Starting phenix.real_space_refine on Sun Apr 7 10:35:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/04_2024/6slu_10240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/04_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_10240/04_2024/6slu_10240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/04_2024/6slu_10240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/04_2024/6slu_10240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6slu_10240/04_2024/6slu_10240.pdb" } 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 Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "F ARG 18": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 7.21, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 3.71 Conformation dependent library (CDL) restraints added in 2.5 seconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 67.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 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: 2.57 Time building geometry restraints manager: 4.08 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: 100.54 - 108.07: 643 108.07 - 115.61: 6468 115.61 - 123.14: 6767 123.14 - 130.67: 430 130.67 - 138.20: 58 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 2.440 nonbonded pdb=" NZ LYS C 30 " pdb=" OE2 GLU C 35 " model vdw 2.202 2.520 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 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: 0.150 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: 1.080 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.860 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- 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 : 1.219 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: 0.2975 time to fit residues: 244.2884 Evaluate side-chains 392 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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: 0.0970 chunk 100 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 103 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 GLN C 5 ASN C 67 GLN C 139 ASN C 192 GLN D 4 GLN D 9 GLN D 112 GLN D 183 ASN E 50 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN F 4 GLN ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10566 Z= 0.203 Angle : 0.625 7.442 14366 Z= 0.312 Chirality : 0.044 0.163 1604 Planarity : 0.005 0.046 1882 Dihedral : 3.399 17.583 1404 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -0.22 (0.22), residues: 1310 helix: 0.40 (0.17), residues: 820 sheet: None (None), residues: 0 loop : -0.97 (0.25), residues: 490 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 0.023 0.002 PHE D 161 TYR 0.016 0.001 TYR E 145 ARG 0.006 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 515 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 1.175 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 28 GLU cc_start: 0.8667 (tt0) cc_final: 0.8294 (pp20) REVERT: A 50 GLN cc_start: 0.9216 (tt0) cc_final: 0.8804 (tm-30) REVERT: A 51 ASP cc_start: 0.9418 (m-30) cc_final: 0.9017 (m-30) REVERT: A 68 MET cc_start: 0.9404 (mtp) cc_final: 0.8794 (mtt) REVERT: A 141 ILE cc_start: 0.9566 (mm) cc_final: 0.9287 (tp) REVERT: A 144 MET cc_start: 0.9212 (tpp) cc_final: 0.8681 (tpp) REVERT: A 167 ARG cc_start: 0.9360 (mtm-85) cc_final: 0.8935 (ptt-90) REVERT: A 215 MET cc_start: 0.8428 (ptm) cc_final: 0.8102 (ptm) REVERT: B 10 MET cc_start: 0.5764 (tmm) cc_final: 0.5412 (tmm) REVERT: B 38 PRO cc_start: 0.9319 (Cg_exo) cc_final: 0.9083 (Cg_endo) REVERT: B 45 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7498 (mm-30) REVERT: B 55 MET cc_start: 0.9516 (ttm) cc_final: 0.9102 (tpp) REVERT: B 96 MET cc_start: 0.4009 (mtm) cc_final: 0.3794 (mtt) REVERT: B 128 GLU cc_start: 0.9443 (mp0) cc_final: 0.8849 (pp20) REVERT: B 129 ILE cc_start: 0.9647 (mm) cc_final: 0.9066 (tp) REVERT: B 141 ILE cc_start: 0.8604 (mt) cc_final: 0.8319 (mt) REVERT: B 190 LEU cc_start: 0.8914 (mt) cc_final: 0.8474 (mt) REVERT: C 9 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7940 (pm20) REVERT: C 13 GLN cc_start: 0.9505 (tp40) cc_final: 0.9305 (tp40) REVERT: C 25 LYS cc_start: 0.8583 (pttt) cc_final: 0.8342 (ttpt) REVERT: C 26 VAL cc_start: 0.8847 (p) cc_final: 0.8573 (p) REVERT: C 35 GLU cc_start: 0.8928 (pt0) cc_final: 0.8108 (tm-30) REVERT: C 68 MET cc_start: 0.9472 (mtp) cc_final: 0.8691 (mtt) REVERT: C 98 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8760 (tm-30) REVERT: C 140 LYS cc_start: 0.9351 (mtmm) cc_final: 0.9109 (ptpp) REVERT: C 141 ILE cc_start: 0.9392 (mt) cc_final: 0.9186 (mm) REVERT: C 154 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7805 (tpp80) REVERT: C 159 GLU cc_start: 0.8899 (mp0) cc_final: 0.8543 (pt0) REVERT: C 167 ARG cc_start: 0.8909 (ttt180) cc_final: 0.8634 (ptt-90) REVERT: C 186 THR cc_start: 0.9060 (p) cc_final: 0.8688 (p) REVERT: C 215 MET cc_start: 0.9035 (ptp) cc_final: 0.8751 (ppp) REVERT: C 216 THR cc_start: 0.8646 (p) cc_final: 0.8033 (p) REVERT: D 16 SER cc_start: 0.9250 (t) cc_final: 0.8870 (p) REVERT: D 23 TRP cc_start: 0.9656 (t-100) cc_final: 0.9379 (t-100) REVERT: D 50 GLN cc_start: 0.9280 (tt0) cc_final: 0.8827 (tm-30) REVERT: D 51 ASP cc_start: 0.9034 (m-30) cc_final: 0.8571 (m-30) REVERT: D 55 MET cc_start: 0.9491 (ttm) cc_final: 0.9216 (ttp) REVERT: D 58 THR cc_start: 0.9227 (p) cc_final: 0.9019 (p) REVERT: D 63 GLN cc_start: 0.9127 (mp10) cc_final: 0.8825 (mp10) REVERT: D 68 MET cc_start: 0.9189 (mtp) cc_final: 0.8616 (mtp) REVERT: D 129 ILE cc_start: 0.9063 (mt) cc_final: 0.8795 (tt) REVERT: D 132 ARG cc_start: 0.9458 (mtp-110) cc_final: 0.8965 (ttm110) REVERT: D 215 MET cc_start: 0.8931 (mtm) cc_final: 0.8563 (mtm) REVERT: E 28 GLU cc_start: 0.8893 (tt0) cc_final: 0.8481 (pt0) REVERT: E 30 LYS cc_start: 0.8924 (tppt) cc_final: 0.8200 (tptp) REVERT: E 55 MET cc_start: 0.9607 (ttm) cc_final: 0.9306 (tpp) REVERT: E 95 GLN cc_start: 0.6685 (mm-40) cc_final: 0.6440 (pt0) REVERT: E 100 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8723 (tpp-160) REVERT: E 128 GLU cc_start: 0.9244 (mp0) cc_final: 0.8664 (tm-30) REVERT: E 129 ILE cc_start: 0.9495 (mm) cc_final: 0.8777 (mm) REVERT: E 141 ILE cc_start: 0.8803 (mt) cc_final: 0.8482 (mt) REVERT: F 13 GLN cc_start: 0.9433 (tp40) cc_final: 0.9210 (tp-100) REVERT: F 38 PRO cc_start: 0.9436 (Cg_exo) cc_final: 0.9193 (Cg_endo) REVERT: F 39 MET cc_start: 0.9207 (tpp) cc_final: 0.8955 (tpp) REVERT: F 68 MET cc_start: 0.9659 (mtp) cc_final: 0.9014 (mtt) REVERT: F 71 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9080 (tm-30) REVERT: F 75 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8644 (tm-30) REVERT: F 79 GLU cc_start: 0.9612 (tt0) cc_final: 0.9194 (tp30) REVERT: F 114 GLN cc_start: 0.8966 (mp-120) cc_final: 0.8081 (mm-40) REVERT: F 117 TRP cc_start: 0.8249 (m-10) cc_final: 0.7333 (m-90) REVERT: F 129 ILE cc_start: 0.9646 (mt) cc_final: 0.9184 (mm) REVERT: F 132 ARG cc_start: 0.9448 (mtp-110) cc_final: 0.9088 (ptm-80) REVERT: F 158 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8221 (mmmt) REVERT: F 164 TYR cc_start: 0.8014 (t80) cc_final: 0.6976 (t80) REVERT: F 168 PHE cc_start: 0.9415 (t80) cc_final: 0.9149 (t80) REVERT: F 169 TYR cc_start: 0.8909 (m-80) cc_final: 0.8703 (m-80) REVERT: F 185 MET cc_start: 0.8973 (ptp) cc_final: 0.8758 (ptp) REVERT: F 190 LEU cc_start: 0.8775 (mt) cc_final: 0.8310 (mt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2941 time to fit residues: 196.0137 Evaluate side-chains 375 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN B 21 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN E 13 GLN E 139 ASN ** F 50 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10566 Z= 0.281 Angle : 0.695 9.148 14366 Z= 0.363 Chirality : 0.045 0.174 1604 Planarity : 0.006 0.076 1882 Dihedral : 3.923 18.584 1404 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % 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: 0.02 (0.22), residues: 1310 helix: 0.50 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.78 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 23 HIS 0.006 0.001 HIS E 62 PHE 0.016 0.003 PHE F 40 TYR 0.008 0.002 TYR F 169 ARG 0.009 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 441 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 440 time to evaluate : 1.198 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: A 10 MET cc_start: 0.5449 (tpt) cc_final: 0.5197 (mmm) REVERT: A 68 MET cc_start: 0.9453 (mtp) cc_final: 0.8789 (mtt) REVERT: A 98 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6568 (mt-10) REVERT: A 128 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8374 (tm-30) REVERT: A 129 ILE cc_start: 0.9103 (mt) cc_final: 0.8701 (mt) REVERT: A 141 ILE cc_start: 0.9592 (mm) cc_final: 0.9354 (tp) REVERT: A 163 ASP cc_start: 0.8917 (m-30) cc_final: 0.8134 (m-30) REVERT: A 167 ARG cc_start: 0.9283 (mtm-85) cc_final: 0.8752 (ptt-90) REVERT: A 214 MET cc_start: 0.9166 (ptp) cc_final: 0.8947 (ptp) REVERT: A 215 MET cc_start: 0.8437 (ptm) cc_final: 0.8220 (ptt) REVERT: B 10 MET cc_start: 0.5758 (tmm) cc_final: 0.5339 (tmm) REVERT: B 55 MET cc_start: 0.9521 (ttm) cc_final: 0.9171 (tpp) REVERT: B 68 MET cc_start: 0.9177 (mtt) cc_final: 0.8857 (mtt) REVERT: B 82 ARG cc_start: 0.8754 (tmm160) cc_final: 0.8546 (ttp80) REVERT: B 128 GLU cc_start: 0.9479 (mp0) cc_final: 0.9028 (mp0) REVERT: B 129 ILE cc_start: 0.9560 (mm) cc_final: 0.9291 (mm) REVERT: B 132 ARG cc_start: 0.9714 (ptp-110) cc_final: 0.9455 (ptp-110) REVERT: B 141 ILE cc_start: 0.9100 (mt) cc_final: 0.8806 (mt) REVERT: B 144 MET cc_start: 0.9005 (ppp) cc_final: 0.8656 (ppp) REVERT: B 212 GLU cc_start: 0.9418 (pt0) cc_final: 0.9188 (pm20) REVERT: C 68 MET cc_start: 0.9555 (mtp) cc_final: 0.9061 (mtt) REVERT: C 71 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8728 (tm-30) REVERT: C 134 ILE cc_start: 0.9497 (mm) cc_final: 0.9205 (mm) REVERT: C 159 GLU cc_start: 0.9074 (mp0) cc_final: 0.8757 (mp0) REVERT: C 167 ARG cc_start: 0.9101 (ttt180) cc_final: 0.8705 (ptp-170) REVERT: D 23 TRP cc_start: 0.9670 (t-100) cc_final: 0.9372 (t-100) REVERT: D 55 MET cc_start: 0.9550 (ttm) cc_final: 0.9092 (ttm) REVERT: D 128 GLU cc_start: 0.9199 (mp0) cc_final: 0.8778 (mp0) REVERT: D 129 ILE cc_start: 0.9176 (mt) cc_final: 0.8887 (tt) REVERT: D 132 ARG cc_start: 0.9333 (mtp-110) cc_final: 0.9115 (ttm110) REVERT: D 138 LEU cc_start: 0.9585 (tp) cc_final: 0.9333 (tp) REVERT: D 163 ASP cc_start: 0.9060 (m-30) cc_final: 0.8716 (m-30) REVERT: D 183 ASN cc_start: 0.9699 (m110) cc_final: 0.9469 (m110) REVERT: D 212 GLU cc_start: 0.9404 (pt0) cc_final: 0.8771 (pm20) REVERT: D 215 MET cc_start: 0.8960 (mtm) cc_final: 0.8722 (mtp) REVERT: E 10 MET cc_start: 0.5039 (tmm) cc_final: 0.4835 (tmm) REVERT: E 13 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8594 (pp30) REVERT: E 28 GLU cc_start: 0.8813 (tt0) cc_final: 0.8315 (pt0) REVERT: E 30 LYS cc_start: 0.8848 (tppt) cc_final: 0.8192 (tptp) REVERT: E 55 MET cc_start: 0.9514 (ttm) cc_final: 0.9253 (tpp) REVERT: E 66 MET cc_start: 0.9210 (mpp) cc_final: 0.8577 (mpp) REVERT: E 68 MET cc_start: 0.8999 (mtp) cc_final: 0.8466 (mtp) REVERT: E 79 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8487 (mm-30) REVERT: E 95 GLN cc_start: 0.5964 (mm-40) cc_final: 0.5667 (pt0) REVERT: E 100 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8679 (tpp-160) REVERT: E 128 GLU cc_start: 0.9279 (mp0) cc_final: 0.9012 (mp0) REVERT: E 131 LYS cc_start: 0.9509 (tttt) cc_final: 0.9302 (tptt) REVERT: E 141 ILE cc_start: 0.9009 (mt) cc_final: 0.8622 (mt) REVERT: E 144 MET cc_start: 0.8079 (ppp) cc_final: 0.7830 (ppp) REVERT: E 215 MET cc_start: 0.9001 (mmp) cc_final: 0.8776 (mmp) REVERT: F 38 PRO cc_start: 0.9524 (Cg_exo) cc_final: 0.9314 (Cg_endo) REVERT: F 39 MET cc_start: 0.9245 (tpp) cc_final: 0.8945 (tpp) REVERT: F 79 GLU cc_start: 0.9640 (tt0) cc_final: 0.9253 (tp30) REVERT: F 97 ARG cc_start: 0.9212 (ptp90) cc_final: 0.8865 (ttp-110) REVERT: F 104 ILE cc_start: 0.9193 (tt) cc_final: 0.8845 (mt) REVERT: F 117 TRP cc_start: 0.8094 (m-10) cc_final: 0.7232 (m-90) REVERT: F 128 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8824 (tm-30) REVERT: F 129 ILE cc_start: 0.9684 (mt) cc_final: 0.9146 (mm) REVERT: F 132 ARG cc_start: 