Starting phenix.real_space_refine on Sun Jun 8 22:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6slq_10239/06_2025/6slq_10239.cif Found real_map, /net/cci-nas-00/data/ceres_data/6slq_10239/06_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_10239/06_2025/6slq_10239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6slq_10239/06_2025/6slq_10239.map" model { file = "/net/cci-nas-00/data/ceres_data/6slq_10239/06_2025/6slq_10239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6slq_10239/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.84, per 1000 atoms: 0.76 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: 2.40 Conformation dependent library (CDL) restraints added in 1.6 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: 0.92 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: 2.57 Time building geometry restraints manager: 2.88 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: 0.170 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.840 Find NCS groups from input model: 0.460 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.618 10572 Z= 0.779 Angle : 0.907 44.170 14378 Z= 0.609 Chirality : 0.045 0.226 1604 Planarity : 0.005 0.070 1882 Dihedral : 9.228 89.602 4028 Min Nonbonded Distance : 1.359 Molprobity Statistics. All-atom Clashscore : 11.86 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 Details of bonding type rmsd hydrogen bonds : bond 0.13362 ( 577) hydrogen bonds : angle 4.66345 ( 1731) SS BOND : bond 0.21515 ( 6) SS BOND : angle 13.84623 ( 12) covalent geometry : bond 0.01200 (10566) covalent geometry : angle 0.81483 (14366) *********************** 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 : 1.196 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: 0.2771 time to fit residues: 218.4878 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 : 1.043 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.136646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102912 restraints weight = 51172.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108189 restraints weight = 25056.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112245 restraints weight = 14503.167| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 10572 Z= 0.151 Angle : 0.646 6.482 14378 Z= 0.332 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 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 577) hydrogen bonds : angle 3.80725 ( 1731) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.94114 ( 12) covalent geometry : bond 0.00343 (10566) covalent geometry : angle 0.64373 (14366) *********************** 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 : 1.195 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: 0.8194 (t80) REVERT: A 100 ARG cc_start: 0.7316 (ttt180) cc_final: 0.6873 (ttp80) REVERT: A 131 LYS cc_start: 0.8751 (tttt) cc_final: 0.8538 (tttt) REVERT: A 133 TRP cc_start: 0.8600 (m-10) cc_final: 0.8180 (m-10) REVERT: A 151 LEU cc_start: 0.8843 (tp) cc_final: 0.8541 (mm) REVERT: A 161 PHE cc_start: 0.8512 (t80) cc_final: 0.8107 (t80) REVERT: A 212 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8268 (pt0) REVERT: A 214 MET cc_start: 0.9157 (ptp) cc_final: 0.8730 (ppp) REVERT: A 215 MET cc_start: 0.8827 (mtm) cc_final: 0.8445 (ptm) REVERT: B 50 GLN cc_start: 0.8380 (tt0) cc_final: 0.7439 (mt0) REVERT: B 68 MET cc_start: 0.7776 (mtp) cc_final: 0.7370 (mmt) REVERT: B 70 LYS cc_start: 0.8074 (ptpt) cc_final: 0.7783 (ptmt) REVERT: B 82 ARG cc_start: 0.8139 (ptm-80) cc_final: 0.7804 (ptm160) REVERT: B 96 MET cc_start: 0.5047 (mmt) cc_final: 0.3844 (mtt) REVERT: B 180 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8548 (pm20) REVERT: B 197 ASP cc_start: 0.7264 (p0) cc_final: 0.6961 (p0) REVERT: B 214 MET cc_start: 0.8688 (mtt) cc_final: 0.8118 (mmt) REVERT: C 28 GLU cc_start: 0.7794 (mp0) cc_final: 0.7408 (mt-10) REVERT: C 35 GLU cc_start: 0.9214 (pt0) cc_final: 0.8681 (pt0) REVERT: C 98 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8563 (pp20) REVERT: C 100 ARG cc_start: 0.7708 (mmp-170) cc_final: 0.7136 (mtm110) REVERT: C 110 THR cc_start: 0.8145 (t) cc_final: 0.7528 (t) REVERT: C 131 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8471 (tttp) REVERT: C 133 TRP cc_start: 0.8188 (m-10) cc_final: 0.7697 (m-10) REVERT: C 173 ARG cc_start: 0.8456 (ttp-170) cc_final: 0.8209 (ttp-170) REVERT: D 57 ASN cc_start: 0.8900 (m-40) cc_final: 0.8625 (m-40) REVERT: D 96 MET cc_start: 0.3057 (mmp) cc_final: 0.2261 (mmt) REVERT: D 213 GLU cc_start: 0.9320 (pt0) cc_final: 0.8934 (pm20) REVERT: D 215 MET cc_start: 0.8503 (mtm) cc_final: 0.7843 (mtt) REVERT: E 10 MET cc_start: 0.3804 (mmm) cc_final: 0.3170 (tmm) REVERT: E 50 GLN cc_start: 0.8608 (mt0) cc_final: 0.8329 (mt0) REVERT: E 84 HIS cc_start: 0.7562 (t-170) cc_final: 0.7333 (t-170) REVERT: E 96 MET cc_start: 0.3748 (mmp) cc_final: 0.2749 (mtt) REVERT: E 112 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8637 (tp40) REVERT: E 141 ILE cc_start: 0.8366 (mt) cc_final: 0.8106 (mt) REVERT: E 144 MET cc_start: 0.8140 (ppp) cc_final: 0.7769 (ppp) REVERT: E 202 LEU cc_start: 0.8498 (mm) cc_final: 0.8116 (pp) REVERT: E 214 MET cc_start: 0.9110 (mtm) cc_final: 0.8476 (tpt) REVERT: F 18 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: F 25 LYS cc_start: 0.8732 (mttt) cc_final: 0.8486 (tttm) REVERT: F 39 MET cc_start: 0.7616 (tpp) cc_final: 0.7314 (ttm) REVERT: F 110 THR cc_start: 0.8440 (t) cc_final: 0.7811 (t) REVERT: F 186 THR cc_start: 0.8884 (p) cc_final: 0.8174 (p) REVERT: F 211 LEU cc_start: 0.9199 (mm) cc_final: 0.8990 (mm) outliers start: 4 outliers final: 0 residues processed: 463 average time/residue: 0.2647 time to fit residues: 163.1784 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 : 1.203 ------------------------------------------------------------------------------- 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: 0.4980 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 C 53 ASN C 179 GLN ** D 114 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 = 0.3886 r_free = 0.3886 target = 0.137069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101413 restraints weight = 55244.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106514 restraints weight = 27327.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.109999 restraints weight = 17156.522| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10572 Z= 0.136 Angle : 0.633 10.251 14378 Z= 0.319 Chirality : 0.044 0.226 1604 Planarity : 0.005 0.053 1882 Dihedral : 3.583 21.921 1404 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.22), residues: 1310 helix: 0.48 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 80 HIS 0.005 0.001 HIS A 12 PHE 0.016 0.002 PHE E 161 TYR 0.017 0.002 TYR C 169 ARG 0.007 0.001 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 577) hydrogen bonds : angle 3.85161 ( 1731) SS BOND : bond 0.00837 ( 6) SS BOND : angle 1.42282 ( 12) covalent geometry : bond 0.00323 (10566) covalent geometry : angle 0.63164 (14366) *********************** 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 436 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 434 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6092 (mmm) cc_final: 0.4097 (ttt) REVERT: A 40 PHE cc_start: 0.8538 (t80) cc_final: 0.8176 (t80) REVERT: A 100 ARG cc_start: 0.7356 (ttt180) cc_final: 0.6983 (ttp80) REVERT: A 133 TRP cc_start: 0.8413 (m-10) cc_final: 0.8003 (m-10) REVERT: A 161 PHE cc_start: 0.8573 (t80) cc_final: 0.8212 (t80) REVERT: A 179 GLN cc_start: 0.8737 (tp40) cc_final: 0.8353 (tp40) REVERT: A 214 MET cc_start: 0.9096 (ptp) cc_final: 0.8604 (ppp) REVERT: B 10 MET cc_start: 0.4912 (tmm) cc_final: 0.4543 (tmm) REVERT: B 50 GLN cc_start: 0.8439 (tt0) cc_final: 0.7757 (mt0) REVERT: B 82 ARG cc_start: 0.8078 (ptm-80) cc_final: 0.7838 (ptm160) REVERT: B 115 ILE cc_start: 0.8649 (mt) cc_final: 0.8230 (mt) REVERT: B 118 MET cc_start: 0.8492 (ptt) cc_final: 0.7696 (tpp) REVERT: B 144 MET cc_start: 0.8516 (ppp) cc_final: 0.8303 (ppp) REVERT: B 197 ASP cc_start: 0.7106 (p0) cc_final: 0.6853 (p0) REVERT: B 214 MET cc_start: 0.8682 (mtt) cc_final: 0.8102 (mmt) REVERT: C 21 ASN cc_start: 0.8180 (m110) cc_final: 0.7673 (m110) REVERT: C 29 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: C 79 GLU cc_start: 0.8366 (pt0) cc_final: 0.7796 (pt0) REVERT: C 98 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8540 (pp20) REVERT: C 100 ARG cc_start: 0.7779 (mmp-170) cc_final: 0.6996 (mtm110) REVERT: C 104 ILE cc_start: 0.8454 (tt) cc_final: 0.8035 (tt) REVERT: C 133 TRP cc_start: 0.7981 (m-10) cc_final: 0.7162 (m-10) REVERT: D 10 MET cc_start: 0.6615 (mmm) cc_final: 0.4427 (ttt) REVERT: D 40 PHE cc_start: 0.8516 (t80) cc_final: 0.8238 (t80) REVERT: D 55 MET cc_start: 0.9159 (ttt) cc_final: 0.8727 (ttm) REVERT: D 96 MET cc_start: 0.2958 (mmp) cc_final: 0.2354 (mmt) REVERT: D 114 GLN cc_start: 0.9165 (pt0) cc_final: 0.8906 (pt0) REVERT: D 131 LYS cc_start: 0.8714 (tttt) cc_final: 0.8385 (tttt) REVERT: D 212 GLU cc_start: 0.8899 (pt0) cc_final: 0.8083 (pm20) REVERT: E 10 MET cc_start: 0.3978 (mmm) cc_final: 0.3235 (tmm) REVERT: E 63 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8034 (mm-40) REVERT: E 96 MET cc_start: 0.3774 (mmp) cc_final: 0.2642 (mtt) REVERT: E 112 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8634 (tp40) REVERT: E 144 MET cc_start: 0.8384 (ppp) cc_final: 0.7581 (ppp) REVERT: E 190 LEU cc_start: 0.9212 (mm) cc_final: 0.8971 (mm) REVERT: E 202 LEU cc_start: 0.8508 (mm) cc_final: 0.8052 (pp) REVERT: E 214 MET cc_start: 0.9212 (mtm) cc_final: 0.8514 (tpt) REVERT: F 25 LYS cc_start: 0.8772 (mttt) cc_final: 0.8489 (ttpp) REVERT: F 131 LYS cc_start: 0.8721 (tttt) cc_final: 0.8368 (tttp) REVERT: F 144 MET cc_start: 0.5937 (tmm) cc_final: 0.5134 (ttp) outliers start: 2 outliers final: 0 residues processed: 435 average time/residue: 0.2455 time to fit residues: 142.7344 Evaluate side-chains 324 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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: 7.9990 chunk 55 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 D 87 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101237 restraints weight = 35990.