Starting phenix.real_space_refine on Fri Feb 14 09:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6slq_10239/02_2025/6slq_10239.cif Found real_map, /net/cci-nas-00/data/ceres_data/6slq_10239/02_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_10239/02_2025/6slq_10239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6slq_10239/02_2025/6slq_10239.map" model { file = "/net/cci-nas-00/data/ceres_data/6slq_10239/02_2025/6slq_10239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6slq_10239/02_2025/6slq_10239.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 7.72, per 1000 atoms: 0.75 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: 2.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.86 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: 2.45 Time building geometry restraints manager: 2.67 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: 0.02 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: 0.090 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.620 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.360 ------------------------------------------------------------------------------- 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 : 0.012 0.618 10566 Z= 0.815 Angle : 0.815 18.322 14366 Z= 0.578 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 : 11.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP F 23 HIS 0.001 0.000 HIS E 62 PHE 0.012 0.001 PHE E 32 TYR 0.004 0.001 TYR B 130 ARG 0.002 0.000 ARG E 143 *********************** 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 : 1.146 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: 0.2791 time to fit residues: 219.8489 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 : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 chunk 34 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 0.3980 overall best weight: 2.6784 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103431 restraints weight = 50889.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108682 restraints weight = 24751.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.112804 restraints weight = 14247.109| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10566 Z= 0.222 Angle : 0.644 6.482 14366 Z= 0.331 Chirality : 0.045 0.223 1604 Planarity : 0.005 0.051 1882 Dihedral : 3.358 22.097 1404 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.35 % Allowed : 2.21 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1310 helix: 0.37 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.07 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 133 HIS 0.005 0.001 HIS B 62 PHE 0.022 0.002 PHE F 168 TYR 0.011 0.002 TYR B 164 ARG 0.006 0.001 ARG C 82 *********************** 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 467 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 463 time to evaluate : 1.159 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: A 40 PHE cc_start: 0.8504 (t80) cc_final: 0.8191 (t80) REVERT: A 100 ARG cc_start: 0.7317 (ttt180) cc_final: 0.6874 (ttp80) REVERT: A 131 LYS cc_start: 0.8754 (tttt) cc_final: 0.8541 (tttt) REVERT: A 133 TRP cc_start: 0.8604 (m-10) cc_final: 0.8179 (m-10) REVERT: A 151 LEU cc_start: 0.8851 (tp) cc_final: 0.8545 (mm) REVERT: A 161 PHE cc_start: 0.8516 (t80) cc_final: 0.8114 (t80) REVERT: A 212 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8286 (pt0) REVERT: A 214 MET cc_start: 0.9160 (ptp) cc_final: 0.8731 (ppp) REVERT: A 215 MET cc_start: 0.8827 (mtm) cc_final: 0.8446 (ptm) REVERT: B 50 GLN cc_start: 0.8390 (tt0) cc_final: 0.7440 (mt0) REVERT: B 68 MET cc_start: 0.7772 (mtp) cc_final: 0.7374 (mmt) REVERT: B 70 LYS cc_start: 0.8075 (ptpt) cc_final: 0.7784 (ptmt) REVERT: B 82 ARG cc_start: 0.8144 (ptm-80) cc_final: 0.7803 (ptm160) REVERT: B 96 MET cc_start: 0.5042 (mmt) cc_final: 0.3847 (mtt) REVERT: B 180 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8539 (pm20) REVERT: B 197 ASP cc_start: 0.7255 (p0) cc_final: 0.6950 (p0) REVERT: B 214 MET cc_start: 0.8692 (mtt) cc_final: 0.8124 (mmt) REVERT: C 28 GLU cc_start: 0.7792 (mp0) cc_final: 0.7408 (mt-10) REVERT: C 35 GLU cc_start: 0.9221 (pt0) cc_final: 0.8686 (pt0) REVERT: C 98 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8563 (pp20) REVERT: C 100 ARG cc_start: 0.7710 (mmp-170) cc_final: 0.7134 (mtm110) REVERT: C 110 THR cc_start: 0.8138 (t) cc_final: 0.7524 (t) REVERT: C 131 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8474 (tttp) REVERT: C 133 TRP cc_start: 0.8191 (m-10) cc_final: 0.7703 (m-10) REVERT: C 173 ARG cc_start: 0.8459 (ttp-170) cc_final: 0.8204 (ttp-170) REVERT: D 57 ASN cc_start: 0.8899 (m-40) cc_final: 0.8629 (m-40) REVERT: D 96 MET cc_start: 0.3058 (mmp) cc_final: 0.2264 (mmt) REVERT: D 213 GLU cc_start: 0.9320 (pt0) cc_final: 0.8931 (pm20) REVERT: D 215 MET cc_start: 0.8501 (mtm) cc_final: 0.7846 (mtt) REVERT: E 10 MET cc_start: 0.3806 (mmm) cc_final: 0.3186 (tmm) REVERT: E 50 GLN cc_start: 0.8616 (mt0) cc_final: 0.8339 (mt0) REVERT: E 84 HIS cc_start: 