0.9525 (mtp-110) cc_final: 0.9109 (ptm-80) REVERT: F 159 GLU cc_start: 0.7272 (pt0) cc_final: 0.6848 (pt0) REVERT: F 164 TYR cc_start: 0.8010 (t80) cc_final: 0.6512 (t80) REVERT: F 168 PHE cc_start: 0.9513 (t80) cc_final: 0.9185 (t80) REVERT: F 185 MET cc_start: 0.9165 (ptp) cc_final: 0.8962 (ptp) REVERT: F 190 LEU cc_start: 0.8716 (mt) cc_final: 0.8318 (mt) outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.3044 time to fit residues: 173.4322 Evaluate side-chains 356 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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: 8.9990 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS E 195 ASN ** F 50 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5897 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= 0.234 Angle : 0.653 6.919 14366 Z= 0.337 Chirality : 0.044 0.150 1604 Planarity : 0.005 0.045 1882 Dihedral : 3.998 19.129 1404 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.30 (0.23), residues: 1310 helix: 0.70 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.59 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 23 HIS 0.003 0.001 HIS F 62 PHE 0.017 0.002 PHE A 40 TYR 0.011 0.002 TYR E 169 ARG 0.009 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 430 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 1.139 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 68 MET cc_start: 0.9207 (mtp) cc_final: 0.8865 (mtt) REVERT: A 98 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6730 (mt-10) REVERT: A 100 ARG cc_start: 0.8974 (ptm-80) cc_final: 0.8753 (ptm-80) REVERT: A 128 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8268 (tm-30) REVERT: A 129 ILE cc_start: 0.9074 (mt) cc_final: 0.8719 (mt) REVERT: A 141 ILE cc_start: 0.9590 (mm) cc_final: 0.9364 (tp) REVERT: A 163 ASP cc_start: 0.8928 (m-30) cc_final: 0.8611 (m-30) REVERT: A 167 ARG cc_start: 0.9116 (mtm-85) cc_final: 0.8686 (ptp90) REVERT: A 214 MET cc_start: 0.9212 (ptp) cc_final: 0.9003 (ptp) REVERT: A 215 MET cc_start: 0.8631 (ptm) cc_final: 0.8411 (ppp) REVERT: B 10 MET cc_start: 0.5831 (tmm) cc_final: 0.5397 (tmm) REVERT: B 55 MET cc_start: 0.9487 (ttm) cc_final: 0.9086 (tpp) REVERT: B 66 MET cc_start: 0.9092 (mpp) cc_final: 0.8804 (mpp) REVERT: B 75 GLU cc_start: 0.9448 (pt0) cc_final: 0.9241 (pp20) REVERT: B 82 ARG cc_start: 0.8630 (tmm160) cc_final: 0.8243 (ttp80) REVERT: B 128 GLU cc_start: 0.9480 (mp0) cc_final: 0.9135 (mp0) REVERT: B 144 MET cc_start: 0.8813 (ppp) cc_final: 0.8604 (ppp) REVERT: B 212 GLU cc_start: 0.9406 (pt0) cc_final: 0.9146 (pm20) REVERT: C 39 MET cc_start: 0.8875 (mmt) cc_final: 0.8643 (mpp) REVERT: C 68 MET cc_start: 0.9553 (mtp) cc_final: 0.9083 (mtt) REVERT: C 71 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8974 (tm-30) REVERT: C 143 ARG cc_start: 0.9024 (mtm110) cc_final: 0.8597 (mtm-85) REVERT: C 154 ARG cc_start: 0.8286 (tpp80) cc_final: 0.7925 (tpp80) REVERT: C 159 GLU cc_start: 0.9103 (mp0) cc_final: 0.8341 (tt0) REVERT: C 167 ARG cc_start: 0.9090 (ttt180) cc_final: 0.8589 (ptp-170) REVERT: C 185 MET cc_start: 0.9114 (ptp) cc_final: 0.8822 (ptp) REVERT: D 23 TRP cc_start: 0.9679 (t-100) cc_final: 0.9312 (t-100) REVERT: D 55 MET cc_start: 0.9549 (ttm) cc_final: 0.9066 (ttm) REVERT: D 68 MET cc_start: 0.8928 (mtt) cc_final: 0.8652 (mtt) REVERT: D 71 GLU cc_start: 0.9123 (pp20) cc_final: 0.8746 (pp20) REVERT: D 128 GLU cc_start: 0.9245 (mp0) cc_final: 0.8823 (mp0) REVERT: D 129 ILE cc_start: 0.9149 (mt) cc_final: 0.8885 (tt) REVERT: D 132 ARG cc_start: 0.9280 (mtp-110) cc_final: 0.9056 (ttm110) REVERT: D 173 ARG cc_start: 0.9583 (ttm-80) cc_final: 0.9076 (ttp80) REVERT: D 212 GLU cc_start: 0.9390 (pt0) cc_final: 0.8991 (pm20) REVERT: D 214 MET cc_start: 0.9438 (mtm) cc_final: 0.9212 (mtt) REVERT: D 215 MET cc_start: 0.8991 (mtm) cc_final: 0.8718 (mtm) REVERT: E 10 MET cc_start: 0.5005 (tmm) cc_final: 0.4665 (tmm) REVERT: E 25 LYS cc_start: 0.9406 (tttp) cc_final: 0.9195 (ttmm) REVERT: E 28 GLU cc_start: 0.8863 (tt0) cc_final: 0.8322 (pt0) REVERT: E 30 LYS cc_start: 0.8923 (tppt) cc_final: 0.8194 (tptp) REVERT: E 55 MET cc_start: 0.9631 (ttm) cc_final: 0.9251 (tpp) REVERT: E 66 MET cc_start: 0.9135 (mpp) cc_final: 0.8489 (mpp) REVERT: E 68 MET cc_start: 0.8997 (mtp) cc_final: 0.8465 (mtp) REVERT: E 95 GLN cc_start: 0.5793 (mm-40) cc_final: 0.5356 (pt0) REVERT: E 100 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8691 (tpp-160) REVERT: E 128 GLU cc_start: 0.9335 (mp0) cc_final: 0.9115 (mp0) REVERT: E 141 ILE cc_start: 0.9012 (mt) cc_final: 0.8526 (mt) REVERT: E 144 MET cc_start: 0.7902 (ppp) cc_final: 0.7645 (ppp) REVERT: F 39 MET cc_start: 0.9251 (tpp) cc_final: 0.8940 (tpp) REVERT: F 79 GLU cc_start: 0.9647 (tt0) cc_final: 0.9284 (tp30) REVERT: F 103 ASP cc_start: 0.8934 (m-30) cc_final: 0.8695 (m-30) REVERT: F 104 ILE cc_start: 0.9203 (tt) cc_final: 0.8965 (mt) REVERT: F 128 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8946 (tm-30) REVERT: F 129 ILE cc_start: 0.9634 (mt) cc_final: 0.9162 (pt) REVERT: F 132 ARG cc_start: 0.9534 (mtp-110) cc_final: 0.9157 (ttp-110) REVERT: F 159 GLU cc_start: 0.6797 (pt0) cc_final: 0.6380 (pt0) REVERT: F 164 TYR cc_start: 0.7801 (t80) cc_final: 0.6708 (t80) REVERT: F 167 ARG cc_start: 0.9148 (mtm-85) cc_final: 0.8791 (mtm180) REVERT: F 168 PHE cc_start: 0.9487 (t80) cc_final: 0.8946 (t80) REVERT: F 190 LEU cc_start: 0.9020 (mt) cc_final: 0.8684 (mt) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.3019 time to fit residues: 166.8135 Evaluate side-chains 352 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN C 139 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10566 Z= 0.346 Angle : 0.744 7.332 14366 Z= 0.391 Chirality : 0.046 0.159 1604 Planarity : 0.005 0.038 1882 Dihedral : 4.521 20.268 1404 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % 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: 0.02 (0.22), residues: 1310 helix: 0.48 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -0.69 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 80 HIS 0.006 0.002 HIS E 12 PHE 0.021 0.003 PHE B 168 