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105091 restraints weight = 20314.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107767 restraints weight = 13730.018| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10572 Z= 0.147 Angle : 0.640 9.608 14378 Z= 0.325 Chirality : 0.044 0.166 1604 Planarity : 0.005 0.052 1882 Dihedral : 3.720 23.605 1404 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.27 % Allowed : 2.39 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.17), residues: 850 sheet: None (None), residues: 0 loop : -0.66 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 80 HIS 0.006 0.001 HIS A 12 PHE 0.018 0.002 PHE D 161 TYR 0.013 0.002 TYR B 164 ARG 0.007 0.001 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 577) hydrogen bonds : angle 3.85459 ( 1731) SS BOND : bond 0.00142 ( 6) SS BOND : angle 1.10515 ( 12) covalent geometry : bond 0.00340 (10566) covalent geometry : angle 0.63922 (14366) *********************** 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 413 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 410 time to evaluate : 1.151 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 118 MET cc_start: 0.7760 (mtt) cc_final: 0.7448 (mmm) REVERT: A 133 TRP cc_start: 0.8551 (m-10) cc_final: 0.7982 (m-10) REVERT: A 161 PHE cc_start: 0.8696 (t80) cc_final: 0.8337 (t80) REVERT: A 179 GLN cc_start: 0.8366 (tp40) cc_final: 0.8104 (tp40) REVERT: A 214 MET cc_start: 0.9010 (ptp) cc_final: 0.8664 (ppp) REVERT: B 10 MET cc_start: 0.5019 (tmm) cc_final: 0.4629 (tmm) REVERT: B 50 GLN cc_start: 0.8521 (tt0) cc_final: 0.7779 (mt0) REVERT: B 82 ARG cc_start: 0.8127 (ptm-80) cc_final: 0.7835 (ptm160) REVERT: B 115 ILE cc_start: 0.8713 (mt) cc_final: 0.8445 (mt) REVERT: B 118 MET cc_start: 0.8444 (ptt) cc_final: 0.7544 (tpp) REVERT: B 144 MET cc_start: 0.8556 (ppp) cc_final: 0.8099 (ppp) REVERT: B 197 ASP cc_start: 0.7127 (p0) cc_final: 0.6835 (p0) REVERT: B 214 MET cc_start: 0.8585 (mtt) cc_final: 0.8234 (mmm) REVERT: C 21 ASN cc_start: 0.8014 (m110) cc_final: 0.7646 (m110) REVERT: C 100 ARG cc_start: 0.7933 (mmp-170) cc_final: 0.7115 (mtm110) REVERT: C 104 ILE cc_start: 0.8546 (tt) cc_final: 0.7997 (tp) REVERT: C 131 LYS cc_start: 0.8644 (tttp) cc_final: 0.8264 (tttp) REVERT: C 132 ARG cc_start: 0.8317 (ptp-170) cc_final: 0.7617 (ttp-110) REVERT: C 133 TRP cc_start: 0.8036 (m-10) cc_final: 0.7016 (m-10) REVERT: D 40 PHE cc_start: 0.8584 (t80) cc_final: 0.8307 (t80) REVERT: D 55 MET cc_start: 0.9203 (ttt) cc_final: 0.8782 (ttm) REVERT: D 68 MET cc_start: 0.8371 (mtp) cc_final: 0.7785 (mtt) REVERT: D 96 MET cc_start: 0.2905 (mmp) cc_final: 0.2698 (mmt) REVERT: D 114 GLN cc_start: 0.9243 (pt0) cc_final: 0.8970 (pt0) REVERT: D 131 LYS cc_start: 0.8682 (tttt) cc_final: 0.8478 (tttt) REVERT: D 212 GLU cc_start: 0.9134 (pt0) cc_final: 0.8117 (pm20) REVERT: E 10 MET cc_start: 0.4115 (mmm) cc_final: 0.3378 (tmm) REVERT: E 96 MET cc_start: 0.4169 (mmp) cc_final: 0.2844 (mtt) REVERT: E 190 LEU cc_start: 0.9248 (mm) cc_final: 0.8979 (mm) REVERT: E 202 LEU cc_start: 0.8460 (mm) cc_final: 0.8049 (pp) REVERT: E 214 MET cc_start: 0.9094 (mtm) cc_final: 0.7931 (tpt) REVERT: E 215 MET cc_start: 0.7968 (mtt) cc_final: 0.7696 (mtt) REVERT: F 25 LYS cc_start: 0.8741 (mttt) cc_final: 0.8535 (tppt) REVERT: F 104 ILE cc_start: 0.8995 (tp) cc_final: 0.8779 (tp) REVERT: F 115 ILE cc_start: 0.9708 (mt) cc_final: 0.9410 (tt) REVERT: F 117 TRP cc_start: 0.8234 (m-10) cc_final: 0.7994 (m-10) REVERT: F 129 ILE cc_start: 0.8704 (pt) cc_final: 0.8477 (pt) REVERT: F 131 LYS cc_start: 0.8791 (tttt) cc_final: 0.8309 (tttp) REVERT: F 133 TRP cc_start: 0.8083 (m-10) cc_final: 0.6918 (m-10) REVERT: F 144 MET cc_start: 0.6890 (tmm) cc_final: 0.5499 (ttp) REVERT: F 161 PHE cc_start: 0.8699 (t80) cc_final: 0.8462 (t80) outliers start: 3 outliers final: 0 residues processed: 410 average time/residue: 0.2599 time to fit residues: 142.2124 Evaluate side-chains 326 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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: 3.9990 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 86 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- 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** B 179 GLN D 84 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094936 restraints weight = 48545.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100077 restraints weight = 24165.