0.7545 (t-170) cc_final: 0.7323 (t-170) REVERT: E 96 MET cc_start: 0.3735 (mmp) cc_final: 0.2754 (mtt) REVERT: E 112 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8634 (tp40) REVERT: E 141 ILE cc_start: 0.8370 (mt) cc_final: 0.8109 (mt) REVERT: E 144 MET cc_start: 0.8147 (ppp) cc_final: 0.7782 (ppp) REVERT: E 202 LEU cc_start: 0.8498 (mm) cc_final: 0.8119 (pp) REVERT: E 214 MET cc_start: 0.9108 (mtm) cc_final: 0.8476 (tpt) REVERT: F 18 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8136 (ttm-80) REVERT: F 25 LYS cc_start: 0.8733 (mttt) cc_final: 0.8484 (tttm) REVERT: F 39 MET cc_start: 0.7622 (tpp) cc_final: 0.7314 (ttm) REVERT: F 110 THR cc_start: 0.8447 (t) cc_final: 0.7815 (t) REVERT: F 186 THR cc_start: 0.8877 (p) cc_final: 0.8166 (p) REVERT: F 211 LEU cc_start: 0.9195 (mm) cc_final: 0.8990 (mm) outliers start: 4 outliers final: 0 residues processed: 463 average time/residue: 0.2662 time to fit residues: 162.5567 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 : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 7.9990 chunk 32 optimal weight: 0.0040 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 92 optimal weight: 0.0970 overall best weight: 1.1994 ------------------------------------------------------------------------------- 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 179 GLN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 179 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 179 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.137313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103912 restraints weight = 54558.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109465 restraints weight = 25217.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113493 restraints weight = 14179.015| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10566 Z= 0.200 Angle : 0.630 11.057 14366 Z= 0.316 Chirality : 0.044 0.186 1604 Planarity : 0.005 0.053 1882 Dihedral : 3.576 21.981 1404 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.18 % Allowed : 2.39 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1310 helix: 0.45 (0.18), residues: 850 sheet: None (None), residues: 0 loop : -0.88 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 80 HIS 0.004 0.001 HIS A 12 PHE 0.017 0.002 PHE E 161 TYR 0.017 0.002 TYR C 169 ARG 0.007 0.001 ARG B 154 *********************** 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 434 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 432 time to evaluate : 1.154 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: A 10 MET cc_start: 0.6040 (mmm) cc_final: 0.4073 (ttt) REVERT: A 40 PHE cc_start: 0.8486 (t80) cc_final: 0.8130 (t80) REVERT: A 100 ARG cc_start: 0.7291 (ttt180) cc_final: 0.6936 (ttp80) REVERT: A 133 TRP cc_start: 0.8412 (m-10) cc_final: 0.8024 (m-10) REVERT: A 161 PHE cc_start: 0.8568 (t80) cc_final: 0.8205 (t80) REVERT: A 179 GLN cc_start: 0.8760 (tp40) cc_final: 0.8371 (tp40) REVERT: A 214 MET cc_start: 0.9102 (ptp) cc_final: 0.8567 (ppp) REVERT: A 215 MET cc_start: 0.8321 (mtm) cc_final: 0.7791 (ptp) REVERT: B 10 MET cc_start: 0.4796 (tmm) cc_final: 0.4431 (tmm) REVERT: B 50 GLN cc_start: 0.8410 (tt0) cc_final: 0.7711 (mt0) REVERT: B 82 ARG cc_start: 0.8050 (ptm-80) cc_final: 0.7813 (ptm160) REVERT: B 96 MET cc_start: 0.4940 (mmt) cc_final: 0.3608 (mtt) REVERT: B 115 ILE cc_start: 0.8635 (mt) cc_final: 0.8218 (mt) REVERT: B 118 MET cc_start: 0.8520 (ptt) cc_final: 0.7719 (tpp) REVERT: B 144 MET cc_start: 0.8527 (ppp) cc_final: 0.8315 (ppp) REVERT: B 197 ASP cc_start: 0.7098 (p0) cc_final: 0.6846 (p0) REVERT: B 214 MET cc_start: 0.8685 (mtt) cc_final: 0.8105 (mmt) REVERT: C 21 ASN cc_start: 0.8128 (m110) cc_final: 0.7618 (m110) REVERT: C 29 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: C 79 GLU cc_start: 0.8386 (pt0) cc_final: 0.7815 (pt0) REVERT: C 98 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8518 (pp20) REVERT: C 100 ARG cc_start: 0.7772 (mmp-170) cc_final: 0.6979 (mtm110) REVERT: C 104 ILE cc_start: 0.8401 (tt) cc_final: 0.8180 (tt) REVERT: C 133 TRP cc_start: 0.7929 (m-10) cc_final: 0.7569 (m-10) REVERT: D 10 MET cc_start: 0.6650 (mmm) cc_final: 0.4343 (ttt) REVERT: D 40 PHE cc_start: 0.8502 (t80) cc_final: 0.8249 (t80) REVERT: D 55 MET cc_start: 0.9106 (ttt) cc_final: 0.8798 (ttm) REVERT: D 96 MET cc_start: 0.2946 (mmp) cc_final: 0.2356 (mmt) REVERT: D 114 GLN cc_start: 0.9187 (pt0) cc_final: 0.8929 (pt0) REVERT: D 131 LYS cc_start: 0.8742 (tttt) cc_final: 0.8438 (tttt) REVERT: D 212 GLU cc_start: 0.8888 (pt0) cc_final: 0.8070 (pm20) REVERT: E 10 MET cc_start: 0.3900 (mmm) cc_final: 0.3148 (tmm) REVERT: E 63 GLN cc_start: 0.8656 (mm-40) cc_final: 0.7964 (mm-40) REVERT: E 96 MET cc_start: 0.3665 (mmp) cc_final: 0.2569 (mtt) REVERT: E 112 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8632 (tp40) REVERT: E 141 ILE cc_start: 0.8486 (mt) cc_final: 0.8275 (mt) REVERT: E 144 MET cc_start: 0.8297 (ppp) cc_final: 0.7493 (ppp) REVERT: E 184 TRP cc_start: 