TYR 0.020 0.002 TYR E 169 ARG 0.011 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 415 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 1.233 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: A 45 GLU cc_start: 0.9426 (tt0) cc_final: 0.8849 (tm-30) REVERT: A 96 MET cc_start: 0.6269 (tpt) cc_final: 0.5838 (tpp) REVERT: A 98 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 117 TRP cc_start: 0.7364 (m-10) cc_final: 0.6868 (m-90) REVERT: A 141 ILE cc_start: 0.9605 (mm) cc_final: 0.9380 (tp) REVERT: A 163 ASP cc_start: 0.8920 (m-30) cc_final: 0.8651 (m-30) REVERT: A 167 ARG cc_start: 0.8924 (mtm-85) cc_final: 0.8301 (mtt180) REVERT: A 214 MET cc_start: 0.9377 (ptp) cc_final: 0.9149 (ptp) REVERT: B 10 MET cc_start: 0.6121 (tmm) cc_final: 0.5730 (tmm) REVERT: B 55 MET cc_start: 0.9429 (ttm) cc_final: 0.8975 (ttm) REVERT: B 68 MET cc_start: 0.8836 (mtt) cc_final: 0.8382 (mtp) REVERT: B 71 GLU cc_start: 0.9278 (pp20) cc_final: 0.9068 (pp20) REVERT: B 72 THR cc_start: 0.9223 (p) cc_final: 0.8663 (p) REVERT: B 128 GLU cc_start: 0.9542 (mp0) cc_final: 0.9222 (mp0) REVERT: B 141 ILE cc_start: 0.9151 (mt) cc_final: 0.8863 (mt) REVERT: B 143 ARG cc_start: 0.8339 (ttt90) cc_final: 0.8080 (ttm170) REVERT: B 144 MET cc_start: 0.8847 (ppp) cc_final: 0.8450 (ppp) REVERT: B 167 ARG cc_start: 0.9292 (ttm110) cc_final: 0.9071 (ttm110) REVERT: B 211 LEU cc_start: 0.9590 (pt) cc_final: 0.9316 (pt) REVERT: B 212 GLU cc_start: 0.9580 (pt0) cc_final: 0.9088 (pm20) REVERT: C 68 MET cc_start: 0.9566 (mtp) cc_final: 0.9096 (mtt) REVERT: C 81 ASP cc_start: 0.9178 (m-30) cc_final: 0.8969 (m-30) REVERT: C 154 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8173 (mmm-85) REVERT: C 167 ARG cc_start: 0.9259 (ttt180) cc_final: 0.8828 (ptp-170) REVERT: C 169 TYR cc_start: 0.9206 (m-80) cc_final: 0.8896 (m-80) REVERT: C 185 MET cc_start: 0.9197 (ptp) cc_final: 0.8950 (ptp) REVERT: C 215 MET cc_start: 0.9064 (ppp) cc_final: 0.8862 (ppp) REVERT: D 28 GLU cc_start: 0.8971 (tt0) cc_final: 0.8624 (pp20) REVERT: D 128 GLU cc_start: 0.9226 (mp0) cc_final: 0.8823 (tm-30) REVERT: D 129 ILE cc_start: 0.9159 (mt) cc_final: 0.8878 (mt) REVERT: D 185 MET cc_start: 0.9600 (ptp) cc_final: 0.9317 (mtt) REVERT: D 210 THR cc_start: 0.9284 (t) cc_final: 0.9078 (t) REVERT: D 214 MET cc_start: 0.9474 (mtm) cc_final: 0.9256 (mtt) REVERT: D 215 MET cc_start: 0.9111 (mtm) cc_final: 0.8861 (mtp) REVERT: E 10 MET cc_start: 0.5287 (tmm) cc_final: 0.4905 (tmm) REVERT: E 25 LYS cc_start: 0.9391 (tttp) cc_final: 0.9129 (ttmm) REVERT: E 28 GLU cc_start: 0.8782 (tt0) cc_final: 0.8382 (tm-30) REVERT: E 30 LYS cc_start: 0.8834 (tppt) cc_final: 0.8217 (tptp) REVERT: E 66 MET cc_start: 0.9318 (mpp) cc_final: 0.8831 (mpp) REVERT: E 68 MET cc_start: 0.9170 (mtp) cc_final: 0.8770 (mtp) REVERT: E 100 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8754 (tpp-160) REVERT: E 128 GLU cc_start: 0.9399 (mp0) cc_final: 0.9184 (mp0) REVERT: E 141 ILE cc_start: 0.9060 (mt) cc_final: 0.8681 (mt) REVERT: E 144 MET cc_start: 0.8091 (ppp) cc_final: 0.7736 (ppp) REVERT: E 167 ARG cc_start: 0.9171 (ttm110) cc_final: 0.8966 (ttm110) REVERT: E 215 MET cc_start: 0.8995 (mmp) cc_final: 0.8719 (mmm) REVERT: F 71 GLU cc_start: 0.8979 (pp20) cc_final: 0.8702 (pp20) REVERT: F 79 GLU cc_start: 0.9652 (tt0) cc_final: 0.9296 (tp30) REVERT: F 104 ILE cc_start: 0.9181 (tt) cc_final: 0.8975 (mt) REVERT: F 134 ILE cc_start: 0.9558 (mm) cc_final: 0.9356 (mm) REVERT: F 158 LYS cc_start: 0.8412 (mmpt) cc_final: 0.8107 (tppt) REVERT: F 164 TYR cc_start: 0.7807 (t80) cc_final: 0.7465 (t80) REVERT: F 167 ARG cc_start: 0.9130 (mtm-85) cc_final: 0.8691 (mtm180) REVERT: F 168 PHE cc_start: 0.9483 (t80) cc_final: 0.8945 (t80) REVERT: F 190 LEU cc_start: 0.8739 (mt) cc_final: 0.8475 (mt) outliers start: 1 outliers final: 1 residues processed: 415 average time/residue: 0.3098 time to fit residues: 164.7660 Evaluate side-chains 333 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 332 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 42 optimal weight: 30.0000 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 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: 0.8144 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10566 Z= 0.221 Angle : 0.663 7.524 14366 Z= 0.339 Chirality : 0.045 0.151 1604 Planarity : 0.004 0.041 1882 Dihedral : 4.378 19.728 1404 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1310 helix: 0.61 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.63 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 23 HIS 0.003 0.001 HIS B 62 PHE 0.019 0.002 PHE A 40 TYR 0.011 0.002 TYR D 169 ARG 0.009 0.001 ARG A 82 *********************** 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 413 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.224 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: A 98 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 115 ILE cc_start: 0.9433 (mm) cc_final: 0.9206 (pt) REVERT: A 117 TRP cc_start: 0.7382 (m-10) cc_final: 0.6963 (m-90) REVERT: A 163 ASP cc_start: 0.8958 (m-30) cc_final: 0.8233 (m-30) REVERT: A 167 ARG cc_start: 0.8931 (mtm-85) cc_final: 0.8357 (ptt-90) REVERT: A 214 MET cc_start: 0.9340 (ptp) cc_final: 0.9083 (ptp) REVERT: B 10 MET cc_start: 0.6194 (tmm) cc_final: 0.5760 (tmm) REVERT: B 29 GLU cc_start: 0.9279 (tm-30) cc_final: 0.9065 (tm-30) REVERT: B 55 MET cc_start: 0.9292 (ttm) cc_final: 0.8953 (ttm) REVERT: B 128 GLU cc_start: 0.9512 (mp0) cc_final: 0.9180 (mp0) REVERT: B 141 ILE cc_start: 0.9063 (mt) cc_final: 0.8718 (mt) REVERT: B 143 ARG cc_start: 0.8295 (ttt90) cc_final: 0.7946 (ttm170) REVERT: B 144 MET cc_start: 0.8600 (ppp) cc_final: 0.8329 (ppp) REVERT: B 211 LEU cc_start: 0.9571 (pt) cc_final: 0.9366 (pt) REVERT: B 212 GLU cc_start: 0.9380 (pt0) cc_final: 0.9050 (pm20) REVERT: C 68 MET cc_start: 0.9558 (mtp) cc_final: 0.9102 (mtt) REVERT: C 81 ASP cc_start: 0.9096 (m-30) cc_final: 0.8867 (m-30) REVERT: C 134 ILE cc_start: 0.9415 (mm) cc_final: 0.9193 (mm) REVERT: C 138 LEU cc_start: 0.9764 (mt) cc_final: 0.9552 (mt) REVERT: C 154 