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102509 restraints weight = 14373.336| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10572 Z= 0.190 Angle : 0.699 8.632 14378 Z= 0.360 Chirality : 0.046 0.190 1604 Planarity : 0.005 0.051 1882 Dihedral : 3.960 19.783 1404 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.09 % Allowed : 2.74 % Favored : 97.17 % 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: -0.06 (0.22), residues: 1310 helix: 0.37 (0.17), residues: 868 sheet: None (None), residues: 0 loop : -0.67 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 133 HIS 0.008 0.001 HIS A 12 PHE 0.017 0.002 PHE F 168 TYR 0.016 0.002 TYR F 169 ARG 0.007 0.001 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 577) hydrogen bonds : angle 4.10400 ( 1731) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.70598 ( 12) covalent geometry : bond 0.00429 (10566) covalent geometry : angle 0.69741 (14366) *********************** 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 : 2.111 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: A 10 MET cc_start: 0.6381 (mmm) cc_final: 0.5139 (ttt) REVERT: A 118 MET cc_start: 0.8120 (mtt) cc_final: 0.7817 (mmm) REVERT: A 161 PHE cc_start: 0.8719 (t80) cc_final: 0.8307 (t80) REVERT: A 214 MET cc_start: 0.9055 (ptp) cc_final: 0.8712 (ppp) REVERT: A 215 MET cc_start: 0.8803 (ptp) cc_final: 0.7854 (ptp) REVERT: B 10 MET cc_start: 0.5138 (tmm) cc_final: 0.4527 (tmm) REVERT: B 50 GLN cc_start: 0.8581 (tt0) cc_final: 0.7647 (mt0) REVERT: B 111 LEU cc_start: 0.8391 (tp) cc_final: 0.7970 (tp) REVERT: B 141 ILE cc_start: 0.8727 (mt) cc_final: 0.8483 (mt) REVERT: B 144 MET cc_start: 0.8448 (ppp) cc_final: 0.8241 (ppp) REVERT: B 190 LEU cc_start: 0.9379 (mt) cc_final: 0.9165 (mt) REVERT: B 193 ASN cc_start: 0.5716 (m110) cc_final: 0.5084 (m110) REVERT: B 197 ASP cc_start: 0.7078 (p0) cc_final: 0.6836 (p0) REVERT: C 21 ASN cc_start: 0.8255 (m110) cc_final: 0.7740 (m-40) REVERT: C 28 GLU cc_start: 0.7855 (mp0) cc_final: 0.7305 (mp0) REVERT: C 100 ARG cc_start: 0.8135 (mmp-170) cc_final: 0.7395 (mtm110) REVERT: C 104 ILE cc_start: 0.8458 (tt) cc_final: 0.8233 (tp) REVERT: C 131 LYS cc_start: 0.8763 (tttp) cc_final: 0.7983 (tptt) REVERT: D 10 MET cc_start: 0.6977 (mmm) cc_final: 0.5525 (ttt) REVERT: D 55 MET cc_start: 0.9143 (ttt) cc_final: 0.8741 (ttm) REVERT: D 66 MET cc_start: 0.9116 (mmm) cc_final: 0.8787 (mmm) REVERT: D 114 GLN cc_start: 0.9298 (pt0) cc_final: 0.9065 (pt0) REVERT: D 154 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6132 (mtm-85) REVERT: D 192 GLN cc_start: 0.8519 (tp-100) cc_final: 0.8284 (tp-100) REVERT: D 212 GLU cc_start: 0.9142 (pt0) cc_final: 0.8299 (pm20) REVERT: D 215 MET cc_start: 0.8964 (ptp) cc_final: 0.8708 (ptp) REVERT: E 10 MET cc_start: 0.4401 (mmm) cc_final: 0.3604 (tmm) REVERT: E 98 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8210 (mm-30) REVERT: E 214 MET cc_start: 0.9193 (mtm) cc_final: 0.8846 (mtp) REVERT: F 25 LYS cc_start: 0.8878 (mttt) cc_final: 0.8558 (tptm) REVERT: F 131 LYS cc_start: 0.8796 (tttt) cc_final: 0.8363 (tttt) REVERT: F 144 MET cc_start: 0.7164 (tmm) cc_final: 0.6143 (ttp) outliers start: 1 outliers final: 0 residues processed: 395 average time/residue: 0.3292 time to fit residues: 175.8789 Evaluate side-chains 310 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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: 5.9990 chunk 10 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 179 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096984 restraints weight = 50621.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101719 restraints weight = 24973.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104908 restraints weight = 15652.396| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10572 Z= 0.135 Angle : 0.660 7.647 14378 Z= 0.338 Chirality : 0.045 0.139 1604 Planarity : 0.005 0.054 1882 Dihedral : 3.913 18.342 1404 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.18 % Allowed : 2.30 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.22), residues: 1310 helix: 0.48 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -0.57 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 133 HIS 0.007 0.001 HIS A 12 PHE 0.013 0.002 PHE E 161 TYR 0.015 0.002 TYR F 164 ARG 0.011 0.001 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 577) hydrogen bonds : angle 4.04992 ( 1731) SS BOND : bond 0.00536 ( 6) SS BOND : angle 1.87959 ( 12) covalent geometry : bond 0.00313 (10566) covalent geometry : angle 0.65760 (14366) *********************** 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 394 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 2.030 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: 0.6512 (mmm) cc_final: 0.5168 (ttt) REVERT: A 113 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8613 (mt-10) REVERT: A 161 PHE cc_start: 0.8617 (t80) cc_final: 0.8288 (t80) REVERT: A 167 ARG cc_start: 0.8794 (ptm160) cc_final: 0.8394 (ptm160) REVERT: A 214 MET cc_start: 0.9096 (ptp) cc_final: 0.8696 (ppp) REVERT: A 215 MET cc_start: 0.8919 (ptp) cc_final: 0.8221 (ptp) REVERT: B 10 MET cc_start: 0.5155 (tmm) cc_final: 0.4405 (tmm) REVERT: B 50 GLN cc_start: 0.8502 (tt0) cc_final: 0.7766 (mt0) REVERT: B 70 LYS cc_start: 0.8818 (pttt) cc_final: 0.8600 (pttt) REVERT: B 115 ILE cc_start: 0.8722 (mt) cc_final: 0.8487 (mt) REVERT: B 118 MET cc_start: 0.8540 (ptt) cc_final: 0.7509 (tpp) REVERT: B 144 MET cc_start: 0.8460 (ppp) cc_final: 0.8237 (ppp) REVERT: B 197 ASP cc_start: 0.6869 (p0) cc_final: 0.6572 (p0) REVERT: B 214 MET cc_start: 0.9122 (ttm) cc_final: 0.8848 (ttm) REVERT: C 28 GLU cc_start: 0.7948 (mp0) cc_final: 0.7369 (mp0) REVERT: C 100 ARG cc_start: 0.8000 (mmp-170) cc_final: 0.7436 (mtm110) REVERT: C 104 ILE cc_start: 0.8492 (tt) cc_final: 