Starting phenix.real_space_refine on Wed Sep 25 09:43:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/09_2024/6slu_10240.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/09_2024/6slu_10240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/09_2024/6slu_10240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/09_2024/6slu_10240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/09_2024/6slu_10240.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/09_2024/6slu_10240.cif" } resolution = 4.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6508 2.51 5 N 1800 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.21, per 1000 atoms: 0.79 Number of scatterers: 10336 At special positions: 0 Unit cell: (114.68, 113.46, 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: 2.78 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: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.512A 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: 4.456A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.698A 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: 4.209A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.587A pdb=" N GLN B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.524A 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: 3.578A pdb=" N LYS B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 4.150A 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: 3.733A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.606A 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: 3.695A 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: 3.624A pdb=" N GLN C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.549A 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: 3.719A 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: 3.532A 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: 3.633A 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: 4.177A 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: 4.189A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.970A pdb=" N MET E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.507A 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: 3.617A 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: 3.568A 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: 4.466A 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: 3.815A 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: 4.587A 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: 2.96 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3210 1.34 - 1.46: 1348 1.46 - 1.57: 5864 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 10566 Sorted by residual: bond pdb=" N PRO D 38 " pdb=" CD PRO D 38 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N PRO A 34 " pdb=" CD PRO A 34 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.83e+01 bond pdb=" C SER A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.335 1.388 -0.054 1.28e-02 6.10e+03 1.77e+01 bond pdb=" N PRO D 34 " pdb=" CD PRO D 34 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N PRO A 38 " pdb=" CD PRO A 38 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 14194 2.64 - 5.28: 155 5.28 - 7.92: 13 7.92 - 10.56: 0 10.56 - 13.20: 4 Bond angle restraints: 14366 Sorted by residual: angle pdb=" CA ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 121.00 114.87 6.13 8.30e-01 1.45e+00 5.45e+01 angle pdb=" N GLU C 29 " pdb=" CA GLU C 29 " pdb=" C GLU C 29 " ideal model delta sigma weight residual 111.36 118.40 -7.04 1.09e+00 8.42e-01 4.18e+01 angle pdb=" N GLU B 29 " pdb=" CA GLU B 29 " pdb=" C GLU B 29 " ideal model delta sigma weight residual 111.36 118.22 -6.86 1.09e+00 8.42e-01 3.96e+01 angle pdb=" C ILE E 37 " pdb=" CA ILE E 37 " pdb=" CB ILE E 37 " ideal model delta sigma weight residual 114.35 107.80 6.55 1.06e+00 8.90e-01 3.82e+01 angle pdb=" O ILE D 37 " pdb=" C ILE D 37 " pdb=" N PRO D 38 " ideal model delta sigma weight residual 120.07 124.09 -4.02 7.10e-01 1.98e+00 3.21e+01 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6209 17.92 - 35.84: 276 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 -12.93 -73.07 1 1.00e+01 1.00e-02 6.80e+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 -117.96 31.96 1 1.00e+01 1.00e-02 1.46e+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 - 0.044: 1223 0.044 - 0.088: 278 0.088 - 0.132: 81 0.132 - 0.177: 16 0.177 - 0.221: 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 2.29 0.22 2.00e-01 2.50e+01 1.22e+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 2.29 0.22 2.00e-01 2.50e+01 1.17e+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 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1601 not shown) Planarity restraints: 1882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 37 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO E 38 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 35 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C GLU F 35 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU F 35 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL F 36 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 19 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C THR E 19 " 0.027 2.00e-02 2.50e+03 pdb=" O THR E 19 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU E 20 " -0.009 2.00e-02 2.50e+03 ... (remaining 1879 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 3 2.14 - 2.83: 3257 2.83 - 3.52: 14581 3.52 - 4.21: 22149 4.21 - 4.90: 38246 Nonbonded interactions: 78236 Sorted by model distance: nonbonded pdb=" O THR D 58 " pdb=" OE2 GLU E 35 " model vdw 1.454 3.040 nonbonded pdb=" O PRO F 17 " pdb=" OD1 ASN F 21 " model vdw 2.029 3.040 nonbonded pdb=" OE1 GLU C 71 " pdb=" OG1 THR D 210 " model vdw 2.099 3.040 nonbonded pdb=" NZ LYS C 30 " pdb=" OE2 GLU C 35 " model vdw 2.202 3.120 nonbonded pdb=" O PRO F 17 " pdb=" CG ASN F 21 " model vdw 2.202 3.270 ... (remaining 78231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.470 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10566 Z= 0.223 Angle : 0.639 13.203 14366 Z= 0.421 Chirality : 0.044 0.221 1604 Planarity : 0.004 0.070 1882 Dihedral : 9.227 89.598 4028 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -1.03 (0.21), residues: 1310 helix: -0.14 (0.17), residues: 814 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 184 HIS 0.001 0.000 HIS E 62 PHE 0.012 0.001 PHE E 32 TYR 0.004 0.001 TYR E 130 ARG 0.002 0.000 ARG B 162 *********************** 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 641 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 639 time to evaluate : 1.308 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 50 GLN cc_start: 0.9257 (tt0) cc_final: 0.8519 (tm-30) REVERT: A 68 MET cc_start: 0.9330 (mtp) cc_final: 0.8284 (mtt) REVERT: A 71 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 115 ILE cc_start: 0.9581 (mm) cc_final: 0.9374 (mm) REVERT: A 117 TRP cc_start: 0.6047 (m-10) cc_final: 0.5720 (m-10) REVERT: A 129 ILE cc_start: 0.9089 (mt) cc_final: 0.8530 (tt) REVERT: A 141 ILE cc_start: 0.9566 (mm) cc_final: 0.9324 (tp) REVERT: A 202 LEU cc_start: 0.9062 (mt) cc_final: 0.8815 (mm) REVERT: B 26 VAL cc_start: 0.9286 (p) cc_final: 0.9070 (m) REVERT: B 38 PRO cc_start: 0.9363 (Cg_exo) cc_final: 0.9057 (Cg_endo) REVERT: B 76 GLU cc_start: 0.9320 (tt0) cc_final: 0.9021 (tp30) REVERT: B 81 ASP cc_start: 0.9302 (t0) cc_final: 0.8508 (t0) REVERT: B 100 ARG cc_start: 0.8984 (ttp80) cc_final: 0.8626 (tpm170) REVERT: B 113 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9279 (mt-10) REVERT: B 114 GLN cc_start: 0.9731 (pt0) cc_final: 0.9073 (pt0) REVERT: B 128 GLU cc_start: 0.9465 (mp0) cc_final: 0.8944 (pp20) REVERT: B 129 ILE cc_start: 0.9656 (mm) cc_final: 0.9208 (tp) REVERT: B 141 ILE cc_start: 0.8869 (mt) cc_final: 0.8299 (mt) REVERT: B 144 MET cc_start: 0.8668 (tmm) cc_final: 0.8459 (ppp) REVERT: B 190 LEU cc_start: 0.9061 (mt) cc_final: 0.8771 (mt) REVERT: C 35 GLU cc_start: 0.8808 (pt0) cc_final: 0.8039 (tm-30) REVERT: C 53 ASN cc_start: 0.8562 (m-40) cc_final: 0.8257 (t0) REVERT: C 68 MET cc_start: 0.9550 (mtp) cc_final: 0.8817 (mtt) REVERT: C 75 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8194 (pp20) REVERT: C 76 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8756 (mm-30) REVERT: C 98 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8736 (tm-30) REVERT: C 129 ILE cc_start: 0.9593 (mt) cc_final: 0.9386 (pt) REVERT: C 159 GLU cc_start: 0.8929 (mp0) cc_final: 0.8344 (pt0) REVERT: C 167 ARG cc_start: 0.8883 (ttt180) cc_final: 0.8622 (ptp-170) REVERT: D 16 SER cc_start: 0.9226 (t) cc_final: 0.8934 (p) REVERT: D 23 TRP cc_start: 0.9287 (t-100) cc_final: 0.8785 (t-100) REVERT: D 32 PHE cc_start: 0.7450 (m-80) cc_final: 0.7066 (m-80) REVERT: D 37 ILE cc_start: 0.9256 (mt) cc_final: 0.9046 (mt) REVERT: D 48 THR cc_start: 0.9592 (p) cc_final: 0.9382 (t) REVERT: D 50 GLN cc_start: 0.9237 (tt0) cc_final: 0.8852 (tm-30) REVERT: D 51 ASP cc_start: 0.9221 (m-30) cc_final: 0.8784 (m-30) REVERT: D 55 MET cc_start: 0.9222 (ttm) cc_final: 0.8982 (ttm) REVERT: D 68 MET cc_start: 0.9208 (mtp) cc_final: 0.8929 (mtp) REVERT: D 71 GLU cc_start: 0.9393 (mt-10) cc_final: 0.8863 (mt-10) REVERT: D 95 GLN cc_start: 0.6789 (tp40) cc_final: 0.6530 (pt0) REVERT: D 128 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 129 ILE cc_start: 0.9091 (mt) cc_final: 0.8646 (tt) REVERT: D 138 LEU cc_start: 0.9493 (mt) cc_final: 0.9252 (tp) REVERT: D 152 ASP cc_start: 0.8092 (m-30) cc_final: 0.7870 (p0) REVERT: D 170 LYS cc_start: 0.9281 (tttt) cc_final: 0.9074 (tptt) REVERT: D 181 VAL cc_start: 0.8561 (p) cc_final: 0.8053 (p) REVERT: D 215 MET cc_start: 0.9067 (mtm) cc_final: 0.8466 (mtm) REVERT: E 28 GLU cc_start: 0.8953 (tt0) cc_final: 0.8546 (pt0) REVERT: E 95 GLN cc_start: 0.6651 (mm110) cc_final: 0.6361 (pt0) REVERT: E 100 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8296 (tpp-160) REVERT: E 128 GLU cc_start: 0.9296 (mp0) cc_final: 0.8781 (pp20) REVERT: E 141 ILE cc_start: 0.8994 (mt) cc_final: 0.8447 (mt) REVERT: E 144 MET cc_start: 0.8239 (ppp) cc_final: 0.7839 (ppp) REVERT: E 161 PHE cc_start: 0.8011 (t80) cc_final: 0.7745 (t80) REVERT: F 52 LEU cc_start: 0.9832 (mp) cc_final: 0.9495 (mp) REVERT: F 68 MET cc_start: 0.9612 (mtp) cc_final: 0.9051 (mtt) REVERT: F 79 GLU cc_start: 0.9572 (tt0) cc_final: 0.9202 (tp30) REVERT: F 98 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8638 (tm-30) REVERT: F 129 ILE cc_start: 0.9596 (mt) cc_final: 0.9276 (pt) REVERT: F 141 ILE cc_start: 0.9231 (mt) cc_final: 0.9017 (mt) REVERT: F 142 VAL cc_start: 0.9263 (m) cc_final: 0.9014 (p) REVERT: F 158 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8275 (mmmt) REVERT: F 159 GLU cc_start: 0.9066 (mp0) cc_final: 0.8569 (pt0) REVERT: F 164 TYR cc_start: 0.8638 (t80) cc_final: 0.7050 (t80) REVERT: F 185 MET cc_start: 0.8997 (ptp) cc_final: 0.8775 (ptp) REVERT: F 191 VAL cc_start: 0.8860 (p) cc_final: 0.8093 (p) REVERT: F 216 THR cc_start: 0.8760 (p) cc_final: 0.8251 (p) outliers start: 2 outliers final: 1 residues processed: 639 average time/residue: 0.2870 time to fit residues: 236.3329 Evaluate side-chains 392 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 0.0980 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 0.0980 chunk 62 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 overall best weight: 0.5120 ------------------------------------------------------------------------------- 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 A 9 GLN A 87 HIS A 95 GLN B 21 ASN B 53 ASN B 95 GLN C 4 GLN C 5 ASN C 67 GLN C 192 GLN D 4 GLN D 9 GLN D 87 HIS D 112 GLN D 183 ASN E 13 GLN E 50 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN F 4 GLN F 139 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10566 Z= 0.211 Angle : 0.634 7.546 14366 Z= 0.320 Chirality : 0.044 0.162 1604 Planarity : 0.005 0.047 1882 Dihedral : 3.378 15.737 1404 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % 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: -0.28 (0.21), residues: 1310 helix: 0.31 (0.17), residues: 830 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 80 HIS 0.005 0.001 HIS E 62 PHE 0.022 0.002 PHE D 161 TYR 0.017 0.001 TYR E 145 ARG 0.005 0.001 ARG D 173 *********************** 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 508 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 507 time to evaluate : 1.165 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: symmetry clash revert: 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: 0.5329 (tpt) cc_final: 0.4938 (mmm) REVERT: A 28 GLU cc_start: 0.8666 (tt0) cc_final: 0.8290 (pp20) REVERT: A 50 GLN cc_start: 0.9200 (tt0) cc_final: 0.8794 (tm-30) REVERT: A 51 ASP cc_start: 0.9406 (m-30) cc_final: 0.8997 (m-30) REVERT: A 68 MET cc_start: 0.9385 (mtp) cc_final: 0.8753 (mtt) REVERT: A 118 MET cc_start: 0.9040 (mmt) cc_final: 0.8817 (mmp) REVERT: A 129 ILE cc_start: 0.8810 (mt) cc_final: 0.8555 (tt) REVERT: A 141 ILE cc_start: 0.9547 (mm) cc_final: 0.9290 (tp) REVERT: A 144 MET cc_start: 0.9214 (tpp) cc_final: 0.8627 (tpp) REVERT: A 167 ARG cc_start: 0.9346 (mtm-85) cc_final: 0.8908 (ptt-90) REVERT: A 215 MET cc_start: 0.8449 (ptm) cc_final: 0.7910 (ptm) REVERT: B 10 MET cc_start: 0.5656 (tmm) cc_final: 0.5288 (tmm) REVERT: B 32 PHE cc_start: 0.5831 (m-80) cc_final: 0.5617 (m-10) REVERT: B 38 PRO cc_start: 0.9310 (Cg_exo) cc_final: 0.9076 (Cg_endo) REVERT: B 55 MET cc_start: 0.9495 (ttm) cc_final: 0.9102 (tpp) REVERT: B 96 MET cc_start: 0.3970 (mtm) cc_final: 0.3750 (mtt) REVERT: B 128 GLU cc_start: 0.9462 (mp0) cc_final: 0.8902 (pp20) REVERT: B 129 ILE cc_start: 0.9650 (mm) cc_final: 0.9054 (tp) REVERT: B 141 ILE cc_start: 0.8599 (mt) cc_final: 0.8357 (mt) REVERT: B 190 