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8241 (tpp80) REVERT: C 159 GLU cc_start: 0.9170 (mp0) cc_final: 0.8942 (mp0) REVERT: C 167 ARG cc_start: 0.9257 (ttt180) cc_final: 0.8794 (ptp-170) REVERT: C 185 MET cc_start: 0.9172 (ptp) cc_final: 0.8953 (ptp) REVERT: C 215 MET cc_start: 0.9023 (ppp) cc_final: 0.8740 (ppp) REVERT: D 23 TRP cc_start: 0.9695 (t-100) cc_final: 0.9170 (t-100) REVERT: D 28 GLU cc_start: 0.8900 (tt0) cc_final: 0.8485 (pp20) REVERT: D 38 PRO cc_start: 0.9280 (Cg_exo) cc_final: 0.9063 (Cg_endo) REVERT: D 40 PHE cc_start: 0.9588 (t80) cc_final: 0.9358 (t80) REVERT: D 55 MET cc_start: 0.9534 (ttm) cc_final: 0.8977 (ttm) REVERT: D 128 GLU cc_start: 0.9265 (mp0) cc_final: 0.8965 (mp0) REVERT: D 132 ARG cc_start: 0.9291 (mtp-110) cc_final: 0.9016 (ttm110) REVERT: D 173 ARG cc_start: 0.9572 (ttm-80) cc_final: 0.9238 (ttp80) REVERT: D 185 MET cc_start: 0.9599 (ptp) cc_final: 0.9352 (mtt) REVERT: D 214 MET cc_start: 0.9462 (mtm) cc_final: 0.9237 (mtt) REVERT: D 215 MET cc_start: 0.9123 (mtm) cc_final: 0.8489 (mtm) REVERT: E 10 MET cc_start: 0.5203 (tmm) cc_final: 0.4657 (tmm) REVERT: E 30 LYS cc_start: 0.8864 (tppt) cc_final: 0.8314 (tptp) REVERT: E 66 MET cc_start: 0.9149 (mpp) cc_final: 0.8542 (mpp) REVERT: E 68 MET cc_start: 0.9122 (mtp) cc_final: 0.8739 (mtp) REVERT: E 100 ARG cc_start: 0.9152 (ttp80) cc_final: 0.8715 (tpp-160) REVERT: E 141 ILE cc_start: 0.9047 (mt) cc_final: 0.8738 (mt) REVERT: E 144 MET cc_start: 0.7996 (ppp) cc_final: 0.7707 (ppp) REVERT: E 167 ARG cc_start: 0.9170 (ttm110) cc_final: 0.8933 (ttm110) REVERT: E 211 LEU cc_start: 0.9696 (pt) cc_final: 0.9455 (pt) REVERT: E 215 MET cc_start: 0.9028 (mmp) cc_final: 0.8645 (mmp) REVERT: F 9 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8172 (pp30) REVERT: F 79 GLU cc_start: 0.9664 (tt0) cc_final: 0.9312 (tp30) REVERT: F 117 TRP cc_start: 0.8105 (m-10) cc_final: 0.7474 (m-10) REVERT: F 132 ARG cc_start: 0.9683 (mtp-110) cc_final: 0.9449 (mtp-110) REVERT: F 154 ARG cc_start: 0.8692 (ttm-80) cc_final: 0.8451 (ttm-80) REVERT: F 158 LYS cc_start: 0.8436 (mmpt) cc_final: 0.8092 (tppt) REVERT: F 159 GLU cc_start: 0.6572 (pt0) cc_final: 0.6149 (pt0) REVERT: F 164 TYR cc_start: 0.7786 (t80) cc_final: 0.6476 (t80) REVERT: F 167 ARG cc_start: 0.9113 (mtm-85) cc_final: 0.8591 (mtm-85) REVERT: F 168 PHE cc_start: 0.9498 (t80) cc_final: 0.9005 (t80) REVERT: F 185 MET cc_start: 0.9227 (ptp) cc_final: 0.8990 (ptp) REVERT: F 190 LEU cc_start: 0.8778 (mt) cc_final: 0.8461 (mt) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.2897 time to fit residues: 154.3752 Evaluate side-chains 340 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 9.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN 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: 0.8127 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10566 Z= 0.200 Angle : 0.660 8.182 14366 Z= 0.333 Chirality : 0.045 0.183 1604 Planarity : 0.004 0.046 1882 Dihedral : 4.291 22.768 1404 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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: 0.39 (0.23), residues: 1310 helix: 0.78 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.53 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 23 HIS 0.002 0.001 HIS E 12 PHE 0.022 0.002 PHE B 40 TYR 0.013 0.002 TYR B 145 ARG 0.007 0.001 ARG E 173 *********************** 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 410 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.9305 (t80) cc_final: 0.9010 (t80) REVERT: A 98 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7025 (mt-10) REVERT: A 115 ILE cc_start: 0.9439 (mm) cc_final: 0.9176 (pt) REVERT: A 143 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8141 (ttp-110) REVERT: A 144 MET cc_start: 0.8828 (tpp) cc_final: 0.8584 (tpt) REVERT: A 163 ASP cc_start: 0.8936 (m-30) cc_final: 0.8662 (m-30) REVERT: A 167 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8308 (mtt180) REVERT: A 176 GLN cc_start: 0.9182 (pm20) cc_final: 0.8693 (pp30) REVERT: A 214 MET cc_start: 0.9294 (ptp) cc_final: 0.9089 (ptp) REVERT: B 10 MET cc_start: 0.6265 (tmm) cc_final: 0.5877 (tmm) REVERT: B 29 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9034 (tm-30) REVERT: B 55 MET cc_start: 0.9533 (ttm) cc_final: 0.9028 (ttm) REVERT: B 66 MET cc_start: 0.9135 (mpp) cc_final: 0.8757 (mpp) REVERT: B 68 MET cc_start: 0.9099 (mtp) cc_final: 0.8564 (mtp) REVERT: B 71 GLU cc_start: 0.9137 (pp20) cc_final: 0.8917 (pp20) REVERT: B 72 THR cc_start: 0.9116 (p) cc_final: 0.8475 (p) REVERT: B 82 ARG cc_start: 0.8644 (tmm160) cc_final: 0.8171 (ttp80) REVERT: B 128 GLU cc_start: 0.9492 (mp0) cc_final: 0.9163 (mp0) REVERT: B 141 ILE cc_start: 0.9052 (mt) cc_final: 0.8837 (mt) REVERT: B 212 GLU cc_start: 0.9295 (pt0) cc_final: 0.8915 (pm20) REVERT: C 68 MET cc_start: 0.9487 (mtp) cc_final: 0.9100 (mtt) REVERT: C 81 ASP cc_start: 0.9051 (m-30) cc_final: 0.8813 (m-30) REVERT: C 134 ILE cc_start: 0.9415 (mm) cc_final: 0.9185 (mm) REVERT: C 138 LEU cc_start: 0.9761 (mt) cc_final: 0.9531 (mt) REVERT: C 154 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8190 (mmm-85) REVERT: C 167 ARG cc_start: 0.9201 (ttt180) cc_final: 0.8790 (ptp-170) REVERT: C 215 MET cc_start: 0.9053 (ppp) cc_final: 0.8839 (ppp) REVERT: C 216 THR cc_start: 0.8653 (p) cc_final: 0.8441 (p) REVERT: D 23 TRP cc_start: 0.9692 (t-100) cc_final: 0.9140 (t-100) REVERT: D 28 GLU cc_start: 0.8841 (tt0) cc_final: 0.8447 (pp20) REVERT: D 38 PRO cc_start: 0.9205 (Cg_exo) cc_final: 0.8951 (Cg_endo) REVERT: D 55 MET cc_start: 0.9541 (ttm) cc_final: 0.8990 (ttm) REVERT: D 128 GLU cc_start: 0.9277 (mp0) cc_final: 0.8954 (mp0) REVERT: D 132 ARG cc_start: 0.9279 (mtp-110) cc_final: 0.9000 (ttm110) REVERT: D 185 MET cc_start: 0.9589 (ptp) cc_final: 0.9374 (mtt) REVERT: D 212 GLU cc_start: 0.9270 (pt0) cc_final: 0.8925 (pm20) REVERT: D 215 MET cc_start: 0.9092 (mtm) cc_final: 0.8412 (mtm) REVERT: E 10 MET cc_start: 0.5172 (tmm) cc_final: 0.4588 (tmm) REVERT: E 30 LYS cc_start: 0.8797 (tppt) cc_final: 0.8273 (tptp) REVERT: E 66 MET cc_start: 0.9169 (mpp) cc_final: 