0.8672 (t60) cc_final: 0.8466 (t60) REVERT: E 190 LEU cc_start: 0.9227 (mm) cc_final: 0.8986 (mm) REVERT: E 202 LEU cc_start: 0.8479 (mm) cc_final: 0.8030 (pp) REVERT: E 214 MET cc_start: 0.9215 (mtm) cc_final: 0.8515 (tpt) REVERT: F 18 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8119 (ttm-80) REVERT: F 25 LYS cc_start: 0.8727 (mttt) cc_final: 0.8430 (ttpp) REVERT: F 131 LYS cc_start: 0.8694 (tttt) cc_final: 0.8332 (tttp) REVERT: F 144 MET cc_start: 0.5888 (tmm) cc_final: 0.5211 (ttt) outliers start: 2 outliers final: 0 residues processed: 433 average time/residue: 0.2580 time to fit residues: 149.1925 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 : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 overall best weight: 5.9988 ------------------------------------------------------------------------------- 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 ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 179 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 74 ASN F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094862 restraints weight = 36709.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098631 restraints weight = 21015.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101309 restraints weight = 14305.246| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10566 Z= 0.340 Angle : 0.748 8.523 14366 Z= 0.391 Chirality : 0.048 0.183 1604 Planarity : 0.006 0.051 1882 Dihedral : 4.188 24.105 1404 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.35 % Allowed : 3.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1310 helix: 0.14 (0.17), residues: 878 sheet: None (None), residues: 0 loop : -0.87 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 80 HIS 0.007 0.002 HIS A 12 PHE 0.018 0.003 PHE F 168 TYR 0.018 0.003 TYR C 169 ARG 0.010 0.001 ARG B 154 *********************** 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 406 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 402 time to evaluate : 1.073 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 100 ARG cc_start: 0.7195 (ttt180) cc_final: 0.6942 (ttp80) REVERT: A 118 MET cc_start: 0.7948 (mtt) cc_final: 0.7563 (mmm) REVERT: A 154 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6376 (mtm-85) REVERT: A 161 PHE cc_start: 0.8709 (t80) cc_final: 0.8303 (t80) REVERT: A 214 MET cc_start: 0.9074 (ptp) cc_final: 0.8709 (ppp) REVERT: A 215 MET cc_start: 0.8723 (mtm) cc_final: 0.7659 (ptp) REVERT: B 10 MET cc_start: 0.5093 (tmm) cc_final: 0.4510 (tmm) REVERT: B 50 GLN cc_start: 0.8530 (tt0) cc_final: 0.7869 (mt0) REVERT: B 82 ARG cc_start: 0.8044 (ptm-80) cc_final: 0.7666 (ptm160) REVERT: B 144 MET cc_start: 0.8481 (ppp) cc_final: 0.8221 (ppp) REVERT: B 190 LEU cc_start: 0.9399 (mt) cc_final: 0.9119 (mt) REVERT: B 197 ASP cc_start: 0.7098 (p0) cc_final: 0.6777 (p0) REVERT: B 214 MET cc_start: 0.8372 (mtt) cc_final: 0.8091 (mmm) REVERT: C 21 ASN cc_start: 0.8108 (m110) cc_final: 0.7670 (m110) REVERT: C 100 ARG cc_start: 0.8097 (mmp-170) cc_final: 0.7380 (mtm110) REVERT: C 115 ILE cc_start: 0.9661 (mt) cc_final: 0.9448 (tt) REVERT: C 131 LYS cc_start: 0.8703 (tttp) cc_final: 0.8059 (tptt) REVERT: C 144 MET cc_start: 0.6903 (tmm) cc_final: 0.6701 (tmm) REVERT: D 51 ASP cc_start: 0.8039 (m-30) cc_final: 0.7833 (m-30) REVERT: D 55 MET cc_start: 0.9213 (ttt) cc_final: 0.8793 (ttm) REVERT: D 66 MET cc_start: 0.9156 (mmm) cc_final: 0.8941 (mmm) REVERT: D 114 GLN cc_start: 0.9252 (pt0) cc_final: 0.9015 (pt0) REVERT: D 154 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.6171 (mtm-85) REVERT: D 212 GLU cc_start: 0.9183 (pt0) cc_final: 0.8051 (pm20) REVERT: E 10 MET cc_start: 0.4461 (mmm) cc_final: 0.3733 (tmm) REVERT: E 96 MET cc_start: 0.4424 (mmp) cc_final: 0.3041 (mtt) REVERT: E 202 LEU cc_start: 0.8498 (mm) cc_final: 0.8051 (pp) REVERT: E 210 THR cc_start: 0.7766 (t) cc_final: 0.7228 (t) REVERT: E 214 MET cc_start: 0.9050 (mtm) cc_final: 0.8216 (tpt) REVERT: F 21 ASN cc_start: 0.8384 (m110) cc_final: 0.8126 (m110) REVERT: F 25 LYS cc_start: 0.8808 (mttt) cc_final: 0.8557 (tppt) REVERT: F 117 TRP cc_start: 0.8362 (m-10) cc_final: 0.8092 (m-10) REVERT: F 129 ILE cc_start: 0.8815 (pt) cc_final: 0.8513 (pt) REVERT: F 131 LYS cc_start: 0.8954 (tttt) cc_final: 0.8539 (tttt) REVERT: F 144 MET cc_start: 0.6910 (tmm) cc_final: 0.6390 (ttt) outliers start: 4 outliers final: 0 residues processed: 402 average time/residue: 0.2637 time to fit residues: 140.5909 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 : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 54 optimal weight: 0.0980 chunk 128 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 9 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 74 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.129384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098430 restraints weight = 47766.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103666 restraints weight = 22303.