0.8265 (tp) REVERT: C 131 LYS cc_start: 0.8492 (tttp) cc_final: 0.8041 (tttt) REVERT: C 132 ARG cc_start: 0.8397 (ptp-170) cc_final: 0.7678 (ttp-110) REVERT: D 40 PHE cc_start: 0.8625 (t80) cc_final: 0.8344 (t80) REVERT: D 55 MET cc_start: 0.9059 (ttt) cc_final: 0.8639 (ttm) REVERT: D 118 MET cc_start: 0.8247 (mtt) cc_final: 0.7808 (mmm) REVERT: D 128 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6714 (tm-30) REVERT: D 154 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6198 (mtm-85) REVERT: D 167 ARG cc_start: 0.8789 (ptm160) cc_final: 0.8579 (ptm160) REVERT: D 212 GLU cc_start: 0.9029 (pt0) cc_final: 0.8218 (pm20) REVERT: E 10 MET cc_start: 0.4439 (mmm) cc_final: 0.3680 (tmm) REVERT: E 84 HIS cc_start: 0.8050 (t-170) cc_final: 0.7149 (t-170) REVERT: E 214 MET cc_start: 0.9199 (mtm) cc_final: 0.8923 (mtp) REVERT: F 25 LYS cc_start: 0.8783 (mttt) cc_final: 0.8389 (tppt) REVERT: F 100 ARG cc_start: 0.8572 (mtp-110) cc_final: 0.8343 (mtm110) REVERT: F 131 LYS cc_start: 0.8689 (tttt) cc_final: 0.7991 (tptt) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.3774 time to fit residues: 201.5544 Evaluate side-chains 298 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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: 5.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 179 GLN D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.128145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094976 restraints weight = 50364.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099483 restraints weight = 25530.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102613 restraints weight = 16118.162| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10572 Z= 0.160 Angle : 0.682 9.416 14378 Z= 0.348 Chirality : 0.045 0.145 1604 Planarity : 0.005 0.053 1882 Dihedral : 4.038 18.702 1404 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.06 (0.22), residues: 1310 helix: 0.44 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -0.55 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 133 HIS 0.005 0.001 HIS B 84 PHE 0.011 0.002 PHE E 161 TYR 0.020 0.002 TYR C 169 ARG 0.008 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 577) hydrogen bonds : angle 4.15032 ( 1731) SS BOND : bond 0.00749 ( 6) SS BOND : angle 1.41425 ( 12) covalent geometry : bond 0.00367 (10566) covalent geometry : angle 0.68066 (14366) *********************** 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 392 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6602 (mmm) cc_final: 0.5276 (ttt) REVERT: A 113 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 161 PHE cc_start: 0.8567 (t80) cc_final: 0.8210 (t80) REVERT: A 212 GLU cc_start: 0.9328 (mt-10) cc_final: 0.8378 (mt-10) REVERT: A 214 MET cc_start: 0.9076 (ptp) cc_final: 0.8723 (ppp) REVERT: A 215 MET cc_start: 0.9097 (ptp) cc_final: 0.8353 (ptp) REVERT: B 2 ILE cc_start: 0.9149 (tp) cc_final: 0.8929 (tp) REVERT: B 10 MET cc_start: 0.5355 (tmm) cc_final: 0.4607 (tmm) REVERT: B 50 GLN cc_start: 0.8441 (tt0) cc_final: 0.7535 (mt0) REVERT: B 115 ILE cc_start: 0.8775 (mt) cc_final: 0.8533 (mt) REVERT: B 118 MET cc_start: 0.8565 (ptt) cc_final: 0.7468 (tpp) REVERT: B 141 ILE cc_start: 0.8826 (mt) cc_final: 0.8622 (mt) REVERT: B 144 MET cc_start: 0.8403 (ppp) cc_final: 0.7931 (ppp) REVERT: B 164 TYR cc_start: 0.8440 (t80) cc_final: 0.8086 (t80) REVERT: B 190 LEU cc_start: 0.9382 (mt) cc_final: 0.9133 (mt) REVERT: B 197 ASP cc_start: 0.6828 (p0) cc_final: 0.6511 (p0) REVERT: B 214 MET cc_start: 0.9115 (ttm) cc_final: 0.8882 (ttm) REVERT: C 28 GLU cc_start: 0.7904 (mp0) cc_final: 0.7295 (mp0) REVERT: C 100 ARG cc_start: 0.8101 (mmp-170) cc_final: 0.7503 (mtm110) REVERT: C 131 LYS cc_start: 0.8513 (tttp) cc_final: 0.8001 (tttt) REVERT: C 132 ARG cc_start: 0.8295 (ptp-170) cc_final: 0.7566 (ttp-110) REVERT: C 143 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7808 (ttm170) REVERT: C 189 LEU cc_start: 0.9050 (mm) cc_final: 0.8771 (mm) REVERT: D 48 THR cc_start: 0.8990 (p) cc_final: 0.8265 (p) REVERT: D 55 MET cc_start: 0.9029 (ttt) cc_final: 0.8642 (ttm) REVERT: D 114 GLN cc_start: 0.9272 (pt0) cc_final: 0.9052 (pt0) REVERT: D 118 MET cc_start: 0.8250 (mtt) cc_final: 0.7829 (mmm) REVERT: D 128 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6708 (tm-30) REVERT: D 129 ILE cc_start: 0.7457 (mt) cc_final: 0.7078 (mt) REVERT: D 154 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.6916 (mtm-85) REVERT: D 189 LEU cc_start: 0.9339 (mm) cc_final: 0.9115 (mm) REVERT: D 193 ASN cc_start: 0.8103 (m-40) cc_final: 0.7627 (t0) REVERT: D 212 GLU cc_start: 0.9094 (pt0) cc_final: 0.8291 (pm20) REVERT: E 10 MET cc_start: 0.4484 (mmm) cc_final: 0.3820 (tmm) REVERT: E 98 GLU cc_start: 0.8255 (tp30) cc_final: 0.7992 (tp30) REVERT: E 112 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8743 (mm-40) REVERT: F 21 ASN cc_start: 0.8185 (m110) cc_final: 0.7884 (m110) REVERT: F 25 LYS cc_start: 0.8809 (mttt) cc_final: 0.8385 (tptm) REVERT: F 100 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8359 (mtm110) REVERT: F 129 ILE cc_start: 0.8643 (pt) cc_final: 0.8412 (pt) REVERT: F 139 ASN cc_start: 0.9240 (m-40) cc_final: 0.9035 (m110) REVERT: F 144 MET cc_start: 0.7201 (tmm) cc_final: 0.6169 (ttp) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.2627 time to fit residues: 141.0698 Evaluate side-chains 309 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS B 179 GLN C 193 ASN D 87 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN F 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097896 restraints weight = 45913.