LEU cc_start: 0.8896 (mt) cc_final: 0.8455 (mt) REVERT: C 9 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8005 (pm20) REVERT: C 13 GLN cc_start: 0.9506 (tp40) cc_final: 0.9301 (tp40) REVERT: C 25 LYS cc_start: 0.8574 (pttt) cc_final: 0.8164 (ttpt) REVERT: C 26 VAL cc_start: 0.8830 (p) cc_final: 0.8235 (p) REVERT: C 35 GLU cc_start: 0.8987 (pt0) cc_final: 0.8205 (tm-30) REVERT: C 53 ASN cc_start: 0.8512 (m-40) cc_final: 0.8295 (t0) REVERT: C 68 MET cc_start: 0.9502 (mtp) cc_final: 0.8773 (mtt) REVERT: C 98 GLU cc_start: 0.9320 (mt-10) cc_final: 0.8758 (tm-30) REVERT: C 140 LYS cc_start: 0.9347 (mtmm) cc_final: 0.9136 (ptpp) REVERT: C 159 GLU cc_start: 0.8900 (mp0) cc_final: 0.8460 (pt0) REVERT: C 167 ARG cc_start: 0.8858 (ttt180) cc_final: 0.8594 (ptp90) REVERT: C 186 THR cc_start: 0.8991 (p) cc_final: 0.8643 (p) REVERT: C 215 MET cc_start: 0.9004 (ptp) cc_final: 0.8772 (ppp) REVERT: C 216 THR cc_start: 0.8669 (p) cc_final: 0.8083 (p) REVERT: D 16 SER cc_start: 0.9250 (t) cc_final: 0.8858 (p) REVERT: D 23 TRP cc_start: 0.9653 (t-100) cc_final: 0.9362 (t-100) REVERT: D 37 ILE cc_start: 0.9502 (mt) cc_final: 0.9223 (mt) REVERT: D 50 GLN cc_start: 0.9256 (tt0) cc_final: 0.8859 (tm-30) REVERT: D 51 ASP cc_start: 0.9012 (m-30) cc_final: 0.8561 (m-30) REVERT: D 55 MET cc_start: 0.9497 (ttm) cc_final: 0.9209 (ttp) REVERT: D 58 THR cc_start: 0.9209 (p) cc_final: 0.9009 (p) REVERT: D 63 GLN cc_start: 0.9150 (mp10) cc_final: 0.8826 (mp10) REVERT: D 67 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9147 (mt0) REVERT: D 111 LEU cc_start: 0.9496 (tp) cc_final: 0.9261 (tp) REVERT: D 129 ILE cc_start: 0.9066 (mt) cc_final: 0.8615 (tt) REVERT: D 132 ARG cc_start: 0.9429 (mtp-110) cc_final: 0.9047 (ttp-110) REVERT: D 215 MET cc_start: 0.8894 (mtm) cc_final: 0.8501 (mtm) REVERT: E 28 GLU cc_start: 0.8899 (tt0) cc_final: 0.8485 (pt0) REVERT: E 30 LYS cc_start: 0.8911 (tppt) cc_final: 0.8188 (tptp) REVERT: E 55 MET cc_start: 0.9649 (ttm) cc_final: 0.9345 (tpp) REVERT: E 95 GLN cc_start: 0.6697 (mm-40) cc_final: 0.6458 (pt0) REVERT: E 100 ARG cc_start: 0.9090 (ttp80) cc_final: 0.8702 (tpp-160) REVERT: E 128 GLU cc_start: 0.9267 (mp0) cc_final: 0.8743 (tm-30) REVERT: E 129 ILE cc_start: 0.9492 (mm) cc_final: 0.8802 (mm) REVERT: E 141 ILE cc_start: 0.8777 (mt) cc_final: 0.8345 (mt) REVERT: E 215 MET cc_start: 0.8520 (mmp) cc_final: 0.8307 (mmp) REVERT: F 13 GLN cc_start: 0.9436 (tp40) cc_final: 0.9198 (tp-100) REVERT: F 38 PRO cc_start: 0.9445 (Cg_exo) cc_final: 0.9200 (Cg_endo) REVERT: F 39 MET cc_start: 0.9215 (tpp) cc_final: 0.8974 (tpp) REVERT: F 68 MET cc_start: 0.9687 (mtp) cc_final: 0.8948 (mtt) REVERT: F 71 GLU cc_start: 0.9276 (tm-30) cc_final: 0.9049 (tm-30) REVERT: F 75 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8641 (tm-30) REVERT: F 79 GLU cc_start: 0.9613 (tt0) cc_final: 0.9185 (tp30) REVERT: F 111 LEU cc_start: 0.8960 (tp) cc_final: 0.8219 (mp) REVERT: F 114 GLN cc_start: 0.9007 (mp-120) cc_final: 0.8123 (mp10) REVERT: F 117 TRP cc_start: 0.8264 (m-10) cc_final: 0.7465 (m-90) REVERT: F 129 ILE cc_start: 0.9643 (mt) cc_final: 0.9168 (mm) REVERT: F 132 ARG cc_start: 0.9453 (mtp-110) cc_final: 0.9100 (ptm-80) REVERT: F 158 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8221 (mmmt) REVERT: F 164 TYR cc_start: 0.8032 (t80) cc_final: 0.6997 (t80) REVERT: F 168 PHE cc_start: 0.9404 (t80) cc_final: 0.9189 (t80) REVERT: F 190 LEU cc_start: 0.8810 (mt) cc_final: 0.8343 (mt) outliers start: 1 outliers final: 0 residues processed: 508 average time/residue: 0.2859 time to fit residues: 187.8812 Evaluate side-chains 385 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.0970 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 112 GLN E 13 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10566 Z= 0.290 Angle : 0.698 8.105 14366 Z= 0.364 Chirality : 0.045 0.158 1604 Planarity : 0.006 0.047 1882 Dihedral : 3.803 15.974 1404 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.18 % Allowed : 3.19 % Favored : 96.64 % 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: 0.07 (0.22), residues: 1310 helix: 0.56 (0.17), residues: 836 sheet: None (None), residues: 0 loop : -0.75 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 23 HIS 0.005 0.001 HIS E 62 PHE 0.018 0.003 PHE B 40 TYR 0.011 0.002 TYR B 145 ARG 0.010 0.001 ARG E 167 *********************** 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 438 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 436 time to evaluate : 1.267 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: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.9494 (mtp) cc_final: 0.9091 (mtt) REVERT: A 98 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6605 (mt-10) REVERT: A 126 VAL cc_start: 0.8465 (m) cc_final: 0.8229 (p) REVERT: A 128 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 129 ILE cc_start: 0.9048 (mt) cc_final: 0.8641 (mt) REVERT: A 141 ILE cc_start: 0.9606 (mm) cc_final: 0.9357 (tp) REVERT: A 163 ASP cc_start: 0.8903 (m-30) cc_final: 0.8578 (m-30) REVERT: A 167 ARG cc_start: 0.9277 (mtm-85) cc_final: 0.8847 (ptp90) REVERT: A 215 MET cc_start: 0.8475 (ptm) cc_final: 0.8049 (ptm) REVERT: B 10 MET cc_start: 0.5718 (tmm) cc_final: 0.5310 (tmm) REVERT: B 32 PHE cc_start: 0.6686 (m-80) cc_final: 0.6477 (m-10) REVERT: B 68 MET cc_start: 0.9180 (mtt) cc_final: 0.8964 (mtt) REVERT: B 128 GLU cc_start: 0.9510 (mp0) cc_final: 0.9057 (mp0) REVERT: B 129 ILE cc_start: 0.9605 (mm) cc_final: 0.9341 (mm) REVERT: B 132 ARG cc_start: 0.9706 (ptp-110) cc_final: 0.9457 (ptp-110) REVERT: B 190 LEU cc_start: 0.9131 (mt) cc_final: 0.8866 (mt) REVERT: C 53 ASN cc_start: 0.8721 (m-40) cc_final: 0.8461 (t0) REVERT: C 68 MET cc_start: 0.9479 (mtp) cc_final: 0.9008 (mtt) REVERT: C 96 MET cc_start: 0.3153 (mpp) cc_final: 0.2878 (mpp) REVERT: C 140 LYS cc_start: 0.9373 (mtmm) cc_final: 0.9117 (ptpp) REVERT: C 159 GLU cc_start: 0.9002 (mp0) cc_final: 0.8743 (mp0) REVERT: C 167 ARG cc_start: 0.9098 (ttt180) cc_final: 0.8703 (ptp-170) REVERT: D 23 TRP cc_start: 0.9676 (t-100) cc_final: 0.9389 (t-100) REVERT: D 55 MET cc_start: 0.9547 (ttm) cc_final: 0.9098 (ttm) REVERT: D 68 MET cc_start: 0.9293 (mtt) cc_final: 0.8909 (mtt) REVERT: D 76 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8504 (mt-10) REVERT: D 98 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6694 (mt-10) REVERT: D 129 ILE cc_start: 0.9075 (mt) cc_final: 0.8664 (tt) REVERT: D 212 GLU cc_start: 0.9310 (pt0) cc_final: 0.8829 (pm20) REVERT: D 215 MET cc_start: 0.8811 (mtm) cc_final: 0.8401 (mtm) REVERT: E 10 MET cc_start: 0.5049 (tmm) cc_final: 0.4823 (tmm) REVERT: E 13 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8484 (pp30) REVERT: E 28 GLU cc_start: 0.8850 (tt0) cc_final: 0.8571 (tm-30) REVERT: E 30 LYS cc_start: 0.8865 (tppt) cc_final: 0.8217 (tptp) REVERT: E 55 MET cc_start: 0.9567 (ttm) cc_final: 0.9220 (tpp) REVERT: E 58 THR cc_start: 0.9319 (p) cc_final: 0.9105 (p) REVERT: E 66 MET cc_start: 0.9031 (mpp) cc_final: 0.8621 (mpp) REVERT: E 68 MET cc_start: 0.8956 (mtp) cc_final: 0.8461 (mtp) REVERT: E 71 GLU cc_start: 0.8563 (pp20) cc_final: 0.8350 (pp20) REVERT: E 95 GLN cc_start: 0.6027 (mm-40) cc_final: 0.5717 (pt0) REVERT: E 100 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8689 (tpp-160) REVERT: E 128 GLU cc_start: 0.9312 (mp0) cc_final: 0.8895 (tm-30) REVERT: E 129 ILE cc_start: 0.9464 (mm) cc_final: 0.9112 (mm) REVERT: E 141 ILE cc_start: 0.8693 (mt) cc_final: 0.8447 (mt) REVERT: E 144 MET cc_start: 0.7920 (ppp) cc_final: 0.7585 (ppp) REVERT: F 38 PRO cc_start: 0.9505 (Cg_exo) cc_final: 0.9304 (Cg_endo) REVERT: F 39 MET cc_start: 0.9229 (tpp) cc_final: 0.8911 (tpp) REVERT: F 68 MET cc_start: 0.9395 (mtp) cc_final: 0.9016 (mtt) REVERT: F 79 GLU cc_start: 0.9638 (tt0) cc_final: 0.9243 (tp30) REVERT: F 117 TRP cc_start: 0.7975 (m-10) cc_final: 0.7407 (m-90) REVERT: F 129 ILE cc_start: 0.9683 (mt) cc_final: 0.9426 (mm) REVERT: F 159 GLU cc_start: 0.7359 (pt0) cc_final: 0.6928 (pt0) REVERT: F 164 TYR cc_start: 0.8168 (t80) cc_final: 0.6606 (t80) REVERT: F 168 PHE cc_start: 0.9482 (t80) cc_final: 0.8925 (t80) REVERT: F 185 MET cc_start: 0.9241 (ptp) cc_final: 0.8848 (ptp) REVERT: F 190 LEU cc_start: 0.8775 (mt) cc_final: 0.8148 (mt) outliers start: 2 outliers final: 1 residues processed: 438 average time/residue: 0.2845 time to fit residues: 160.9416 Evaluate side-chains 352 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 350 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 139 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10566 Z= 0.218 Angle : 0.641 7.312 14366 Z= 0.331 Chirality : 0.044 0.184 1604 Planarity : 0.005 0.050 1882 Dihedral : 3.878 15.656 1404 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1310 helix: 0.58 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.59 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 23 HIS 0.003 0.001 HIS A 12 PHE 0.020 0.003 PHE A 40 TYR 0.023 0.002 TYR B 145 ARG 0.010 0.001 ARG E 167 *********************** 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 425 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 98 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6950 (mt-10) REVERT: A 132 ARG cc_start: 0.9389 (mtp-110) cc_final: 0.9165 (ttm110) REVERT: A 141 ILE cc_start: 0.9616 (mm) cc_final: 0.9384 (tp) REVERT: A 144 MET cc_start: 0.9313 (tpp) cc_final: 0.8926 (tpp) REVERT: A 167 ARG cc_start: 0.9130 (mtm-85) cc_final: 0.8552 (ptt-90) REVERT: A 215 MET cc_start: 0.8436 (ptm) cc_final: 0.8074 (ptm) REVERT: B 10 MET cc_start: 0.5808 (tmm) cc_final: 0.5513 (tmm) REVERT: B 66 MET cc_start: 0.9062 (mpp) cc_final: 0.8849 (mpp) REVERT: B 71 GLU cc_start: 0.8936 (pp20) cc_final: 0.8636 (pp20) REVERT: B 72 THR cc_start: 0.9072 (p) cc_final: 0.8597 (p) REVERT: B 128 GLU cc_start: 0.9495 (mp0) cc_final: 0.9178 (mp0) REVERT: B 141 ILE cc_start: 0.9059 (mt) cc_final: 0.8800 (mt) REVERT: B 144 MET cc_start: 0.8876 (ppp) cc_final: 0.8296 (ppp) REVERT: B 190 LEU cc_start: 0.9201 (mt) cc_final: 0.8964 (mt) REVERT: B 212 GLU cc_start: 0.9363 (pt0) cc_final: 0.8702 (pm20) REVERT: C 9 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8222 (tm-30) REVERT: C 21 ASN cc_start: 0.9232 (m110) cc_final: 0.9006 (m110) REVERT: C 53 ASN cc_start: 0.8807 (m-40) cc_final: 0.8474 (t0) REVERT: C 68 MET cc_start: 0.9589 (mtp) cc_final: 0.9274 (mtm) REVERT: C 71 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8845 (tm-30) REVERT: C 97 ARG cc_start: 0.9175 (ttp-110) cc_final: 0.8850 (ttp-110) REVERT: C 117 TRP cc_start: 0.7914 (m-10) cc_final: 0.7098 (m-90) REVERT: C 159 GLU cc_start: 0.9033 (mp0) cc_final: 0.8798 (mp0) REVERT: C 167 ARG cc_start: 0.9048 (ttt180) cc_final: 0.8596 (ptp90) REVERT: C 185 MET cc_start: 0.9114 (ptp) cc_final: 0.8729 (ptp) REVERT: D 23 TRP cc_start: 0.9693 (t-100) cc_final: 0.9394 (t-100) REVERT: D 55 MET cc_start: 0.9549 (ttm) cc_final: 0.9090 (ttm) REVERT: D 117 TRP cc_start: 0.7363 (m-10) cc_final: 0.7057 (m-90) REVERT: D 173 ARG cc_start: 0.9513 (ttm-80) cc_final: 0.9186 (ttp80) REVERT: E 10 MET cc_start: 0.5018 (tmm) cc_final: 0.4670 (tmm) REVERT: E 25 LYS cc_start: 0.9396 (tttp) cc_final: 0.9166 (ttmm) REVERT: E 28 GLU cc_start: 0.8795 (tt0) cc_final: 0.8291 (pt0) REVERT: E 30 LYS cc_start: 0.8913 (tppt) cc_final: 0.8148 (tptp) REVERT: E 55 MET cc_start: 0.9634 (ttm) cc_final: 0.9296 (tpp) REVERT: E 66 MET cc_start: 0.9015 (mpp) cc_final: 0.8529 (mpp) REVERT: E 68 MET cc_start: 0.8993 (mtp) cc_final: 0.8405 (mtp) REVERT: E 72 THR cc_start: 0.8979 (p) cc_final: 0.8400 (p) REVERT: E 95 GLN cc_start: 0.5847 (mm-40) cc_final: 0.5486 (pt0) REVERT: E 100 ARG cc_start: 0.9064 (ttp80) cc_final: 0.8700 (tpp-160) REVERT: E 128 GLU cc_start: 0.9382 (mp0) cc_final: 0.8855 (tm-30) REVERT: E 129 ILE cc_start: 0.9535 (mm) cc_final: 0.8967 (mm) REVERT: E 132 ARG cc_start: 0.9466 (mtm110) cc_final: 0.9066 (mtm110) REVERT: E 141 ILE cc_start: 0.8714 (mt) cc_final: 0.8473 (mt) REVERT: E 144 MET cc_start: 0.7794 (ppp) cc_final: 0.7593 (ppp) REVERT: F 38 PRO cc_start: 0.9527 (Cg_exo) cc_final: 0.9285 (Cg_endo) REVERT: F 68 MET cc_start: 0.9469 (mtp) cc_final: 0.8895 (mtt) REVERT: F 71 GLU cc_start: 0.9339 (tm-30) cc_final: 0.9138 (tm-30) REVERT: F 79 GLU cc_start: 0.9638 (tt0) cc_final: 0.9298 (tp30) REVERT: F 103 ASP cc_start: 0.8997 (m-30) cc_final: 0.8726 (m-30) REVERT: F 129 ILE cc_start: 0.9698 (mt) cc_final: 0.9464 (mm) REVERT: F 132 ARG cc_start: 0.9590 (mtp-110) cc_final: 0.9298 (ptm-80) REVERT: F 158 LYS cc_start: 0.8333 (mmpt) cc_final: 0.8057 (tppt) REVERT: F 159 GLU cc_start: 0.6839 (pt0) cc_final: 0.6007 (pt0) REVERT: F 164 TYR cc_start: 0.7858 (t80) cc_final: 0.6618 (t80) REVERT: F 167 ARG cc_start: 0.9170 (mtm-85) cc_final: 0.8734 (mtm180) REVERT: F 185 MET cc_start: 0.9180 (ptp) cc_final: 0.8851 (ptp) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.2800 time to fit residues: 154.0131 Evaluate side-chains 360 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.4980 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 chunk 108 optimal weight: 0.1980 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 0.