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107068 restraints weight = 12641.688| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10566 Z= 0.199 Angle : 0.643 7.805 14366 Z= 0.325 Chirality : 0.045 0.194 1604 Planarity : 0.005 0.050 1882 Dihedral : 3.904 21.280 1404 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1310 helix: 0.49 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -0.64 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 23 HIS 0.007 0.001 HIS A 12 PHE 0.015 0.002 PHE E 161 TYR 0.013 0.002 TYR E 169 ARG 0.014 0.001 ARG B 154 *********************** 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 396 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 1.232 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: 0.6400 (mmm) cc_final: 0.5072 (ttt) REVERT: A 144 MET cc_start: 0.8305 (tmm) cc_final: 0.8074 (ppp) REVERT: A 161 PHE cc_start: 0.8659 (t80) cc_final: 0.8313 (t80) REVERT: A 167 ARG cc_start: 0.8756 (ptm160) cc_final: 0.8392 (ptm160) REVERT: A 214 MET cc_start: 0.9007 (ptp) cc_final: 0.8665 (ppp) REVERT: A 215 MET cc_start: 0.8705 (mtm) cc_final: 0.8009 (ptp) REVERT: B 2 ILE cc_start: 0.9064 (tp) cc_final: 0.8858 (tp) REVERT: B 10 MET cc_start: 0.5040 (tmm) cc_final: 0.4358 (tmm) REVERT: B 50 GLN cc_start: 0.8567 (tt0) cc_final: 0.7557 (mt0) REVERT: B 82 ARG cc_start: 0.8075 (ptm-80) cc_final: 0.7781 (ptm160) REVERT: B 111 LEU cc_start: 0.8496 (tp) cc_final: 0.7993 (tp) REVERT: B 115 ILE cc_start: 0.8740 (mt) cc_final: 0.8453 (mt) REVERT: B 118 MET cc_start: 0.8582 (ptt) cc_final: 0.7428 (tpp) REVERT: B 141 ILE cc_start: 0.8758 (mt) cc_final: 0.8539 (mt) REVERT: B 197 ASP cc_start: 0.7115 (p0) cc_final: 0.6864 (p0) REVERT: B 210 THR cc_start: 0.8108 (t) cc_final: 0.7858 (t) REVERT: B 214 MET cc_start: 0.8416 (mtt) cc_final: 0.8215 (mmm) REVERT: C 100 ARG cc_start: 0.8007 (mmp-170) cc_final: 0.7396 (mtm110) REVERT: C 131 LYS cc_start: 0.8527 (tttp) cc_final: 0.8038 (tttt) REVERT: C 132 ARG cc_start: 0.8341 (ptp-170) cc_final: 0.7673 (ttp-110) REVERT: C 133 TRP cc_start: 0.8104 (m-10) cc_final: 0.7098 (m-10) REVERT: C 144 MET cc_start: 0.6760 (tmm) cc_final: 0.6426 (tmm) REVERT: D 10 MET cc_start: 0.6899 (mmm) cc_final: 0.5312 (ttt) REVERT: D 40 PHE cc_start: 0.8536 (t80) cc_final: 0.8257 (t80) REVERT: D 55 MET cc_start: 0.9137 (ttt) cc_final: 0.8812 (ttm) REVERT: D 66 MET cc_start: 0.9113 (mmm) cc_final: 0.8733 (mmm) REVERT: D 154 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.6073 (mtm-85) REVERT: D 212 GLU cc_start: 0.9021 (pt0) cc_final: 0.8141 (pm20) REVERT: E 10 MET cc_start: 0.4332 (mmm) cc_final: 0.3561 (tmm) REVERT: E 112 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8731 (mm-40) REVERT: E 165 VAL cc_start: 0.9496 (m) cc_final: 0.9295 (m) REVERT: E 190 LEU cc_start: 0.9309 (mm) cc_final: 0.9032 (mm) REVERT: E 202 LEU cc_start: 0.8545 (mm) cc_final: 0.8134 (pp) REVERT: E 214 MET cc_start: 0.9209 (mtm) cc_final: 0.8454 (mmp) REVERT: F 25 LYS cc_start: 0.8817 (mttt) cc_final: 0.8483 (tptp) REVERT: F 52 LEU cc_start: 0.9143 (mp) cc_final: 0.8913 (mp) REVERT: F 129 ILE cc_start: 0.8575 (pt) cc_final: 0.8337 (pt) REVERT: F 131 LYS cc_start: 0.8678 (tttt) cc_final: 0.7916 (tptt) REVERT: F 144 MET cc_start: 0.6865 (tmm) cc_final: 0.6013 (ttt) outliers start: 1 outliers final: 0 residues processed: 395 average time/residue: 0.2666 time to fit residues: 141.6383 Evaluate side-chains 301 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 84 HIS A 87 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 193 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 87 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS F 53 ASN F 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097165 restraints weight = 50984.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101830 restraints weight = 25666.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104950 restraints weight = 16310.877| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10566 Z= 0.193 Angle : 0.634 9.144 14366 Z= 0.321 Chirality : 0.044 0.147 1604 Planarity : 0.005 0.050 1882 Dihedral : 3.874 18.614 1404 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.27 % Allowed : 1.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1310 helix: 0.56 (0.17), residues: 862 sheet: None (None), residues: 0 loop : -0.56 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 23 HIS 0.005 0.001 HIS A 12 PHE 0.017 0.002 PHE D 161 TYR 0.016 0.002 TYR E 169 ARG 0.007 0.001 ARG B 143 *********************** 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 396 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 393 time to evaluate : 1.150 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: 0.6463 (mmm) cc_final: 0.5025 (ttt) REVERT: A 154 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6427 (mtm-85) REVERT: A 161 PHE cc_start: 0.8620 (t80) cc_final: 0.8305 (t80) REVERT: A 199 LYS cc_start: 0.8473 (pttt) cc_final: 0.8245 (pttp) REVERT: A 214 MET cc_start: 0.9160 (ptp) cc_final: 0.8605 (ppp) REVERT: A 215 MET