0.8527 (mpp) REVERT: E 68 MET cc_start: 0.9173 (mtp) cc_final: 0.8809 (mtp) REVERT: E 72 THR cc_start: 0.9178 (p) cc_final: 0.8799 (p) REVERT: E 100 ARG cc_start: 0.9172 (ttp80) cc_final: 0.8720 (tpp-160) REVERT: E 128 GLU cc_start: 0.9418 (mp0) cc_final: 0.9193 (mp0) REVERT: E 141 ILE cc_start: 0.9071 (mt) cc_final: 0.8545 (mt) REVERT: E 144 MET cc_start: 0.7885 (ppp) cc_final: 0.7637 (ppp) REVERT: E 167 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8965 (ttm110) REVERT: E 211 LEU cc_start: 0.9691 (pt) cc_final: 0.9464 (pt) REVERT: E 215 MET cc_start: 0.8985 (mmp) cc_final: 0.8691 (mmp) REVERT: F 9 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8179 (pp30) REVERT: F 53 ASN cc_start: 0.8827 (t0) cc_final: 0.8553 (t0) REVERT: F 68 MET cc_start: 0.9028 (mtm) cc_final: 0.8772 (mtp) REVERT: F 79 GLU cc_start: 0.9653 (tt0) cc_final: 0.9277 (tp30) REVERT: F 81 ASP cc_start: 0.9065 (m-30) cc_final: 0.8836 (m-30) REVERT: F 158 LYS cc_start: 0.8432 (mmpt) cc_final: 0.8098 (tppt) REVERT: F 159 GLU cc_start: 0.6763 (pt0) cc_final: 0.6186 (pt0) REVERT: F 164 TYR cc_start: 0.7814 (t80) cc_final: 0.6107 (t80) REVERT: F 167 ARG cc_start: 0.9134 (mtm-85) cc_final: 0.8583 (mtm-85) REVERT: F 168 PHE cc_start: 0.9490 (t80) cc_final: 0.9028 (t80) REVERT: F 185 MET cc_start: 0.9223 (ptp) cc_final: 0.8990 (ptp) REVERT: F 190 LEU cc_start: 0.8731 (mt) cc_final: 0.8459 (mt) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.3037 time to fit residues: 160.5730 Evaluate side-chains 342 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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: 30.0000 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 0.1980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.7214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10566 Z= 0.210 Angle : 0.676 7.848 14366 Z= 0.345 Chirality : 0.046 0.183 1604 Planarity : 0.005 0.044 1882 Dihedral : 4.273 22.722 1404 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1310 helix: 0.78 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -0.56 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 23 HIS 0.002 0.001 HIS E 12 PHE 0.018 0.002 PHE A 40 TYR 0.010 0.001 TYR D 169 ARG 0.012 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 404 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 1.226 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: A 40 PHE cc_start: 0.9329 (t80) cc_final: 0.9011 (t80) REVERT: A 98 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7218 (mt-10) REVERT: A 129 ILE cc_start: 0.9050 (mt) cc_final: 0.8746 (mt) REVERT: A 143 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8029 (ttp-170) REVERT: A 144 MET cc_start: 0.8844 (tpp) cc_final: 0.8586 (tpt) REVERT: A 163 ASP cc_start: 0.8956 (m-30) cc_final: 0.8284 (m-30) REVERT: A 167 ARG cc_start: 0.9029 (mtm-85) cc_final: 0.8446 (ptt-90) REVERT: A 215 MET cc_start: 0.8309 (ppp) cc_final: 0.8047 (ppp) REVERT: B 10 MET cc_start: 0.6287 (tmm) cc_final: 0.6044 (tmm) REVERT: B 29 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8986 (tm-30) REVERT: B 55 MET cc_start: 0.9383 (ttm) cc_final: 0.9018 (ttm) REVERT: B 66 MET cc_start: 0.9150 (mpp) cc_final: 0.8768 (mpp) REVERT: B 68 MET cc_start: 0.9098 (mtp) cc_final: 0.8579 (mtp) REVERT: B 71 GLU cc_start: 0.9138 (pp20) cc_final: 0.8924 (pp20) REVERT: B 72 THR cc_start: 0.9056 (p) cc_final: 0.8407 (p) REVERT: B 128 GLU cc_start: 0.9479 (mp0) cc_final: 0.9144 (mp0) REVERT: B 141 ILE cc_start: 0.9090 (mt) cc_final: 0.8780 (mt) REVERT: B 144 MET cc_start: 0.8480 (ppp) cc_final: 0.8098 (ppp) REVERT: C 53 ASN cc_start: 0.8778 (t0) cc_final: 0.8520 (t0) REVERT: C 68 MET cc_start: 0.9575 (mtp) cc_final: 0.9130 (mtt) REVERT: C 71 GLU cc_start: 0.9274 (tm-30) cc_final: 0.9054 (tm-30) REVERT: C 81 ASP cc_start: 0.9180 (m-30) cc_final: 0.8955 (m-30) REVERT: C 134 ILE cc_start: 0.9441 (mm) cc_final: 0.9202 (mm) REVERT: C 138 LEU cc_start: 0.9750 (mt) cc_final: 0.9545 (mt) REVERT: C 167 ARG cc_start: 0.9136 (ttt180) cc_final: 0.8729 (ptp-170) REVERT: C 185 MET cc_start: 0.9183 (ptp) cc_final: 0.8941 (ptp) REVERT: C 215 MET cc_start: 0.9113 (ppp) cc_final: 0.8838 (ppp) REVERT: C 216 THR cc_start: 0.8595 (p) cc_final: 0.8335 (p) REVERT: D 23 TRP cc_start: 0.9686 (t-100) cc_final: 0.9121 (t-100) REVERT: D 55 MET cc_start: 0.9560 (ttm) cc_final: 0.9012 (ttm) REVERT: D 128 GLU cc_start: 0.9292 (mp0) cc_final: 0.9085 (mp0) REVERT: D 212 GLU cc_start: 0.9390 (pt0) cc_final: 0.9032 (pm20) REVERT: D 215 MET cc_start: 0.9119 (mtm) cc_final: 0.8663 (mtm) REVERT: E 10 MET cc_start: 0.5347 (tmm) cc_final: 0.4779 (tmm) REVERT: E 30 LYS cc_start: 0.8841 (tppt) cc_final: 0.8305 (tptp) REVERT: E 50 GLN cc_start: 0.9224 (mt0) cc_final: 0.8781 (mt0) REVERT: E 55 MET cc_start: 0.9236 (ttm) cc_final: 0.8927 (tpp) REVERT: E 66 MET cc_start: 0.9185 (mpp) cc_final: 0.8526 (mpp) REVERT: E 68 MET cc_start: 0.9110 (mtp) cc_final: 0.8746 (mtp) REVERT: E 72 THR cc_start: 0.9153 (p) cc_final: 0.8739 (p) REVERT: E 100 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8753 (tpp-160) REVERT: E 128 GLU cc_start: 0.9399 (mp0) cc_final: 0.9157 (mp0) REVERT: E 141 ILE cc_start: 0.8989 (mt) cc_final: 0.8503 (mt) REVERT: E 167 ARG cc_start: 0.9173 (ttm110) cc_final: 0.8937 (ttm110) REVERT: E 173 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.9097 (mmm160) REVERT: E 211 LEU cc_start: 0.9653 (pt) cc_final: 0.9424 (pt) REVERT: E 215 MET cc_start: 0.8932 (mmp) cc_final: 0.8643 (mmp) REVERT: F 9 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8128 (pp30) REVERT: F 53 ASN cc_start: 0.8824 (t0) cc_final: 0.8559 (t0) REVERT: F 79 GLU cc_start: 0.9648 (tt0) cc_final: 0.9272 (tp30) REVERT: F 81 ASP cc_start: 0.9283 (m-30) cc_final: 0.9072 (m-30) REVERT: F 97 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8353 (ttp-110) REVERT: F 117 TRP cc_start: 0.8223 (m-10) cc_final: 0.6934 (m-10) REVERT: F 118 MET cc_start: 0.8340 (mmp) cc_final: 0.8128 (mmp) REVERT: F 158 LYS cc_start: 0.8440 (mmpt) cc_final: 0.8103 (tppt) REVERT: F 159 GLU cc_start: 0.6771 (pt0) cc_final: 0.6180 (pt0) REVERT: F 164 TYR cc_start: 