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102301 restraints weight = 23419.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105306 restraints weight = 14959.926| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10572 Z= 0.125 Angle : 0.654 9.418 14378 Z= 0.334 Chirality : 0.045 0.152 1604 Planarity : 0.005 0.060 1882 Dihedral : 3.981 17.941 1404 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.18 % Allowed : 1.06 % Favored : 98.76 % 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: 0.10 (0.22), residues: 1310 helix: 0.45 (0.17), residues: 868 sheet: None (None), residues: 0 loop : -0.50 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 80 HIS 0.007 0.001 HIS A 12 PHE 0.013 0.001 PHE E 161 TYR 0.016 0.002 TYR E 169 ARG 0.007 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 577) hydrogen bonds : angle 4.10235 ( 1731) SS BOND : bond 0.00279 ( 6) SS BOND : angle 1.40000 ( 12) covalent geometry : bond 0.00281 (10566) covalent geometry : angle 0.65309 (14366) *********************** 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 405 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 403 time to evaluate : 1.128 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: 0.6527 (mmm) cc_final: 0.5345 (ttt) REVERT: A 144 MET cc_start: 0.8451 (tmm) cc_final: 0.8218 (ttp) REVERT: A 161 PHE cc_start: 0.8593 (t80) cc_final: 0.8306 (t80) REVERT: A 167 ARG cc_start: 0.8697 (ptm160) cc_final: 0.8317 (ptm160) REVERT: A 214 MET cc_start: 0.8980 (ptp) cc_final: 0.8633 (ppp) REVERT: A 215 MET cc_start: 0.8799 (ptp) cc_final: 0.8338 (ptt) REVERT: B 10 MET cc_start: 0.5326 (tmm) cc_final: 0.4604 (tmm) REVERT: B 50 GLN cc_start: 0.8483 (tt0) cc_final: 0.7636 (mt0) REVERT: B 98 GLU cc_start: 0.7910 (tp30) cc_final: 0.7679 (tp30) REVERT: B 111 LEU cc_start: 0.8465 (tp) cc_final: 0.8254 (tp) REVERT: B 118 MET cc_start: 0.8543 (ptt) cc_final: 0.7546 (tpp) REVERT: B 141 ILE cc_start: 0.8752 (mt) cc_final: 0.8535 (mt) REVERT: B 144 MET cc_start: 0.8130 (ppp) cc_final: 0.7652 (ppp) REVERT: B 164 TYR cc_start: 0.8267 (t80) cc_final: 0.7834 (t80) REVERT: B 190 LEU cc_start: 0.9343 (mt) cc_final: 0.9091 (mt) REVERT: B 197 ASP cc_start: 0.6835 (p0) cc_final: 0.6523 (p0) REVERT: B 202 LEU cc_start: 0.8384 (pp) cc_final: 0.8097 (pp) REVERT: B 214 MET cc_start: 0.9054 (ttm) cc_final: 0.8777 (ttt) REVERT: C 28 GLU cc_start: 0.7608 (mp0) cc_final: 0.6903 (mp0) REVERT: C 100 ARG cc_start: 0.7945 (mmp-170) cc_final: 0.7382 (mtm110) REVERT: C 131 LYS cc_start: 0.8520 (tttp) cc_final: 0.7733 (tptt) REVERT: C 132 ARG cc_start: 0.8297 (ptp-170) cc_final: 0.7629 (ttp-110) REVERT: C 133 TRP cc_start: 0.8118 (m-10) cc_final: 0.7754 (m-10) REVERT: C 144 MET cc_start: 0.6017 (tmm) cc_final: 0.5616 (tmm) REVERT: C 193 ASN cc_start: 0.7296 (m-40) cc_final: 0.6166 (t0) REVERT: D 10 MET cc_start: 0.6934 (mmm) cc_final: 0.5587 (ttt) REVERT: D 40 PHE cc_start: 0.8594 (t80) cc_final: 0.8302 (t80) REVERT: D 48 THR cc_start: 0.9139 (p) cc_final: 0.8260 (p) REVERT: D 55 MET cc_start: 0.8962 (ttt) cc_final: 0.8574 (ttm) REVERT: D 114 GLN cc_start: 0.9274 (pt0) cc_final: 0.9069 (pt0) REVERT: D 118 MET cc_start: 0.8229 (mtt) cc_final: 0.7977 (mmm) REVERT: D 128 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6579 (tm-30) REVERT: D 129 ILE cc_start: 0.7492 (mt) cc_final: 0.7268 (mt) REVERT: D 131 LYS cc_start: 0.8415 (tttt) cc_final: 0.8096 (tptm) REVERT: D 133 TRP cc_start: 0.8344 (m-10) cc_final: 0.7867 (m-10) REVERT: D 154 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6116 (mtm-85) REVERT: D 212 GLU cc_start: 0.9074 (pt0) cc_final: 0.8224 (pm20) REVERT: E 10 MET cc_start: 0.4441 (mmm) cc_final: 0.3739 (tmm) REVERT: E 112 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8747 (mm-40) REVERT: E 115 ILE cc_start: 0.8810 (mt) cc_final: 0.8437 (mt) REVERT: E 118 MET cc_start: 0.8561 (ptt) cc_final: 0.7665 (tpp) REVERT: E 214 MET cc_start: 0.9208 (mtp) cc_final: 0.8801 (mtp) REVERT: F 21 ASN cc_start: 0.8180 (m110) cc_final: 0.7927 (m110) REVERT: F 25 LYS cc_start: 0.8662 (mttt) cc_final: 0.8266 (tppt) REVERT: F 28 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7297 (mp0) REVERT: F 66 MET cc_start: 0.8355 (mpp) cc_final: 0.7658 (ttm) REVERT: F 100 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.8249 (mtm110) REVERT: F 131 LYS cc_start: 0.8655 (tttt) cc_final: 0.8053 (tptt) outliers start: 2 outliers final: 0 residues processed: 403 average time/residue: 0.2356 time to fit residues: 128.3281 Evaluate side-chains 312 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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: 10.0000 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 129 optimal weight: 0.0980 chunk 61 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 179 GLN D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.131262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096424 restraints weight = 54252.