cc_start: 0.8382 (mtm) cc_final: 0.7335 (ptp) REVERT: B 10 MET cc_start: 0.5066 (tmm) cc_final: 0.4251 (tmm) REVERT: B 50 GLN cc_start: 0.8464 (tt0) cc_final: 0.7720 (mt0) REVERT: B 63 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8183 (mm-40) REVERT: B 82 ARG cc_start: 0.8197 (ptm-80) cc_final: 0.7880 (ptm160) REVERT: B 114 GLN cc_start: 0.8668 (pt0) cc_final: 0.7915 (pp30) REVERT: B 115 ILE cc_start: 0.8758 (mt) cc_final: 0.8387 (mt) REVERT: B 118 MET cc_start: 0.8512 (ptt) cc_final: 0.7573 (tpp) REVERT: B 141 ILE cc_start: 0.8770 (mt) cc_final: 0.8507 (mt) REVERT: B 197 ASP cc_start: 0.6999 (p0) cc_final: 0.6667 (p0) REVERT: B 202 LEU cc_start: 0.8210 (pp) cc_final: 0.7994 (pp) REVERT: B 210 THR cc_start: 0.8144 (t) cc_final: 0.7874 (t) REVERT: C 28 GLU cc_start: 0.8126 (mp0) cc_final: 0.7880 (mp0) REVERT: C 29 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: C 39 MET cc_start: 0.7635 (mtt) cc_final: 0.7433 (tpp) REVERT: C 100 ARG cc_start: 0.7933 (mmp-170) cc_final: 0.7374 (mtm110) REVERT: C 104 ILE cc_start: 0.8489 (tt) cc_final: 0.7844 (tp) REVERT: C 131 LYS cc_start: 0.8550 (tttp) cc_final: 0.7982 (tptt) REVERT: C 132 ARG cc_start: 0.8358 (ptp-170) cc_final: 0.7687 (ttp-110) REVERT: C 133 TRP cc_start: 0.8096 (m-10) cc_final: 0.7073 (m-10) REVERT: C 144 MET cc_start: 0.6659 (tmm) cc_final: 0.6184 (tmm) REVERT: D 10 MET cc_start: 0.6653 (mmm) cc_final: 0.5145 (ttt) REVERT: D 40 PHE cc_start: 0.8662 (t80) cc_final: 0.8289 (t80) REVERT: D 55 MET cc_start: 0.9006 (ttt) cc_final: 0.8526 (ttm) REVERT: D 66 MET cc_start: 0.9131 (mmm) cc_final: 0.8905 (mmm) REVERT: D 114 GLN cc_start: 0.9286 (pt0) cc_final: 0.9025 (pt0) REVERT: D 118 MET cc_start: 0.8196 (mtt) cc_final: 0.7890 (mmm) REVERT: D 131 LYS cc_start: 0.8394 (tttt) cc_final: 0.7919 (tptm) REVERT: D 145 TYR cc_start: 0.7089 (t80) cc_final: 0.6673 (t80) REVERT: D 212 GLU cc_start: 0.9055 (pt0) cc_final: 0.8205 (pm20) REVERT: E 10 MET cc_start: 0.4397 (mmm) cc_final: 0.3629 (tmm) REVERT: E 190 LEU cc_start: 0.9311 (mm) cc_final: 0.9014 (mm) REVERT: E 202 LEU cc_start: 0.8589 (mm) cc_final: 0.8115 (pp) REVERT: E 210 THR cc_start: 0.7773 (t) cc_final: 0.7456 (t) REVERT: E 214 MET cc_start: 0.9038 (mtm) cc_final: 0.8228 (tpt) REVERT: F 25 LYS cc_start: 0.8866 (mttt) cc_final: 0.8482 (tptm) REVERT: F 52 LEU cc_start: 0.9113 (mp) cc_final: 0.8837 (mp) REVERT: F 100 ARG cc_start: 0.8530 (mtp-110) cc_final: 0.8159 (mtm110) REVERT: F 131 LYS cc_start: 0.8595 (tttt) cc_final: 0.7928 (tptt) REVERT: F 144 MET cc_start: 0.6643 (tmm) cc_final: 0.6243 (ttt) outliers start: 3 outliers final: 0 residues processed: 394 average time/residue: 0.2531 time to fit residues: 133.6074 Evaluate side-chains 309 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 179 GLN B 193 ASN D 84 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094127 restraints weight = 51335.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098837 restraints weight = 26083.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101998 restraints weight = 16594.558| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10566 Z= 0.228 Angle : 0.668 9.171 14366 Z= 0.344 Chirality : 0.045 0.170 1604 Planarity : 0.005 0.049 1882 Dihedral : 3.972 17.276 1404 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1310 helix: 0.54 (0.17), residues: 858 sheet: None (None), residues: 0 loop : -0.54 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 133 HIS 0.006 0.001 HIS A 12 PHE 0.015 0.002 PHE D 161 TYR 0.016 0.002 TYR B 164 ARG 0.006 0.001 ARG B 143 *********************** 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 396 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.111 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: 0.6634 (mmm) cc_final: 0.5284 (ttt) REVERT: A 161 PHE cc_start: 0.8647 (t80) cc_final: 0.8322 (t80) REVERT: A 214 MET cc_start: 0.9085 (ptp) cc_final: 0.8721 (ppp) REVERT: A 215 MET cc_start: 0.8973 (mtm) cc_final: 0.8067 (ptp) REVERT: B 10 MET cc_start: 0.5164 (tmm) cc_final: 0.4373 (tmm) REVERT: B 50 GLN cc_start: 0.8570 (tt0) cc_final: 0.7303 (mt0) REVERT: B 63 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8171 (mm-40) REVERT: B 118 MET cc_start: 0.8584 (ptt) cc_final: 0.7548 (tpp) REVERT: B 141 ILE cc_start: 0.8855 (mt) cc_final: 0.8492 (mt) REVERT: B 144 MET cc_start: 0.8419 (ppp) cc_final: 0.7964 (ppp) REVERT: B 197 ASP cc_start: 0.7069 (p0) cc_final: 0.6745 (p0) REVERT: C 28 GLU cc_start: 0.7997 (mp0) cc_final: 0.7573 (mp0) REVERT: C 39 MET cc_start: 0.8052 (mtt) cc_final: 0.7634 (tpp) REVERT: C 100 ARG cc_start: 0.8055 (mmp-170) cc_final: 0.7503 (mtm110) REVERT: C 131 LYS cc_start: 0.8539 (tttp) cc_final: 0.7816 (tptt) REVERT: C 132 ARG cc_start: 0.8344 (ptp-170) cc_final: 0.7791 (ttp-110) REVERT: C 189 LEU cc_start: 0.9009 (mm) cc_final: 0.8802 (mm) REVERT: C 193 ASN cc_start: 0.7447 (m-40) cc_final: 0.7195 (m-40) REVERT: D 10 MET cc_start: 0.6974 (mmm) cc_final: 0.5599 (ttt) REVERT: D 40 PHE cc_start: 0.8606 (t80) cc_final: 