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 12 HIS ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10566 Z= 0.204 Angle : 0.645 7.185 14366 Z= 0.329 Chirality : 0.044 0.160 1604 Planarity : 0.005 0.043 1882 Dihedral : 3.921 17.918 1404 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 0.28 (0.22), residues: 1310 helix: 0.64 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.47 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 23 HIS 0.002 0.000 HIS C 12 PHE 0.033 0.003 PHE B 32 TYR 0.012 0.001 TYR E 130 ARG 0.010 0.001 ARG E 167 *********************** 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 429 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 427 time to evaluate : 1.259 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7199 (mt-10) REVERT: A 128 GLU cc_start: 0.8745 (pm20) cc_final: 0.8441 (tm-30) REVERT: A 163 ASP cc_start: 0.8856 (m-30) cc_final: 0.8165 (m-30) REVERT: A 167 ARG cc_start: 0.9115 (mtm-85) cc_final: 0.8541 (ptt-90) REVERT: A 212 GLU cc_start: 0.9310 (pt0) cc_final: 0.9102 (pm20) REVERT: A 215 MET cc_start: 0.8513 (ptm) cc_final: 0.8182 (ptm) REVERT: B 10 MET cc_start: 0.5885 (tmm) cc_final: 0.5553 (tmm) REVERT: B 55 MET cc_start: 0.9533 (ttm) cc_final: 0.9170 (tpp) REVERT: B 66 MET cc_start: 0.9074 (mpp) cc_final: 0.8744 (mpp) REVERT: B 128 GLU cc_start: 0.9513 (mp0) cc_final: 0.9193 (mp0) REVERT: B 141 ILE cc_start: 0.8995 (mt) cc_final: 0.8794 (mt) REVERT: B 144 MET cc_start: 0.8784 (ppp) cc_final: 0.8336 (ppp) REVERT: C 9 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 35 GLU cc_start: 0.9248 (pt0) cc_final: 0.8384 (tm-30) REVERT: C 53 ASN cc_start: 0.8795 (m-40) cc_final: 0.8479 (t0) REVERT: C 68 MET cc_start: 0.9646 (mtp) cc_final: 0.8888 (mtp) REVERT: C 97 ARG cc_start: 0.9213 (ttp-110) cc_final: 0.8902 (ttp-110) REVERT: C 117 TRP cc_start: 0.8151 (m-10) cc_final: 0.7132 (m-90) REVERT: C 143 ARG cc_start: 0.8550 (mtt180) cc_final: 0.7946 (mmt-90) REVERT: C 159 GLU cc_start: 0.9051 (mp0) cc_final: 0.8811 (mp0) REVERT: C 167 ARG cc_start: 0.9024 (ttt180) cc_final: 0.8575 (ptp-170) REVERT: C 185 MET cc_start: 0.9101 (ptp) cc_final: 0.8753 (ptp) REVERT: D 23 TRP cc_start: 0.9699 (t-100) cc_final: 0.9318 (t-100) REVERT: D 55 MET cc_start: 0.9558 (ttm) cc_final: 0.9149 (ttp) REVERT: D 96 MET cc_start: 0.7026 (tpt) cc_final: 0.6809 (tpp) REVERT: D 117 TRP cc_start: 0.7441 (m-10) cc_final: 0.7086 (m-90) REVERT: D 128 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8618 (tm-30) REVERT: D 129 ILE cc_start: 0.9094 (mt) cc_final: 0.8674 (mt) REVERT: D 185 MET cc_start: 0.9603 (ptp) cc_final: 0.9369 (mtt) REVERT: E 10 MET cc_start: 0.5240 (tmm) cc_final: 0.4843 (tmm) REVERT: E 25 LYS cc_start: 0.9385 (tttp) cc_final: 0.9063 (ttmm) REVERT: E 28 GLU cc_start: 0.8808 (tt0) cc_final: 0.8176 (pt0) REVERT: E 30 LYS cc_start: 0.8884 (tppt) cc_final: 0.8319 (tptp) REVERT: E 55 MET cc_start: 0.9553 (ttm) cc_final: 0.9190 (tpp) REVERT: E 66 MET cc_start: 0.9070 (mpp) cc_final: 0.8660 (mpp) REVERT: E 68 MET cc_start: 0.8956 (mtp) cc_final: 0.8452 (mtp) REVERT: E 95 GLN cc_start: 0.5831 (mm-40) cc_final: 0.5346 (pt0) REVERT: E 100 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8696 (tpp-160) REVERT: E 128 GLU cc_start: 0.9411 (mp0) cc_final: 0.8799 (tm-30) REVERT: E 129 ILE cc_start: 0.9543 (mm) cc_final: 0.8882 (mm) REVERT: E 132 ARG cc_start: 0.9469 (mtm110) cc_final: 0.9016 (mtm110) REVERT: E 141 ILE cc_start: 0.8737 (mt) cc_final: 0.8520 (mt) REVERT: E 144 MET cc_start: 0.7823 (ppp) cc_final: 0.7572 (ppp) REVERT: F 38 PRO cc_start: 0.9480 (Cg_exo) cc_final: 0.9245 (Cg_endo) REVERT: F 50 GLN cc_start: 0.8798 (mp10) cc_final: 0.8395 (mp10) REVERT: F 68 MET cc_start: 0.9245 (mtp) cc_final: 0.8819 (mtt) REVERT: F 71 GLU cc_start: 0.9309 (tm-30) cc_final: 0.8975 (tm-30) REVERT: F 79 GLU cc_start: 0.9638 (tt0) cc_final: 0.9272 (tp30) REVERT: F 128 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8839 (tm-30) REVERT: F 129 ILE cc_start: 0.9725 (mt) cc_final: 0.9008 (mm) REVERT: F 132 ARG cc_start: 0.9594 (mtp-110) cc_final: 0.9270 (ttp80) REVERT: F 158 LYS cc_start: 0.8309 (mmpt) cc_final: 0.8019 (tppt) REVERT: F 164 TYR cc_start: 0.7803 (t80) cc_final: 0.6510 (t80) REVERT: F 167 ARG cc_start: 0.9236 (mtm-85) cc_final: 0.8618 (ptt-90) REVERT: F 185 MET cc_start: 0.9205 (ptp) cc_final: 0.8911 (ptp) outliers start: 2 outliers final: 1 residues processed: 429 average time/residue: 0.2841 time to fit residues: 157.9778 Evaluate side-chains 355 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 67 optimal weight: 0.0370 chunk 123 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10566 Z= 0.192 Angle : 0.679 7.390 14366 Z= 0.346 Chirality : 0.045 0.189 1604 Planarity : 0.005 0.043 1882 Dihedral : 3.994 17.527 1404 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 0.32 (0.23), residues: 1310 helix: 0.66 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.43 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 117 HIS 0.003 0.000 HIS F 62 PHE 0.023 0.002 PHE A 40 TYR 0.025 0.002 TYR E 169 ARG 0.011 0.001 ARG E 167 *********************** 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 434 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 1.164 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: symmetry clash REVERT: A 10 MET cc_start: 0.5434 (mmm) cc_final: 0.5131 (mmm) REVERT: A 40 PHE cc_start: 0.9389 (t80) cc_final: 0.9005 (t80) REVERT: A 96 MET cc_start: 0.5872 (tpt) cc_final: 0.5604 (tpp) REVERT: A 129 ILE cc_start: 0.9156 (mt) cc_final: 0.8881 (mt) REVERT: A 131 LYS cc_start: 0.9280 (tttt) cc_final: 0.9069 (tttt) REVERT: A 163 ASP cc_start: 0.8841 (m-30) cc_final: 0.8050 (m-30) REVERT: A 167 ARG cc_start: 0.9104 (mtm-85) cc_final: 0.8493 (ptt-90) REVERT: A 215 MET cc_start: 0.8503 (ptm) cc_final: 0.8159 (ptm) REVERT: B 10 MET cc_start: 0.5874 (tmm) cc_final: 0.5547 (tmm) REVERT: B 55 MET cc_start: 0.9500 (ttm) cc_final: 0.9258 (ttm) REVERT: B 82 ARG cc_start: 0.8615 (tmm160) cc_final: 0.8368 (ttp80) REVERT: B 128 GLU cc_start: 0.9483 (mp0) cc_final: 0.9157 (mp0) REVERT: B 144 MET cc_start: 0.8794 (ppp) cc_final: 0.8473 (ppp) REVERT: B 212 GLU cc_start: 0.9295 (pt0) cc_final: 0.9021 (pm20) REVERT: C 29 GLU cc_start: 0.8463 (pp20) cc_final: 0.7584 (pt0) REVERT: C 35 GLU cc_start: 0.9309 (pt0) cc_final: 0.8523 (tm-30) REVERT: C 66 MET cc_start: 0.9395 (mpp) cc_final: 0.9163 (mpp) REVERT: C 68 MET cc_start: 0.9597 (mtp) cc_final: 0.9077 (mtt) REVERT: C 97 ARG cc_start: 0.9189 (ttp-110) cc_final: 0.8857 (ttp-110) REVERT: C 113 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8928 (tt0) REVERT: C 117 TRP cc_start: 0.7931 (m-10) cc_final: 0.7049 (m-10) REVERT: C 159 GLU cc_start: 0.9083 (mp0) cc_final: 0.8831 (mp0) REVERT: C 167 ARG cc_start: 0.9063 (ttt180) cc_final: 0.8593 (ptp-170) REVERT: C 185 MET cc_start: 0.9048 (ptp) cc_final: 0.8755 (ptp) REVERT: D 23 TRP cc_start: 0.9719 (t-100) cc_final: 0.9452 (t-100) REVERT: D 55 MET cc_start: 0.9567 (ttm) cc_final: 0.9211 (ttm) REVERT: D 70 LYS cc_start: 0.9545 (mtpt) cc_final: 0.9181 (ptpt) REVERT: D 98 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6760 (mt-10) REVERT: D 117 TRP cc_start: 0.7451 (m-10) cc_final: 0.7089 (m-90) REVERT: D 129 ILE cc_start: 0.9045 (mt) cc_final: 0.8749 (tt) REVERT: D 173 ARG cc_start: 0.9541 (ttm-80) cc_final: 0.9147 (ttp80) REVERT: E 10 MET cc_start: 0.5318 (tmm) cc_final: 0.4891 (tmm) REVERT: E 25 LYS cc_start: 0.9380 (tttp) cc_final: 0.9066 (ttmm) REVERT: E 28 GLU cc_start: 0.8813 (tt0) cc_final: 