0.7824 (t80) cc_final: 0.6128 (t80) REVERT: F 167 ARG cc_start: 0.9146 (mtm-85) cc_final: 0.8573 (mtm-85) REVERT: F 168 PHE cc_start: 0.9487 (t80) cc_final: 0.9047 (t80) REVERT: F 185 MET cc_start: 0.9247 (ptp) cc_final: 0.9046 (ptp) REVERT: F 190 LEU cc_start: 0.8683 (mt) cc_final: 0.8472 (mt) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2848 time to fit residues: 150.3514 Evaluate side-chains 335 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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: 20.0000 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 77 optimal weight: 0.0060 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10566 Z= 0.218 Angle : 0.703 14.384 14366 Z= 0.358 Chirality : 0.045 0.179 1604 Planarity : 0.005 0.046 1882 Dihedral : 4.333 18.266 1404 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: 0.31 (0.23), residues: 1310 helix: 0.71 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -0.57 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 23 HIS 0.002 0.001 HIS E 12 PHE 0.020 0.002 PHE B 161 TYR 0.014 0.002 TYR C 164 ARG 0.011 0.001 ARG D 82 *********************** 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 402 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 1.216 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: A 45 GLU cc_start: 0.9314 (tt0) cc_final: 0.8763 (pm20) REVERT: A 98 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 115 ILE cc_start: 0.9446 (mm) cc_final: 0.9164 (pt) REVERT: A 144 MET cc_start: 0.8847 (tpp) cc_final: 0.8259 (tmm) REVERT: A 163 ASP cc_start: 0.8896 (m-30) cc_final: 0.8638 (m-30) REVERT: A 167 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.8352 (mtt180) REVERT: A 214 MET cc_start: 0.9171 (ptp) cc_final: 0.8950 (ptp) REVERT: A 215 MET cc_start: 0.8140 (ppp) cc_final: 0.7938 (ppp) REVERT: B 10 MET cc_start: 0.6318 (tmm) cc_final: 0.6076 (tmm) REVERT: B 55 MET cc_start: 0.9349 (ttm) cc_final: 0.8848 (ttp) REVERT: B 68 MET cc_start: 0.9095 (mtp) cc_final: 0.8594 (mtp) REVERT: B 71 GLU cc_start: 0.9145 (pp20) cc_final: 0.8922 (pp20) REVERT: B 72 THR cc_start: 0.9042 (p) cc_final: 0.8396 (p) REVERT: B 128 GLU cc_start: 0.9478 (mp0) cc_final: 0.9134 (mp0) REVERT: B 141 ILE cc_start: 0.9101 (mt) cc_final: 0.8776 (mt) REVERT: B 144 MET cc_start: 0.8408 (ppp) cc_final: 0.8005 (ppp) REVERT: B 167 ARG cc_start: 0.9330 (ttm110) cc_final: 0.9112 (ttm110) REVERT: B 212 GLU cc_start: 0.9265 (pt0) cc_final: 0.9005 (pm20) REVERT: C 53 ASN cc_start: 0.8792 (t0) cc_final: 0.8514 (t0) REVERT: C 68 MET cc_start: 0.9551 (mtp) cc_final: 0.8972 (mtt) REVERT: C 71 GLU cc_start: 0.9277 (tm-30) cc_final: 0.8884 (tm-30) REVERT: C 81 ASP cc_start: 0.9186 (m-30) cc_final: 0.8962 (m-30) REVERT: C 97 ARG cc_start: 0.9161 (ttp-110) cc_final: 0.8699 (ttp-110) REVERT: C 117 TRP cc_start: 0.8290 (m-10) cc_final: 0.7697 (m-90) REVERT: C 134 ILE cc_start: 0.9442 (mm) cc_final: 0.9216 (mm) REVERT: C 138 LEU cc_start: 0.9751 (mt) cc_final: 0.9551 (mt) REVERT: C 167 ARG cc_start: 0.9114 (ttt180) cc_final: 0.8741 (ptp-170) REVERT: C 185 MET cc_start: 0.9211 (ptp) cc_final: 0.8967 (ptp) REVERT: C 215 MET cc_start: 0.9143 (ppp) cc_final: 0.8819 (ppp) REVERT: C 216 THR cc_start: 0.8588 (p) cc_final: 0.8358 (p) REVERT: D 23 TRP cc_start: 0.9671 (t-100) cc_final: 0.9129 (t-100) REVERT: D 40 PHE cc_start: 0.9563 (t80) cc_final: 0.9361 (t80) REVERT: D 55 MET cc_start: 0.9553 (ttm) cc_final: 0.9039 (ttm) REVERT: D 128 GLU cc_start: 0.9290 (mp0) cc_final: 0.9074 (mp0) REVERT: D 212 GLU cc_start: 0.9325 (pt0) cc_final: 0.8793 (pm20) REVERT: D 215 MET cc_start: 0.9116 (mtm) cc_final: 0.8601 (mtm) REVERT: E 10 MET cc_start: 0.5362 (tmm) cc_final: 0.4794 (tmm) REVERT: E 30 LYS cc_start: 0.8841 (tppt) cc_final: 0.8453 (tptp) REVERT: E 35 GLU cc_start: 0.9169 (pp20) cc_final: 0.8781 (pp20) REVERT: E 50 GLN cc_start: 0.9208 (mt0) cc_final: 0.8740 (mt0) REVERT: E 66 MET cc_start: 0.9192 (mpp) cc_final: 0.8535 (mpp) REVERT: E 68 MET cc_start: 0.9069 (mtp) cc_final: 0.8779 (mtp) REVERT: E 72 THR cc_start: 0.9148 (p) cc_final: 0.8748 (p) REVERT: E 100 ARG cc_start: 0.9213 (ttp80) cc_final: 0.8755 (tpp-160) REVERT: E 128 GLU cc_start: 0.9409 (mp0) cc_final: 0.9170 (mp0) REVERT: E 141 ILE cc_start: 0.8980 (mt) cc_final: 0.8488 (mt) REVERT: E 144 MET cc_start: 0.7738 (ppp) cc_final: 0.7484 (ppp) REVERT: E 167 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8909 (ttm110) REVERT: E 173 ARG cc_start: 0.9343 (mmm-85) cc_final: 0.9071 (mmm160) REVERT: E 215 MET cc_start: 0.9058 (mmp) cc_final: 0.8754 (mmp) REVERT: F 9 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8134 (pp30) REVERT: F 53 ASN cc_start: 0.8820 (t0) cc_final: 0.8510 (t0) REVERT: F 79 GLU cc_start: 0.9658 (tt0) cc_final: 0.9299 (tp30) REVERT: F 81 ASP cc_start: 0.9272 (m-30) cc_final: 0.9050 (m-30) REVERT: F 97 ARG cc_start: 0.8969 (ttp-110) cc_final: 0.8719 (ttp-110) REVERT: F 103 ASP cc_start: 0.8915 (m-30) cc_final: 0.8532 (m-30) REVERT: F 112 GLN cc_start: 0.9389 (mp10) cc_final: 0.9167 (mp10) REVERT: F 134 ILE cc_start: 0.9540 (mm) cc_final: 0.9310 (mm) REVERT: F 158 LYS cc_start: 0.8450 (mmpt) cc_final: 0.8185 (tppt) REVERT: F 164 TYR cc_start: 0.7774 (t80) cc_final: 0.6522 (t80) REVERT: F 167 ARG cc_start: 0.9135 (mtm-85) cc_final: 0.8677 (ptt-90) REVERT: F 168 PHE cc_start: 0.9503 (t80) cc_final: 0.9046 (t80) REVERT: F 190 LEU cc_start: 0.8655 (mt) cc_final: 0.8341 (mt) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2738 time to fit residues: 143.6863 Evaluate side-chains 337 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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: 9.9990 chunk 87 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 111 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 155 GLN ** 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: 0.8109 moved from start: 0.7402 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= 0.194 Angle : 0.721 9.156 14366 Z= 0.362 Chirality : 0.046 0.189 1604 Planarity : 0.005 0.043 1882 Dihedral : 4.204 19.437 1404 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1310 