0.8221 (t80) REVERT: D 55 MET cc_start: 0.9055 (ttt) cc_final: 0.8599 (ttm) REVERT: D 66 MET cc_start: 0.9195 (mmm) cc_final: 0.8904 (mmm) REVERT: D 96 MET cc_start: 0.3209 (mmt) cc_final: 0.2972 (mmt) REVERT: D 114 GLN cc_start: 0.9305 (pt0) cc_final: 0.9073 (pt0) REVERT: D 118 MET cc_start: 0.8258 (mtt) cc_final: 0.7995 (mmm) REVERT: D 128 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6787 (tm-30) REVERT: D 154 ARG cc_start: 0.7235 (mtm-85) cc_final: 0.6689 (mtm-85) REVERT: D 212 GLU cc_start: 0.9070 (pt0) cc_final: 0.8186 (pm20) REVERT: E 10 MET cc_start: 0.4450 (mmm) cc_final: 0.3701 (tmm) REVERT: E 165 VAL cc_start: 0.9501 (m) cc_final: 0.9297 (m) REVERT: E 190 LEU cc_start: 0.9272 (mm) cc_final: 0.8913 (mm) REVERT: E 202 LEU cc_start: 0.8581 (mm) cc_final: 0.8188 (pp) REVERT: E 214 MET cc_start: 0.9129 (mtm) cc_final: 0.8146 (tpt) REVERT: F 21 ASN cc_start: 0.8202 (m110) cc_final: 0.7901 (m110) REVERT: F 25 LYS cc_start: 0.8811 (mttt) cc_final: 0.8428 (tptm) REVERT: F 52 LEU cc_start: 0.9147 (mp) cc_final: 0.8838 (mp) REVERT: F 100 ARG cc_start: 0.8574 (mtp-110) cc_final: 0.8331 (mtm110) REVERT: F 129 ILE cc_start: 0.8555 (pt) cc_final: 0.8256 (pt) REVERT: F 131 LYS cc_start: 0.8651 (tttt) cc_final: 0.8031 (tptt) REVERT: F 144 MET cc_start: 0.6914 (tmm) cc_final: 0.6231 (ttp) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.2475 time to fit residues: 132.3254 Evaluate side-chains 304 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 B 179 GLN B 193 ASN D 87 HIS D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 84 HIS ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093569 restraints weight = 46887.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097949 restraints weight = 24177.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.100939 restraints weight = 15527.012| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10566 Z= 0.264 Angle : 0.692 6.980 14366 Z= 0.363 Chirality : 0.047 0.170 1604 Planarity : 0.006 0.060 1882 Dihedral : 4.207 18.433 1404 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.18 % Allowed : 0.80 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1310 helix: 0.32 (0.17), residues: 874 sheet: None (None), residues: 0 loop : -0.49 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 133 HIS 0.007 0.001 HIS A 12 PHE 0.019 0.002 PHE E 32 TYR 0.017 0.003 TYR E 164 ARG 0.006 0.001 ARG B 143 *********************** 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 393 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 1.193 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: 0.6833 (mmm) cc_final: 0.5761 (ttt) REVERT: A 161 PHE cc_start: 0.8612 (t80) cc_final: 0.8317 (t80) REVERT: A 203 LYS cc_start: 0.8933 (mttt) cc_final: 0.8630 (mtmm) REVERT: A 214 MET cc_start: 0.9213 (ptp) cc_final: 0.8719 (ptp) REVERT: B 10 MET cc_start: 0.4873 (tmm) cc_final: 0.4190 (tmm) REVERT: B 50 GLN cc_start: 0.8479 (tt0) cc_final: 0.7106 (mt0) REVERT: B 98 GLU cc_start: 0.7879 (tp30) cc_final: 0.7622 (tp30) REVERT: B 118 MET cc_start: 0.8557 (ptt) cc_final: 0.7519 (tpp) REVERT: B 141 ILE cc_start: 0.8880 (mt) cc_final: 0.8528 (mt) REVERT: B 144 MET cc_start: 0.8309 (ppp) cc_final: 0.7805 (ppp) REVERT: B 190 LEU cc_start: 0.9469 (mt) cc_final: 0.9175 (mt) REVERT: B 197 ASP cc_start: 0.7070 (p0) cc_final: 0.6728 (p0) REVERT: C 28 GLU cc_start: 0.7653 (mp0) cc_final: 0.7077 (mp0) REVERT: C 100 ARG cc_start: 0.8225 (mmp-170) cc_final: 0.7704 (mtm110) REVERT: C 131 LYS cc_start: 0.8641 (tttp) cc_final: 0.7891 (tptt) REVERT: C 132 ARG cc_start: 0.8340 (ptp-170) cc_final: 0.7583 (ttp-110) REVERT: D 10 MET cc_start: 0.7204 (mmm) cc_final: 0.5981 (ttt) REVERT: D 48 THR cc_start: 0.8920 (p) cc_final: 0.8199 (p) REVERT: D 55 MET cc_start: 0.9021 (ttt) cc_final: 0.8640 (ttm) REVERT: D 66 MET cc_start: 0.9137 (mmm) cc_final: 0.8908 (mmm) REVERT: D 114 GLN cc_start: 0.9299 (pt0) cc_final: 0.9095 (pt0) REVERT: D 118 MET cc_start: 0.8312 (mtt) cc_final: 0.7988 (mmm) REVERT: D 128 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6596 (tm-30) REVERT: D 154 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6781 (mtm-85) REVERT: D 189 LEU cc_start: 0.9350 (mm) cc_final: 0.9113 (mm) REVERT: D 193 ASN cc_start: 0.8165 (m-40) cc_final: 0.7695 (t0) REVERT: D 212 GLU cc_start: 0.9017 (pt0) cc_final: 0.8315 (pm20) REVERT: E 10 MET cc_start: 0.4558 (mmm) cc_final: 0.3871 (tmm) REVERT: E 98 GLU cc_start: 0.8618 (tp30) cc_final: 0.8352 (tp30) REVERT: E 190 LEU cc_start: 0.9380 (mm) cc_final: 0.9074 (mm) REVERT: E 202 LEU cc_start: 0.8609 (mm) cc_final: 0.8196 (pp) REVERT: E 214 MET cc_start: 0.9071 (mtm) cc_final: 0.8283 (tpt) REVERT: F 21 ASN cc_start: 0.8175 (m110) cc_final: 0.7827 (m110) REVERT: F 25 LYS cc_start: 0.8659 (mttt) cc_final: 0.8414 (tppt) REVERT: F 52 LEU cc_start: 0.9165 (mp) cc_final: 0.8880 (mp) REVERT: F 135 ILE cc_start: 0.9356 (mt) cc_final: 0.9143 (mt) REVERT: F 139 ASN cc_start: 0.9259 (m-40) cc_final: 0.9010 (m-40) outliers start: 2 outliers final: 0 residues processed: 391 average time/residue: 0.2454 time to fit residues: 129.4987 Evaluate side-chains 297 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 108 optimal weight: 0.0470 chunk 129 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 84 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 193 ASN D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.129167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094611 restraints weight = 56100.