0.8225 (pt0) REVERT: E 30 LYS cc_start: 0.8817 (tppt) cc_final: 0.8251 (tptp) REVERT: E 32 PHE cc_start: 0.7517 (m-80) cc_final: 0.7233 (m-80) REVERT: E 55 MET cc_start: 0.9557 (ttm) cc_final: 0.9208 (tpp) REVERT: E 66 MET cc_start: 0.9032 (mpp) cc_final: 0.8601 (mpp) REVERT: E 68 MET cc_start: 0.8919 (mtp) cc_final: 0.8368 (mtp) REVERT: E 72 THR cc_start: 0.8976 (p) cc_final: 0.8441 (p) REVERT: E 100 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8706 (tpp-160) REVERT: E 128 GLU cc_start: 0.9371 (mp0) cc_final: 0.8788 (tm-30) REVERT: E 129 ILE cc_start: 0.9548 (mm) cc_final: 0.8791 (mm) REVERT: E 141 ILE cc_start: 0.8741 (mt) cc_final: 0.8487 (mt) REVERT: E 144 MET cc_start: 0.7939 (ppp) cc_final: 0.7716 (ppp) REVERT: F 38 PRO cc_start: 0.9462 (Cg_exo) cc_final: 0.9192 (Cg_endo) REVERT: F 50 GLN cc_start: 0.8785 (mp10) cc_final: 0.8343 (mp10) REVERT: F 68 MET cc_start: 0.9285 (mtp) cc_final: 0.8924 (mtt) REVERT: F 79 GLU cc_start: 0.9646 (tt0) cc_final: 0.9297 (tp30) REVERT: F 128 GLU cc_start: 0.9268 (tm-30) cc_final: 0.9052 (tm-30) REVERT: F 129 ILE cc_start: 0.9665 (mt) cc_final: 0.9140 (pt) REVERT: F 132 ARG cc_start: 0.9600 (mtp-110) cc_final: 0.9233 (ttp-110) REVERT: F 143 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8681 (mmm-85) REVERT: F 164 TYR cc_start: 0.7956 (t80) cc_final: 0.6579 (t80) REVERT: F 167 ARG cc_start: 0.9262 (mtm-85) cc_final: 0.8957 (mtm-85) REVERT: F 185 MET cc_start: 0.9190 (ptp) cc_final: 0.8868 (ptp) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.2763 time to fit residues: 155.3749 Evaluate side-chains 349 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10566 Z= 0.204 Angle : 0.679 8.309 14366 Z= 0.345 Chirality : 0.046 0.169 1604 Planarity : 0.005 0.054 1882 Dihedral : 4.006 16.901 1404 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.09 % Allowed : 1.42 % Favored : 98.50 % 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: 0.33 (0.23), residues: 1310 helix: 0.65 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.41 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 117 HIS 0.003 0.001 HIS B 62 PHE 0.021 0.003 PHE B 40 TYR 0.022 0.002 TYR E 169 ARG 0.010 0.001 ARG D 82 *********************** 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 424 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 1.187 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5488 (mmm) cc_final: 0.5238 (mmm) REVERT: A 40 PHE cc_start: 0.9376 (t80) cc_final: 0.9147 (t80) REVERT: A 55 MET cc_start: 0.9655 (ttm) cc_final: 0.9439 (ttp) REVERT: A 96 MET cc_start: 0.5886 (tpt) cc_final: 0.5624 (tpp) REVERT: A 98 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7292 (mt-10) REVERT: A 144 MET cc_start: 0.9160 (tpt) cc_final: 0.8892 (tpp) REVERT: A 163 ASP cc_start: 0.8886 (m-30) cc_final: 0.8116 (m-30) REVERT: A 167 ARG cc_start: 0.9132 (mtm-85) cc_final: 0.8518 (ptt-90) REVERT: A 214 MET cc_start: 0.9158 (ptp) cc_final: 0.8954 (ptp) REVERT: A 215 MET cc_start: 0.8523 (ptm) cc_final: 0.8108 (ptm) REVERT: B 10 MET cc_start: 0.6048 (tmm) cc_final: 0.5661 (tmm) REVERT: B 55 MET cc_start: 0.9462 (ttm) cc_final: 0.9200 (ttm) REVERT: B 82 ARG cc_start: 0.8581 (tmm160) cc_final: 0.8152 (ttp80) REVERT: B 128 GLU cc_start: 0.9488 (mp0) cc_final: 0.9178 (mp0) REVERT: B 141 ILE cc_start: 0.8937 (mt) cc_final: 0.8597 (mt) REVERT: B 212 GLU cc_start: 0.9262 (pt0) cc_final: 0.9037 (pt0) REVERT: C 33 SER cc_start: 0.8881 (t) cc_final: 0.8658 (t) REVERT: C 35 GLU cc_start: 0.9328 (pt0) cc_final: 0.8625 (tm-30) REVERT: C 68 MET cc_start: 0.9442 (mtp) cc_final: 0.8700 (mtt) REVERT: C 97 ARG cc_start: 0.9181 (ttp-110) cc_final: 0.8847 (ttp-110) REVERT: C 113 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8911 (tt0) REVERT: C 117 TRP cc_start: 0.7982 (m-10) cc_final: 0.7067 (m-10) REVERT: C 159 GLU cc_start: 0.9117 (mp0) cc_final: 0.8874 (mp0) REVERT: C 167 ARG cc_start: 0.9075 (ttt180) cc_final: 0.8585 (ptp90) REVERT: C 185 MET cc_start: 0.9129 (ptp) cc_final: 0.8803 (ptp) REVERT: D 55 MET cc_start: 0.9569 (ttm) cc_final: 0.9238 (ttm) REVERT: D 56 LEU cc_start: 0.9522 (mt) cc_final: 0.9321 (pp) REVERT: D 70 LYS cc_start: 0.9548 (mtpt) cc_final: 0.9145 (ptpt) REVERT: D 71 GLU cc_start: 0.9240 (pp20) cc_final: 0.8842 (pp20) REVERT: D 98 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6824 (mt-10) REVERT: D 117 TRP cc_start: 0.7660 (m-10) cc_final: 0.7319 (m-90) REVERT: D 173 ARG cc_start: 0.9530 (ttm-80) cc_final: 0.9143 (ttp80) REVERT: D 185 MET cc_start: 0.7825 (mtt) cc_final: 0.7622 (ptp) REVERT: D 214 MET cc_start: 0.9103 (ptp) cc_final: 0.8776 (ptp) REVERT: D 215 MET cc_start: 0.8829 (ptm) cc_final: 0.8572 (ptm) REVERT: E 10 MET cc_start: 0.5359 (tmm) cc_final: 0.4892 (tmm) REVERT: E 25 LYS cc_start: 0.9384 (tttp) cc_final: 0.9057 (ttmm) REVERT: E 28 GLU cc_start: 0.8787 (tt0) cc_final: 0.8186 (pt0) REVERT: E 30 LYS cc_start: 0.8826 (tppt) cc_final: 0.8267 (tptp) REVERT: E 32 PHE cc_start: 0.7534 (m-80) cc_final: 0.7249 (m-80) REVERT: E 66 MET cc_start: 0.8949 (mpp) cc_final: 0.8543 (mpp) REVERT: E 68 MET cc_start: 0.8958 (mtp) cc_final: 0.8404 (mtp) REVERT: E 100 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8707 (tpp-160) REVERT: E 128 GLU cc_start: 0.9377 (mp0) cc_final: 0.8843 (tm-30) REVERT: E 129 ILE cc_start: 0.9417 (mm) cc_final: 0.8777 (mm) REVERT: E 132 ARG cc_start: 0.9367 (mtm110) cc_final: 0.8989 (mtm110) REVERT: E 140 LYS cc_start: 0.9354 (mtpt) cc_final: 0.8887 (mtmm) REVERT: E 141 ILE cc_start: 0.8770 (mt) cc_final: 0.8540 (mt) REVERT: E 144 MET cc_start: 0.8067 (ppp) cc_final: 0.7836 (ppp) REVERT: F 50 GLN cc_start: 0.8777 (mp10) cc_final: 0.8510 (mp10) REVERT: F 68 MET cc_start: 0.9208 (mtp) cc_final: 0.8793 (mtt) REVERT: F 71 GLU cc_start: 0.8701 (pp20) cc_final: 0.8331 (pp20) REVERT: F 79 GLU cc_start: 0.9644 (tt0) cc_final: 0.9296 (tp30) REVERT: F 159 GLU cc_start: 0.8875 (mp0) cc_final: 0.8640 (mp0) REVERT: F 164 TYR cc_start: 0.8144 (t80) cc_final: 0.6872 (t80) REVERT: F 167 ARG cc_start: 0.9308 (mtm-85) cc_final: 0.9050 (mtm180) REVERT: F 185 MET cc_start: 0.9182 (ptp) cc_final: 0.8958 (ptp) outliers start: 1 outliers final: 0 residues processed: 424 average time/residue: 0.2875 time to fit residues: 160.1012 Evaluate side-chains 354 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 chunk 100 optimal weight: 0.1980 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10566 Z= 0.196 Angle : 0.703 7.999 14366 Z= 0.360 Chirality : 0.047 0.171 1604 Planarity : 0.005 0.051 1882 Dihedral : 4.009 16.621 1404 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1310 helix: 0.57 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.40 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 23 HIS 0.003 0.000 HIS B 62 PHE 0.021 0.002 PHE A 40 TYR 0.022 0.002 TYR E 169 ARG 0.008 0.001 ARG D 82 *********************** 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 