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101256 restraints weight = 26709.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104542 restraints weight = 16764.196| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.6560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10572 Z= 0.126 Angle : 0.671 7.984 14378 Z= 0.343 Chirality : 0.045 0.165 1604 Planarity : 0.005 0.057 1882 Dihedral : 4.003 20.751 1404 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.14 (0.22), residues: 1310 helix: 0.46 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -0.42 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 23 HIS 0.005 0.001 HIS A 12 PHE 0.019 0.002 PHE A 40 TYR 0.018 0.002 TYR E 169 ARG 0.007 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 577) hydrogen bonds : angle 4.18793 ( 1731) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.27483 ( 12) covalent geometry : bond 0.00285 (10566) covalent geometry : angle 0.67050 (14366) *********************** 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 406 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.195 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: 0.6558 (mmm) cc_final: 0.5371 (ttt) REVERT: A 118 MET cc_start: 0.8035 (mtt) cc_final: 0.7735 (mmm) REVERT: A 161 PHE cc_start: 0.8633 (t80) cc_final: 0.8296 (t80) REVERT: A 167 ARG cc_start: 0.8695 (ptm160) cc_final: 0.8313 (ptm160) REVERT: A 214 MET cc_start: 0.8917 (ptp) cc_final: 0.8582 (ppp) REVERT: A 215 MET cc_start: 0.8831 (ptp) cc_final: 0.8306 (ptp) REVERT: B 10 MET cc_start: 0.5213 (tmm) cc_final: 0.4504 (tmm) REVERT: B 50 GLN cc_start: 0.8440 (tt0) cc_final: 0.7864 (mt0) REVERT: B 98 GLU cc_start: 0.7952 (tp30) cc_final: 0.7749 (tp30) REVERT: B 118 MET cc_start: 0.8395 (ptt) cc_final: 0.7590 (tpp) REVERT: B 144 MET cc_start: 0.8259 (ppp) cc_final: 0.7780 (ppp) REVERT: B 164 TYR cc_start: 0.8290 (t80) cc_final: 0.7842 (t80) REVERT: B 197 ASP cc_start: 0.6957 (p0) cc_final: 0.6641 (p0) REVERT: B 202 LEU cc_start: 0.8379 (pp) cc_final: 0.8079 (pp) REVERT: B 214 MET cc_start: 0.9117 (ttm) cc_final: 0.8839 (ttt) REVERT: C 28 GLU cc_start: 0.7707 (mp0) cc_final: 0.7093 (mp0) REVERT: C 100 ARG cc_start: 0.7925 (mmp-170) cc_final: 0.7182 (mtm110) REVERT: C 131 LYS cc_start: 0.8487 (tttp) cc_final: 0.7723 (tptt) REVERT: C 132 ARG cc_start: 0.8222 (ptp-170) cc_final: 0.7587 (ttp-110) REVERT: C 133 TRP cc_start: 0.8136 (m-10) cc_final: 0.7683 (m-10) REVERT: C 193 ASN cc_start: 0.7247 (m-40) cc_final: 0.6499 (t0) REVERT: D 10 MET cc_start: 0.6907 (mmm) cc_final: 0.5603 (ttt) REVERT: D 48 THR cc_start: 0.9076 (p) cc_final: 0.8203 (p) REVERT: D 55 MET cc_start: 0.8956 (ttt) cc_final: 0.8633 (ttm) REVERT: D 66 MET cc_start: 0.8967 (mmm) cc_final: 0.8610 (mmm) REVERT: D 118 MET cc_start: 0.8286 (mtt) cc_final: 0.8047 (mmm) REVERT: D 128 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6564 (tm-30) REVERT: D 131 LYS cc_start: 0.8317 (tttt) cc_final: 0.8063 (tptm) REVERT: D 154 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6048 (mtm-85) REVERT: D 183 ASN cc_start: 0.8901 (m110) cc_final: 0.8684 (m-40) REVERT: D 199 LYS cc_start: 0.8550 (pttt) cc_final: 0.8338 (pttp) REVERT: D 215 MET cc_start: 0.8555 (ptp) cc_final: 0.8097 (pmm) REVERT: E 10 MET cc_start: 0.4428 (mmm) cc_final: 0.3779 (tmm) REVERT: E 98 GLU cc_start: 0.8421 (tp30) cc_final: 0.8195 (tp30) REVERT: E 112 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8780 (mm-40) REVERT: E 115 ILE cc_start: 0.8822 (mt) cc_final: 0.8479 (mt) REVERT: E 118 MET cc_start: 0.8403 (ptt) cc_final: 0.7747 (tpp) REVERT: F 21 ASN cc_start: 0.8281 (m110) cc_final: 0.7918 (m110) REVERT: F 25 LYS cc_start: 0.8657 (mttt) cc_final: 0.8235 (tppt) REVERT: F 28 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7279 (mp0) REVERT: F 66 MET cc_start: 0.8337 (mpp) cc_final: 0.7651 (ttm) REVERT: F 100 ARG cc_start: 0.8472 (mtp-110) cc_final: 0.8199 (mtm110) REVERT: F 131 LYS cc_start: 0.8685 (tttt) cc_final: 0.8131 (tptt) REVERT: F 139 ASN cc_start: 0.9162 (m-40) cc_final: 0.8939 (m-40) REVERT: F 144 MET cc_start: 0.6656 (tmm) cc_final: 0.5961 (ttt) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.2540 time to fit residues: 139.9111 Evaluate side-chains 324 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 23 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 overall best weight: 3.7200 ------------------------------------------------------------------------------- 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 179 GLN D 87 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095814 restraints weight = 40653.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099964 restraints weight = 22075.