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099405 restraints weight = 26701.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102707 restraints weight = 16516.160| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10566 Z= 0.187 Angle : 0.664 9.003 14366 Z= 0.339 Chirality : 0.045 0.183 1604 Planarity : 0.005 0.060 1882 Dihedral : 4.048 16.429 1404 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1310 helix: 0.61 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 80 HIS 0.007 0.001 HIS A 84 PHE 0.014 0.001 PHE E 161 TYR 0.018 0.002 TYR B 164 ARG 0.005 0.001 ARG A 154 *********************** 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 394 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.126 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: 0.6748 (mmm) cc_final: 0.5572 (ttt) REVERT: A 141 ILE cc_start: 0.9085 (mt) cc_final: 0.8512 (mt) REVERT: A 161 PHE cc_start: 0.8618 (t80) cc_final: 0.8385 (t80) REVERT: A 167 ARG cc_start: 0.8734 (ptm160) cc_final: 0.8424 (ptm160) REVERT: A 214 MET cc_start: 0.9187 (ptp) cc_final: 0.8669 (ptp) REVERT: B 10 MET cc_start: 0.5229 (tmm) cc_final: 0.4478 (tmm) REVERT: B 50 GLN cc_start: 0.8478 (tt0) cc_final: 0.7556 (mt0) REVERT: B 70 LYS cc_start: 0.8922 (ptmt) cc_final: 0.8697 (pttt) REVERT: B 98 GLU cc_start: 0.7963 (tp30) cc_final: 0.7724 (tp30) REVERT: B 114 GLN cc_start: 0.8565 (pt0) cc_final: 0.7852 (pp30) REVERT: B 115 ILE cc_start: 0.9054 (mt) cc_final: 0.8652 (mt) REVERT: B 118 MET cc_start: 0.8549 (ptt) cc_final: 0.7611 (tpp) REVERT: B 141 ILE cc_start: 0.8793 (mt) cc_final: 0.8488 (mt) REVERT: B 144 MET cc_start: 0.8070 (ppp) cc_final: 0.7509 (ppp) REVERT: B 180 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8623 (pm20) REVERT: B 197 ASP cc_start: 0.7086 (p0) cc_final: 0.6780 (p0) REVERT: B 214 MET cc_start: 0.9200 (ttm) cc_final: 0.7932 (tpt) REVERT: C 28 GLU cc_start: 0.7731 (mp0) cc_final: 0.7113 (mp0) REVERT: C 100 ARG cc_start: 0.7974 (mmp-170) cc_final: 0.7455 (mtm110) REVERT: C 131 LYS cc_start: 0.8584 (tttp) cc_final: 0.7849 (tptt) REVERT: C 132 ARG cc_start: 0.8294 (ptp-170) cc_final: 0.7633 (ttp-110) REVERT: C 133 TRP cc_start: 0.8083 (m-10) cc_final: 0.7728 (m-10) REVERT: C 143 ARG cc_start: 0.8071 (mtt180) cc_final: 0.7693 (ttm110) REVERT: C 193 ASN cc_start: 0.7364 (m-40) cc_final: 0.6580 (t0) REVERT: D 10 MET cc_start: 0.7082 (mmm) cc_final: 0.6012 (ttm) REVERT: D 40 PHE cc_start: 0.8368 (t80) cc_final: 0.8161 (t80) REVERT: D 48 THR cc_start: 0.9175 (p) cc_final: 0.8353 (p) REVERT: D 55 MET cc_start: 0.8931 (ttt) cc_final: 0.8553 (ttm) REVERT: D 66 MET cc_start: 0.9118 (mmm) cc_final: 0.8756 (mmm) REVERT: D 114 GLN cc_start: 0.9273 (pt0) cc_final: 0.9050 (pt0) REVERT: D 118 MET cc_start: 0.8251 (mtt) cc_final: 0.7938 (mmm) REVERT: D 128 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6704 (tm-30) REVERT: D 212 GLU cc_start: 0.8888 (pt0) cc_final: 0.8323 (pm20) REVERT: D 214 MET cc_start: 0.8533 (tmm) cc_final: 0.8280 (tmm) REVERT: D 215 MET cc_start: 0.8696 (pmm) cc_final: 0.7748 (pmm) REVERT: E 10 MET cc_start: 0.4501 (mmm) cc_final: 0.3802 (tmm) REVERT: E 68 MET cc_start: 0.7714 (ttm) cc_final: 0.7432 (ttm) REVERT: E 115 ILE cc_start: 0.8840 (mt) cc_final: 0.8486 (mt) REVERT: E 118 MET cc_start: 0.8502 (ptt) cc_final: 0.7612 (tpp) REVERT: E 190 LEU cc_start: 0.9314 (mm) cc_final: 0.9107 (mm) REVERT: E 202 LEU cc_start: 0.8591 (mm) cc_final: 0.8274 (pp) REVERT: E 214 MET cc_start: 0.9211 (mtm) cc_final: 0.8264 (tpt) REVERT: F 21 ASN cc_start: 0.8301 (m110) cc_final: 0.7903 (m110) REVERT: F 25 LYS cc_start: 0.8788 (mttt) cc_final: 0.8290 (tptp) REVERT: F 52 LEU cc_start: 0.9255 (mp) cc_final: 0.8921 (mp) REVERT: F 66 MET cc_start: 0.8324 (mpp) cc_final: 0.7724 (ttm) REVERT: F 131 LYS cc_start: 0.8578 (tttt) cc_final: 0.7959 (tptt) REVERT: F 144 MET cc_start: 0.6416 (tmm) cc_final: 0.6154 (ttp) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.2440 time to fit residues: 130.3039 Evaluate side-chains 319 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 179 GLN B 193 ASN D 87 HIS D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096372 restraints weight = 40222.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100518 restraints weight = 21509.