431 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 1.262 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5460 (mmm) cc_final: 0.5201 (mmm) REVERT: A 96 MET cc_start: 0.5892 (tpt) cc_final: 0.5645 (tpp) REVERT: A 98 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 131 LYS cc_start: 0.9567 (ttpp) cc_final: 0.9336 (ptpp) REVERT: A 144 MET cc_start: 0.9145 (tpt) cc_final: 0.8572 (tmm) REVERT: A 163 ASP cc_start: 0.8847 (m-30) cc_final: 0.8075 (m-30) REVERT: A 167 ARG cc_start: 0.9134 (mtm-85) cc_final: 0.8548 (ptt-90) REVERT: A 175 GLU cc_start: 0.7546 (pm20) cc_final: 0.7343 (pm20) REVERT: A 176 GLN cc_start: 0.8949 (pm20) cc_final: 0.8057 (pp30) REVERT: A 214 MET cc_start: 0.9154 (ptp) cc_final: 0.8950 (ptp) REVERT: A 215 MET cc_start: 0.8630 (ptm) cc_final: 0.8295 (ptm) REVERT: B 10 MET cc_start: 0.6003 (tmm) cc_final: 0.5646 (tmm) REVERT: B 128 GLU cc_start: 0.9479 (mp0) cc_final: 0.9129 (mp0) REVERT: B 141 ILE cc_start: 0.8937 (mt) cc_final: 0.8594 (mt) REVERT: B 212 GLU cc_start: 0.9232 (pt0) cc_final: 0.8880 (pm20) REVERT: C 29 GLU cc_start: 0.8507 (pp20) cc_final: 0.7670 (pt0) REVERT: C 35 GLU cc_start: 0.9345 (pt0) cc_final: 0.8638 (tm-30) REVERT: C 68 MET cc_start: 0.9448 (mtp) cc_final: 0.9032 (mtt) REVERT: C 103 ASP cc_start: 0.8983 (m-30) cc_final: 0.8767 (m-30) REVERT: C 154 ARG cc_start: 0.8510 (tpp80) cc_final: 0.8080 (mmm-85) REVERT: C 159 GLU cc_start: 0.9111 (mp0) cc_final: 0.8895 (mp0) REVERT: C 167 ARG cc_start: 0.9047 (ttt180) cc_final: 0.8540 (ptp90) REVERT: C 185 MET cc_start: 0.9044 (ptp) cc_final: 0.8723 (ptp) REVERT: D 70 LYS cc_start: 0.9546 (mtpt) cc_final: 0.9175 (ptpt) REVERT: D 98 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6822 (mt-10) REVERT: D 132 ARG cc_start: 0.9433 (mtp-110) cc_final: 0.8973 (ttm110) REVERT: D 173 ARG cc_start: 0.9503 (ttm-80) cc_final: 0.9173 (ttp80) REVERT: D 185 MET cc_start: 0.7800 (mtt) cc_final: 0.7561 (ptp) REVERT: D 190 LEU cc_start: 0.9513 (tp) cc_final: 0.9304 (tp) REVERT: E 10 MET cc_start: 0.5338 (tmm) cc_final: 0.4853 (tmm) REVERT: E 30 LYS cc_start: 0.8833 (tppt) cc_final: 0.8249 (tptp) REVERT: E 32 PHE cc_start: 0.7474 (m-80) cc_final: 0.7223 (m-80) REVERT: E 55 MET cc_start: 0.9651 (ttm) cc_final: 0.9347 (tpp) REVERT: E 66 MET cc_start: 0.9098 (mpp) cc_final: 0.8639 (mpp) REVERT: E 68 MET cc_start: 0.8936 (mtp) cc_final: 0.8368 (mtp) REVERT: E 72 THR cc_start: 0.9117 (p) cc_final: 0.8643 (p) REVERT: E 96 MET cc_start: 0.3901 (tpt) cc_final: 0.2729 (mtt) REVERT: E 100 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8702 (tpp-160) REVERT: E 128 GLU cc_start: 0.9397 (mp0) cc_final: 0.8943 (pp20) REVERT: E 130 TYR cc_start: 0.9353 (t80) cc_final: 0.9008 (t80) REVERT: E 132 ARG cc_start: 0.9425 (mtm110) cc_final: 0.8938 (mtm110) REVERT: E 140 LYS cc_start: 0.9340 (mtpt) cc_final: 0.8898 (mtmm) REVERT: E 141 ILE cc_start: 0.8738 (mt) cc_final: 0.8526 (mt) REVERT: F 50 GLN cc_start: 0.8769 (mp10) cc_final: 0.8529 (mp10) REVERT: F 55 MET cc_start: 0.8640 (tmm) cc_final: 0.8386 (tmm) REVERT: F 68 MET cc_start: 0.9267 (mtp) cc_final: 0.8875 (mtt) REVERT: F 79 GLU cc_start: 0.9630 (tt0) cc_final: 0.9294 (tp30) REVERT: F 103 ASP cc_start: 0.8958 (m-30) cc_final: 0.8742 (m-30) REVERT: F 132 ARG cc_start: 0.9668 (mtm110) cc_final: 0.9298 (ptm-80) REVERT: F 164 TYR cc_start: 0.8061 (t80) cc_final: 0.6230 (t80) REVERT: F 167 ARG cc_start: 0.9305 (mtm-85) cc_final: 0.8924 (mtm-85) REVERT: F 179 GLN cc_start: 0.9328 (tp-100) cc_final: 0.9126 (tp-100) REVERT: F 185 MET cc_start: 0.9169 (ptp) cc_final: 0.8939 (ptp) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.2773 time to fit residues: 154.7641 Evaluate side-chains 352 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 139 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10566 Z= 0.268 Angle : 0.746 8.946 14366 Z= 0.394 Chirality : 0.048 0.160 1604 Planarity : 0.005 0.044 1882 Dihedral : 4.255 21.275 1404 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1310 helix: 0.50 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.52 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 23 HIS 0.008 0.001 HIS B 62 PHE 0.023 0.003 PHE B 40 TYR 0.025 0.002 TYR E 169 ARG 0.009 0.001 ARG E 173 *********************** 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 400 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.217 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 45 GLU cc_start: 0.9240 (tt0) cc_final: 0.8724 (mm-30) REVERT: A 144 MET cc_start: 0.9141 (tpt) cc_final: 0.8516 (tmm) REVERT: A 163 ASP cc_start: 0.8849 (m-30) cc_final: 0.8144 (m-30) REVERT: A 167 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8440 (ptt-90) REVERT: A 214 MET cc_start: 0.9226 (ptp) cc_final: 0.8995 (ptp) REVERT: A 215 MET cc_start: 0.8657 (ptm) cc_final: 0.8237 (ptm) REVERT: B 10 MET cc_start: 0.6242 (tmm) cc_final: 0.5723 (tmm) REVERT: B 55 MET cc_start: 0.9297 (ttm) cc_final: 0.8678 (ttp) REVERT: B 66 MET cc_start: 0.9212 (mpp) cc_final: 0.8836 (mpp) REVERT: B 82 ARG cc_start: 0.8675 (tmm160) cc_final: 0.8431 (ttp80) REVERT: B 128 GLU cc_start: 0.9459 (mp0) cc_final: 0.9055 (mp0) REVERT: B 141 ILE cc_start: 0.9030 (mt) cc_final: 0.8698 (mt) REVERT: B 212 GLU cc_start: 0.9386 (pt0) cc_final: 0.9074 (pt0) REVERT: C 35 GLU cc_start: 0.9258 (pt0) cc_final: 0.8373 (tm-30) REVERT: C 39 MET cc_start: 0.9254 (tpp) cc_final: 0.8775 (tpp) REVERT: C 68 MET cc_start: 0.9494 (mtp) cc_final: 0.9140 (mtt) REVERT: C 97 ARG cc_start: 0.9139 (ttp-110) cc_final: 0.8682 (ptt90) REVERT: C 144 MET cc_start: 0.8527 (ptm) cc_final: 0.8307 (ptm) REVERT: C 167 ARG cc_start: 0.9102 (ttt180) cc_final: 0.8643 (ptp90) REVERT: C 185 MET cc_start: 0.9124 (ptp) cc_final: 0.8841 (ptp) REVERT: D 68 MET cc_start: 0.8987 (mtt) cc_final: 0.8295 (mtt) REVERT: D 71 GLU cc_start: 0.9282 (pp20) cc_final: 0.8843 (pp20) REVERT: D 96 MET cc_start: 0.5696 (tpp) cc_final: 0.5306 (tpp) REVERT: D 128 GLU cc_start: 0.9358 (mp0) cc_final: 0.9068 (mp0) REVERT: D 132 ARG cc_start: 0.9386 (mtp-110) cc_final: 0.8958 (ttm110) REVERT: D 143 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7844 (mpt180) REVERT: D 173 ARG cc_start: 0.9558 (ttm-80) cc_final: 0.9139 (ttp80) REVERT: D 185 MET cc_start: 0.7809 (mtt) cc_final: 0.7592 (mtt) REVERT: D 214 MET cc_start: 0.9203 (ptp) cc_final: 0.8900 (ptp) REVERT: D 215 MET cc_start: 0.8894 (ptm) cc_final: 0.8521 (ppp) REVERT: E 10 MET cc_start: 0.5512 (tmm) cc_final: 0.4885 (tmm) REVERT: E 29 GLU cc_start: 0.9320 (tt0) cc_final: 0.8983 (tt0) REVERT: E 30 LYS cc_start: 0.8821 (tppt) cc_final: 0.8338 (tptp) REVERT: E 32 PHE cc_start: 0.7588 (m-80) cc_final: 0.7354 (m-80) REVERT: E 55 MET cc_start: 0.9585 (ttm) cc_final: 0.9288 (tpp) REVERT: E 66 MET cc_start: 0.9082 (mpp) cc_final: 0.8635 (mpp) REVERT: E 68 MET cc_start: 0.9048 (mtp) cc_final: 0.8552 (mtp) REVERT: E 72 THR cc_start: 0.9157 (p) cc_final: 