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102859 restraints weight = 14431.640| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10572 Z= 0.173 Angle : 0.726 8.382 14378 Z= 0.379 Chirality : 0.047 0.192 1604 Planarity : 0.005 0.061 1882 Dihedral : 4.251 22.616 1404 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.22), residues: 1310 helix: 0.26 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -0.49 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 133 HIS 0.006 0.001 HIS A 12 PHE 0.013 0.002 PHE F 168 TYR 0.018 0.003 TYR D 169 ARG 0.008 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 577) hydrogen bonds : angle 4.38867 ( 1731) SS BOND : bond 0.00128 ( 6) SS BOND : angle 1.17509 ( 12) covalent geometry : bond 0.00393 (10566) covalent geometry : angle 0.72593 (14366) ********************** 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 398 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6797 (mmm) cc_final: 0.5728 (ttt) REVERT: A 118 MET cc_start: 0.8086 (mtt) cc_final: 0.7794 (mmm) REVERT: A 161 PHE cc_start: 0.8680 (t80) cc_final: 0.8323 (t80) REVERT: A 214 MET cc_start: 0.8931 (ptp) cc_final: 0.8617 (ppp) REVERT: A 215 MET cc_start: 0.8690 (ptp) cc_final: 0.8237 (ptp) REVERT: B 10 MET cc_start: 0.5251 (tmm) cc_final: 0.4584 (tmm) REVERT: B 50 GLN cc_start: 0.8463 (tt0) cc_final: 0.7595 (mt0) REVERT: B 98 GLU cc_start: 0.8084 (tp30) cc_final: 0.7724 (tp30) REVERT: B 118 MET cc_start: 0.8482 (ptt) cc_final: 0.7637 (tpp) REVERT: B 164 TYR cc_start: 0.8321 (t80) cc_final: 0.7864 (t80) REVERT: B 190 LEU cc_start: 0.9393 (mt) cc_final: 0.9175 (mt) REVERT: B 197 ASP cc_start: 0.7019 (p0) cc_final: 0.6673 (p0) REVERT: B 202 LEU cc_start: 0.8423 (pp) cc_final: 0.8098 (pp) REVERT: B 214 MET cc_start: 0.9046 (ttm) cc_final: 0.8758 (ttt) REVERT: C 28 GLU cc_start: 0.7756 (mp0) cc_final: 0.7044 (mp0) REVERT: C 100 ARG cc_start: 0.8194 (mmp-170) cc_final: 0.7393 (mtm110) REVERT: C 131 LYS cc_start: 0.8567 (tttp) cc_final: 0.7870 (tptt) REVERT: C 143 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7755 (ttm170) REVERT: C 193 ASN cc_start: 0.7316 (m-40) cc_final: 0.6779 (t0) REVERT: C 201 ILE cc_start: 0.8821 (pt) cc_final: 0.8583 (pt) REVERT: C 214 MET cc_start: 0.8727 (mtm) cc_final: 0.8511 (mtt) REVERT: D 10 MET cc_start: 0.7119 (mmm) cc_final: 0.6001 (ttt) REVERT: D 48 THR cc_start: 0.8929 (p) cc_final: 0.8106 (p) REVERT: D 55 MET cc_start: 0.9067 (ttt) cc_final: 0.8675 (ttm) REVERT: D 79 GLU cc_start: 0.8665 (pm20) cc_final: 0.8322 (pm20) REVERT: D 128 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6415 (tm-30) REVERT: D 129 ILE cc_start: 0.7388 (mt) cc_final: 0.7121 (mt) REVERT: D 131 LYS cc_start: 0.8429 (tttt) cc_final: 0.8118 (tptm) REVERT: D 133 TRP cc_start: 0.8411 (m-10) cc_final: 0.8055 (m-10) REVERT: D 154 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.6783 (mtm-85) REVERT: D 189 LEU cc_start: 0.9345 (mm) cc_final: 0.9119 (mm) REVERT: D 193 ASN cc_start: 0.8187 (m-40) cc_final: 0.7865 (t0) REVERT: D 213 GLU cc_start: 0.9207 (pt0) cc_final: 0.8845 (pm20) REVERT: D 215 MET cc_start: 0.8571 (ptp) cc_final: 0.8124 (pmm) REVERT: E 10 MET cc_start: 0.4478 (mmm) cc_final: 0.3859 (tmm) REVERT: E 68 MET cc_start: 0.7912 (ttm) cc_final: 0.7630 (ttm) REVERT: E 112 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8781 (mm-40) REVERT: E 115 ILE cc_start: 0.8839 (mt) cc_final: 0.8471 (mt) REVERT: E 118 MET cc_start: 0.8506 (ptt) cc_final: 0.7675 (tpp) REVERT: F 21 ASN cc_start: 0.8194 (m110) cc_final: 0.7828 (m110) REVERT: F 25 LYS cc_start: 0.8633 (mttt) cc_final: 0.8308 (tppt) REVERT: F 28 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7309 (mp0) REVERT: F 66 MET cc_start: 0.8470 (mpp) cc_final: 0.7768 (ttm) REVERT: F 131 LYS cc_start: 0.8736 (tttt) cc_final: 0.8181 (tptt) REVERT: F 144 MET cc_start: 0.6617 (tmm) cc_final: 0.6104 (ttt) outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.2522 time to fit residues: 134.5877 Evaluate side-chains 317 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096737 restraints weight = 38169.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.100729 restraints weight = 21206.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103500 restraints weight = 14097.282| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 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 = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10572 Z= 0.139 Angle : 0.711 8.831 14378 Z= 0.364 Chirality : 0.047 0.160 1604 Planarity : 0.005 0.060 1882 Dihedral : 4.273 24.554 1404 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % 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: 0.04 (0.22), residues: 1310 helix: 0.39 (0.17), residues: 860 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 23 HIS 0.003 0.001 HIS A 12 PHE 0.016 0.002 PHE C 168 TYR 0.018 0.002 TYR F 164 ARG 0.007 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 577) hydrogen bonds : angle 4.33840 ( 1731) SS BOND : bond 0.00178 ( 6) SS BOND : angle 1.24121 ( 12) covalent geometry : bond 0.00322 (10566) covalent geometry : angle 0.71006 (14366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4579.85 seconds wall clock time: 83 minutes 8.42 seconds (4988.42 seconds total)