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.103353 restraints weight = 13952.118| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10566 Z= 0.216 Angle : 0.671 7.959 14366 Z= 0.347 Chirality : 0.046 0.156 1604 Planarity : 0.005 0.062 1882 Dihedral : 4.062 16.117 1404 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.09 % Allowed : 0.53 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1310 helix: 0.57 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -0.46 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 133 HIS 0.005 0.001 HIS A 12 PHE 0.014 0.002 PHE A 40 TYR 0.020 0.002 TYR B 164 ARG 0.007 0.001 ARG B 143 ********************** 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 393 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 1.214 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: A 10 MET cc_start: 0.6769 (mmm) cc_final: 0.5663 (ttt) REVERT: A 118 MET cc_start: 0.7996 (mtt) cc_final: 0.7670 (mmm) REVERT: A 161 PHE cc_start: 0.8550 (t80) cc_final: 0.8258 (t80) REVERT: A 203 LYS cc_start: 0.8943 (mttt) cc_final: 0.8647 (mtmm) REVERT: A 214 MET cc_start: 0.9154 (ptp) cc_final: 0.8565 (ptp) REVERT: B 10 MET cc_start: 0.5349 (tmm) cc_final: 0.4507 (tmm) REVERT: B 50 GLN cc_start: 0.8484 (tt0) cc_final: 0.7696 (mt0) REVERT: B 70 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8657 (pttt) REVERT: B 114 GLN cc_start: 0.8800 (pt0) cc_final: 0.8172 (pt0) REVERT: B 115 ILE cc_start: 0.8999 (mt) cc_final: 0.8651 (mt) REVERT: B 118 MET cc_start: 0.8501 (ptt) cc_final: 0.7544 (tpp) REVERT: B 141 ILE cc_start: 0.8877 (mt) cc_final: 0.8544 (mt) REVERT: B 144 MET cc_start: 0.8197 (ppp) cc_final: 0.7702 (ppp) REVERT: B 190 LEU cc_start: 0.9350 (mt) cc_final: 0.9135 (mt) REVERT: B 197 ASP cc_start: 0.7090 (p0) cc_final: 0.6758 (p0) REVERT: B 214 MET cc_start: 0.9170 (ttm) cc_final: 0.7984 (tpt) REVERT: C 28 GLU cc_start: 0.7623 (mp0) cc_final: 0.6960 (mp0) REVERT: C 39 MET cc_start: 0.8158 (mtt) cc_final: 0.7646 (tpp) REVERT: C 100 ARG cc_start: 0.8175 (mmp-170) cc_final: 0.7524 (mtm110) REVERT: C 131 LYS cc_start: 0.8624 (tttp) cc_final: 0.7824 (tptt) REVERT: C 132 ARG cc_start: 0.8230 (ptp-170) cc_final: 0.7546 (ttp-110) REVERT: C 133 TRP cc_start: 0.8051 (m-10) cc_final: 0.7158 (m-10) REVERT: C 143 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7580 (tpt90) REVERT: C 193 ASN cc_start: 0.7402 (m-40) cc_final: 0.6846 (t0) REVERT: C 201 ILE cc_start: 0.8737 (pt) cc_final: 0.8478 (pt) REVERT: C 214 MET cc_start: 0.8836 (mtm) cc_final: 0.8593 (mtt) REVERT: D 10 MET cc_start: 0.7159 (mmm) cc_final: 0.6207 (ttm) REVERT: D 48 THR cc_start: 0.8968 (p) cc_final: 0.8121 (p) REVERT: D 55 MET cc_start: 0.8997 (ttt) cc_final: 0.8677 (ttm) REVERT: D 66 MET cc_start: 0.9127 (mmm) cc_final: 0.8858 (mmm) REVERT: D 70 LYS cc_start: 0.8578 (tttt) cc_final: 0.8317 (tttp) REVERT: D 118 MET cc_start: 0.8270 (mtt) cc_final: 0.7973 (mmm) REVERT: D 128 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6665 (tm-30) REVERT: D 154 ARG cc_start: 0.7158 (mtm-85) cc_final: 0.6040 (mtm-85) REVERT: D 183 ASN cc_start: 0.8948 (m110) cc_final: 0.8723 (m-40) REVERT: D 212 GLU cc_start: 0.9025 (pt0) cc_final: 0.8334 (pm20) REVERT: E 10 MET cc_start: 0.4511 (mmm) cc_final: 0.3838 (tmm) REVERT: E 68 MET cc_start: 0.7871 (ttm) cc_final: 0.7560 (ttm) REVERT: E 115 ILE cc_start: 0.8849 (mt) cc_final: 0.8490 (mt) REVERT: E 118 MET cc_start: 0.8461 (ptt) cc_final: 0.7596 (tpp) REVERT: E 125 PRO cc_start: 0.8483 (Cg_endo) cc_final: 0.8155 (Cg_exo) REVERT: E 190 LEU cc_start: 0.9356 (mm) cc_final: 0.9064 (mm) REVERT: E 202 LEU cc_start: 0.8614 (mm) cc_final: 0.8106 (pp) REVERT: E 214 MET cc_start: 0.9125 (mtm) cc_final: 0.8381 (tpt) REVERT: F 21 ASN cc_start: 0.8185 (m110) cc_final: 0.7734 (m110) REVERT: F 25 LYS cc_start: 0.8634 (mttt) cc_final: 0.8367 (ttpt) REVERT: F 52 LEU cc_start: 0.9270 (mp) cc_final: 0.8952 (mp) REVERT: F 66 MET cc_start: 0.8379 (mpp) cc_final: 0.7746 (ttm) REVERT: F 129 ILE cc_start: 0.8532 (pt) cc_final: 0.8160 (pt) outliers start: 1 outliers final: 0 residues processed: 392 average time/residue: 0.2379 time to fit residues: 126.4357 Evaluate side-chains 319 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 0.0000 chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 69 optimal weight: 0.0010 chunk 99 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 B 193 ASN D 95 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.097008 restraints weight = 38338.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100993 restraints weight = 21340.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103783 restraints weight = 14301.791| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10566 Z= 0.193 Angle : 0.695 10.688 14366 Z= 0.355 Chirality : 0.045 0.164 1604 Planarity : 0.005 0.061 1882 Dihedral : 4.000 17.202 1404 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1310 helix: 0.57 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -0.37 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 23 HIS 0.004 0.001 HIS D 12 PHE 0.017 0.002 PHE A 40 TYR 0.018 0.002 TYR B 164 ARG 0.007 0.001 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3801.27 seconds wall clock time: 68 minutes 37.34 seconds (4117.34 seconds total)