helix: 0.76 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.49 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 23 HIS 0.001 0.000 HIS D 62 PHE 0.019 0.002 PHE A 40 TYR 0.014 0.001 TYR F 145 ARG 0.010 0.001 ARG D 82 ********************** 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: 1 poor density : 403 time to evaluate : 1.252 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 28 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8037 (pp20) REVERT: A 29 GLU cc_start: 0.7800 (pt0) cc_final: 0.7590 (pt0) REVERT: A 45 GLU cc_start: 0.9316 (tt0) cc_final: 0.8755 (pm20) REVERT: A 98 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 115 ILE cc_start: 0.9474 (mm) cc_final: 0.9187 (pt) REVERT: A 129 ILE cc_start: 0.9042 (mt) cc_final: 0.8680 (mt) REVERT: A 144 MET cc_start: 0.8804 (tpp) cc_final: 0.8212 (tmm) REVERT: A 163 ASP cc_start: 0.8915 (m-30) cc_final: 0.8241 (m-30) REVERT: A 167 ARG cc_start: 0.9089 (mtm-85) cc_final: 0.8526 (ptt-90) REVERT: A 214 MET cc_start: 0.9143 (ptp) cc_final: 0.8840 (ptp) REVERT: A 215 MET cc_start: 0.8386 (ppp) cc_final: 0.7660 (ppp) REVERT: B 10 MET cc_start: 0.6328 (tmm) cc_final: 0.5978 (tmm) REVERT: B 68 MET cc_start: 0.9045 (mtp) cc_final: 0.8555 (mtp) REVERT: B 72 THR cc_start: 0.9005 (p) cc_final: 0.8381 (p) REVERT: B 128 GLU cc_start: 0.9486 (mp0) cc_final: 0.9139 (mp0) REVERT: B 141 ILE cc_start: 0.9077 (mt) cc_final: 0.8869 (mt) REVERT: B 144 MET cc_start: 0.8295 (ppp) cc_final: 0.7923 (ppp) REVERT: C 53 ASN cc_start: 0.8763 (t0) cc_final: 0.8479 (t0) REVERT: C 68 MET cc_start: 0.9556 (mtp) cc_final: 0.9012 (mtt) REVERT: C 71 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8862 (tm-30) REVERT: C 81 ASP cc_start: 0.9123 (m-30) cc_final: 0.8891 (m-30) REVERT: C 97 ARG cc_start: 0.9164 (ttp-110) cc_final: 0.8724 (ttp-110) REVERT: C 117 TRP cc_start: 0.8216 (m-10) cc_final: 0.7661 (m-90) REVERT: C 134 ILE cc_start: 0.9415 (mm) cc_final: 0.9184 (mm) REVERT: C 138 LEU cc_start: 0.9719 (mt) cc_final: 0.9491 (mt) REVERT: C 167 ARG cc_start: 0.9085 (ttt180) cc_final: 0.8654 (ptp-170) REVERT: C 185 MET cc_start: 0.9204 (ptp) cc_final: 0.8970 (ptp) REVERT: C 215 MET cc_start: 0.9154 (ppp) cc_final: 0.8826 (ppp) REVERT: C 216 THR cc_start: 0.8538 (p) cc_final: 0.8294 (p) REVERT: D 23 TRP cc_start: 0.9679 (t-100) cc_final: 0.9140 (t-100) REVERT: D 40 PHE cc_start: 0.9537 (t80) cc_final: 0.9335 (t80) REVERT: D 55 MET cc_start: 0.9594 (ttm) cc_final: 0.9062 (ttm) REVERT: D 70 LYS cc_start: 0.9485 (mtpt) cc_final: 0.9055 (ptpp) REVERT: D 185 MET cc_start: 0.9558 (mtm) cc_final: 0.9319 (mtm) REVERT: D 212 GLU cc_start: 0.9285 (pt0) cc_final: 0.8757 (pm20) REVERT: D 215 MET cc_start: 0.9100 (mtm) cc_final: 0.8566 (mtm) REVERT: E 10 MET cc_start: 0.5326 (tmm) cc_final: 0.4762 (tmm) REVERT: E 30 LYS cc_start: 0.8851 (tppt) cc_final: 0.8350 (tptp) REVERT: E 35 GLU cc_start: 0.9163 (pp20) cc_final: 0.8781 (pp20) REVERT: E 50 GLN cc_start: 0.9149 (mt0) cc_final: 0.8720 (mt0) REVERT: E 55 MET cc_start: 0.9041 (tpp) cc_final: 0.8773 (tpp) REVERT: E 66 MET cc_start: 0.9138 (mpp) cc_final: 0.8459 (mpp) REVERT: E 68 MET cc_start: 0.9032 (mtp) cc_final: 0.8797 (mtp) REVERT: E 72 THR cc_start: 0.9137 (p) cc_final: 0.8734 (p) REVERT: E 100 ARG cc_start: 0.9211 (ttp80) cc_final: 0.8754 (tpp-160) REVERT: E 128 GLU cc_start: 0.9404 (mp0) cc_final: 0.9177 (mp0) REVERT: E 136 LEU cc_start: 0.9737 (tt) cc_final: 0.9317 (pp) REVERT: E 140 LYS cc_start: 0.9381 (mtpt) cc_final: 0.8923 (mtmm) REVERT: E 141 ILE cc_start: 0.8965 (mt) cc_final: 0.8423 (mt) REVERT: E 144 MET cc_start: 0.7682 (ppp) cc_final: 0.7431 (ppp) REVERT: E 167 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8900 (ttm110) REVERT: E 173 ARG cc_start: 0.9342 (mmm-85) cc_final: 0.9090 (mmm160) REVERT: E 211 LEU cc_start: 0.9619 (pt) cc_final: 0.9329 (pt) REVERT: E 215 MET cc_start: 0.8891 (mmp) cc_final: 0.8655 (mmp) REVERT: F 9 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8160 (pp30) REVERT: F 53 ASN cc_start: 0.8764 (t0) cc_final: 0.8463 (t0) REVERT: F 79 GLU cc_start: 0.9650 (tt0) cc_final: 0.9286 (tp30) REVERT: F 97 ARG cc_start: 0.8943 (ttp-110) cc_final: 0.8712 (ttp-110) REVERT: F 103 ASP cc_start: 0.8876 (m-30) cc_final: 0.8501 (m-30) REVERT: F 112 GLN cc_start: 0.9393 (mp10) cc_final: 0.9187 (mp10) REVERT: F 132 ARG cc_start: 0.9645 (mtm110) cc_final: 0.9303 (ptm-80) REVERT: F 158 LYS cc_start: 0.8435 (mmpt) cc_final: 0.8106 (tppt) REVERT: F 164 TYR cc_start: 0.7926 (t80) cc_final: 0.6438 (t80) REVERT: F 167 ARG cc_start: 0.9300 (mtm-85) cc_final: 0.8854 (mtm-85) REVERT: F 168 PHE cc_start: 0.9487 (t80) cc_final: 0.9081 (t80) REVERT: F 185 MET cc_start: 0.9247 (ptp) cc_final: 0.9045 (ptp) REVERT: F 190 LEU cc_start: 0.8598 (mt) cc_final: 0.8320 (mt) outliers start: 1 outliers final: 1 residues processed: 404 average time/residue: 0.2729 time to fit residues: 144.6286 Evaluate side-chains 341 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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: 0.0870 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063839 restraints weight = 58459.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067023 restraints weight = 33681.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069278 restraints weight = 23040.326| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 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 = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.7501 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= 0.195 Angle : 0.694 9.159 14366 Z= 0.353 Chirality : 0.045 0.185 1604 Planarity : 0.005 0.042 1882 Dihedral : 4.153 19.555 1404 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.23), residues: 1310 helix: 0.76 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -0.47 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 23 HIS 0.001 0.000 HIS F 12 PHE 0.021 0.002 PHE B 40 TYR 0.018 0.001 TYR C 169 ARG 0.010 0.001 ARG E 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3071.95 seconds wall clock time: 56 minutes 20.77 seconds (3380.77 seconds total)