0.8708 (p) REVERT: E 96 MET cc_start: 0.3975 (tpt) cc_final: 0.3042 (mtt) REVERT: E 100 ARG cc_start: 0.9152 (ttp80) cc_final: 0.8731 (tpp-160) REVERT: E 128 GLU cc_start: 0.9400 (mp0) cc_final: 0.8861 (tm-30) REVERT: E 129 ILE cc_start: 0.9436 (mm) cc_final: 0.8932 (mm) REVERT: E 132 ARG cc_start: 0.9414 (mtm110) cc_final: 0.9059 (mtm110) REVERT: E 140 LYS cc_start: 0.9370 (mtpt) cc_final: 0.8941 (mtmm) REVERT: E 141 ILE cc_start: 0.8861 (mt) cc_final: 0.8598 (mt) REVERT: E 144 MET cc_start: 0.8058 (ppp) cc_final: 0.7829 (ppp) REVERT: E 211 LEU cc_start: 0.9684 (pt) cc_final: 0.9484 (pt) REVERT: F 9 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8258 (pp30) REVERT: F 50 GLN cc_start: 0.8772 (mp10) cc_final: 0.8563 (mp10) REVERT: F 68 MET cc_start: 0.9252 (mtp) cc_final: 0.9051 (mtt) REVERT: F 79 GLU cc_start: 0.9635 (tt0) cc_final: 0.9307 (tp30) REVERT: F 81 ASP cc_start: 0.9076 (m-30) cc_final: 0.8843 (m-30) REVERT: F 103 ASP cc_start: 0.8953 (m-30) cc_final: 0.8674 (m-30) REVERT: F 132 ARG cc_start: 0.9626 (mtm110) cc_final: 0.9373 (mtm110) REVERT: F 164 TYR cc_start: 0.8073 (t80) cc_final: 0.6354 (t80) REVERT: F 167 ARG cc_start: 0.9301 (mtm-85) cc_final: 0.8875 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.2838 time to fit residues: 147.2569 Evaluate side-chains 337 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 2.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.7218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10566 Z= 0.231 Angle : 0.744 7.625 14366 Z= 0.388 Chirality : 0.048 0.222 1604 Planarity : 0.005 0.051 1882 Dihedral : 4.351 24.167 1404 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: 0.08 (0.23), residues: 1310 helix: 0.49 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.58 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 117 HIS 0.003 0.001 HIS B 62 PHE 0.014 0.002 PHE B 168 TYR 0.021 0.002 TYR C 169 ARG 0.008 0.001 ARG F 97 ********************** 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 404 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 1.121 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: A 71 GLU cc_start: 0.9303 (pp20) cc_final: 0.8915 (pp20) REVERT: A 98 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 144 MET cc_start: 0.9154 (tpt) cc_final: 0.8508 (tmm) REVERT: A 163 ASP cc_start: 0.8837 (m-30) cc_final: 0.8130 (m-30) REVERT: A 167 ARG cc_start: 0.9009 (mtm-85) cc_final: 0.8403 (ptt-90) REVERT: A 176 GLN cc_start: 0.8999 (pm20) cc_final: 0.8086 (pp30) REVERT: A 214 MET cc_start: 0.9173 (ptp) cc_final: 0.8946 (ptp) REVERT: A 215 MET cc_start: 0.8623 (ptm) cc_final: 0.8291 (ptm) REVERT: B 10 MET cc_start: 0.6086 (tmm) cc_final: 0.5588 (tmm) REVERT: B 55 MET cc_start: 0.9439 (ttm) cc_final: 0.8663 (ttp) REVERT: B 66 MET cc_start: 0.9230 (mpp) cc_final: 0.8866 (mpp) REVERT: B 82 ARG cc_start: 0.8610 (tmm160) cc_final: 0.8168 (ttp80) REVERT: B 128 GLU cc_start: 0.9507 (mp0) cc_final: 0.9195 (mp0) REVERT: B 141 ILE cc_start: 0.9047 (mt) cc_final: 0.8734 (mt) REVERT: B 212 GLU cc_start: 0.9361 (pt0) cc_final: 0.9094 (pt0) REVERT: C 35 GLU cc_start: 0.9247 (pt0) cc_final: 0.8683 (tm-30) REVERT: C 68 MET cc_start: 0.9467 (mtp) cc_final: 0.9189 (mtt) REVERT: C 75 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8506 (tm-30) REVERT: C 97 ARG cc_start: 0.9131 (ttp-110) cc_final: 0.8646 (ptt90) REVERT: C 154 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7928 (mmm-85) REVERT: C 167 ARG cc_start: 0.9079 (ttt180) cc_final: 0.8613 (ptp90) REVERT: C 185 MET cc_start: 0.9129 (ptp) cc_final: 0.8851 (ptp) REVERT: D 68 MET cc_start: 0.9039 (mtt) cc_final: 0.8355 (mtt) REVERT: D 71 GLU cc_start: 0.9252 (pp20) cc_final: 0.8809 (pp20) REVERT: D 96 MET cc_start: 0.5747 (tpp) cc_final: 0.5339 (tpp) REVERT: D 128 GLU cc_start: 0.9331 (mp0) cc_final: 0.9068 (mp0) REVERT: D 132 ARG cc_start: 0.9380 (mtp-110) cc_final: 0.8943 (ttm110) REVERT: D 143 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.7898 (mpt180) REVERT: D 173 ARG cc_start: 0.9552 (ttm-80) cc_final: 0.9125 (ttp80) REVERT: D 185 MET cc_start: 0.7809 (mtt) cc_final: 0.7598 (mtt) REVERT: D 215 MET cc_start: 0.8722 (ptm) cc_final: 0.8508 (ppp) REVERT: E 10 MET cc_start: 0.5356 (tmm) cc_final: 0.4873 (tmm) REVERT: E 30 LYS cc_start: 0.8832 (tppt) cc_final: 0.8316 (tptp) REVERT: E 55 MET cc_start: 0.9627 (ttm) cc_final: 0.9295 (tpp) REVERT: E 66 MET cc_start: 0.9089 (mpp) cc_final: 0.8627 (mpp) REVERT: E 68 MET cc_start: 0.9006 (mtp) cc_final: 0.8583 (mtp) REVERT: E 72 THR cc_start: 0.9136 (p) cc_final: 0.8701 (p) REVERT: E 96 MET cc_start: 0.3889 (tpt) cc_final: 0.3100 (mtt) REVERT: E 100 ARG cc_start: 0.9177 (ttp80) cc_final: 0.8725 (tpp-160) REVERT: E 128 GLU cc_start: 0.9375 (mp0) cc_final: 0.8942 (pp20) REVERT: E 132 ARG cc_start: 0.9408 (mtm110) cc_final: 0.9077 (mtm110) REVERT: E 140 LYS cc_start: 0.9362 (mtpt) cc_final: 0.8929 (mtmm) REVERT: E 141 ILE cc_start: 0.8816 (mt) cc_final: 0.8582 (mt) REVERT: E 144 MET cc_start: 0.8055 (ppp) cc_final: 0.7818 (ppp) REVERT: E 173 ARG cc_start: 0.9329 (mmm-85) cc_final: 0.9094 (mmm160) REVERT: F 9 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8280 (pp30) REVERT: F 50 GLN cc_start: 0.8767 (mp10) cc_final: 0.8538 (mp10) REVERT: F 79 GLU cc_start: 0.9630 (tt0) cc_final: 0.9320 (tp30) REVERT: F 96 MET cc_start: 0.3527 (mpp) cc_final: 0.3154 (mpp) REVERT: F 103 ASP cc_start: 0.8921 (m-30) cc_final: 0.8659 (m-30) REVERT: F 132 ARG cc_start: 0.9695 (mtm110) cc_final: 0.9266 (ptm-80) REVERT: F 164 TYR cc_start: 0.8039 (t80) cc_final: 0.6546 (t80) REVERT: F 167 ARG cc_start: 0.9314 (mtm-85) cc_final: 0.8937 (mtm-85) REVERT: F 185 MET cc_start: 0.9225 (ptp) cc_final: 0.8978 (ptp) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2753 time to fit residues: 144.2681 Evaluate side-chains 331 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN D 193 ASN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 183 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.088935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.063649 restraints weight = 59392.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.066697 restraints weight = 35107.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.068889 restraints weight = 24406.385| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10566 Z= 0.253 Angle : 0.764 9.006 14366 Z= 0.400 Chirality : 0.049 0.210 1604 Planarity : 0.005 0.043 1882 Dihedral : 4.353 22.380 1404 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.22), residues: 1310 helix: 0.42 (0.17), residues: 836 sheet: None (None), residues: 0 loop : -0.59 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 23 HIS 0.004 0.001 HIS B 62 PHE 0.021 0.003 PHE A 40 TYR 0.017 0.002 TYR C 130 ARG 0.009 0.001 ARG F 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.78 seconds wall clock time: 55 minutes 31.54 seconds (3331.54 seconds total)