Starting phenix.real_space_refine on Sun Feb 18 08:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6n_29775/02_2024/8g6n_29775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6n_29775/02_2024/8g6n_29775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6n_29775/02_2024/8g6n_29775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6n_29775/02_2024/8g6n_29775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6n_29775/02_2024/8g6n_29775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6n_29775/02_2024/8g6n_29775.pdb" } resolution = 3.5 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6800 2.51 5 N 1875 2.21 5 O 2026 1.98 5 H 10672 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ASP 166": "OD1" <-> "OD2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 166": "OD1" <-> "OD2" Residue "C ASP 197": "OD1" <-> "OD2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "F ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21450 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3057 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3115 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2721 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3269 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3116 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3115 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3057 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 10.10, per 1000 atoms: 0.47 Number of scatterers: 21450 At special positions: 0 Unit cell: (109.2, 135.2, 126.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 O 2026 8.00 N 1875 7.00 C 6800 6.00 H 10672 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 16.58 Conformation dependent library (CDL) restraints added in 2.7 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 1 sheets defined 76.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.757A pdb=" N LYS G 30 " --> pdb=" O VAL G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.746A pdb=" N TYR G 130 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 176 removed outlier: 3.509A pdb=" N GLN G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.007A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'A' and resid 16 through 31 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 120 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.719A pdb=" N ASP A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.855A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.593A pdb=" N THR A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'B' and resid 16 through 30 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 106 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 174 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.446A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.924A pdb=" N ALA C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 60 removed outlier: 3.548A pdb=" N THR C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.538A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 4.219A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.991A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 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 105 Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 194 removed outlier: 4.287A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.923A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 103 through 107 removed outlier: 4.224A pdb=" N THR E 107 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 160 through 176 removed outlier: 3.559A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.320A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.937A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 30 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 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 146 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.844A pdb=" N GLN F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.773A pdb=" N TRP F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 4.169A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 715 hydrogen bonds defined for protein. 2124 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: 7.19 Time building geometry restraints manager: 17.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10660 1.03 - 1.23: 30 1.23 - 1.42: 4397 1.42 - 1.62: 6458 1.62 - 1.82: 142 Bond restraints: 21687 Sorted by residual: bond pdb=" N HIS F 12 " pdb=" CA HIS F 12 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N HIS G 12 " pdb=" CA HIS G 12 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" CB MET C 144 " pdb=" CG MET C 144 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 bond pdb=" N HIS G 12 " pdb=" H HIS G 12 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" N HIS F 12 " pdb=" H HIS F 12 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 21682 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.12: 325 105.12 - 112.40: 25366 112.40 - 119.68: 5778 119.68 - 126.96: 7630 126.96 - 134.24: 220 Bond angle restraints: 39319 Sorted by residual: angle pdb=" CB MET D 68 " pdb=" CG MET D 68 " pdb=" SD MET D 68 " ideal model delta sigma weight residual 112.70 99.60 13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CA MET E 144 " pdb=" CB MET E 144 " pdb=" CG MET E 144 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA MET D 68 " pdb=" CB MET D 68 " pdb=" CG MET D 68 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.71e+00 angle pdb=" CB MET A 68 " pdb=" CG MET A 68 " pdb=" SD MET A 68 " ideal model delta sigma weight residual 112.70 103.51 9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" CB MET F 118 " pdb=" CG MET F 118 " pdb=" SD MET F 118 " ideal model delta sigma weight residual 112.70 121.66 -8.96 3.00e+00 1.11e-01 8.92e+00 ... (remaining 39314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 8752 17.49 - 34.98: 1001 34.98 - 52.47: 389 52.47 - 69.96: 81 69.96 - 87.45: 19 Dihedral angle restraints: 10242 sinusoidal: 5703 harmonic: 4539 Sorted by residual: dihedral pdb=" CA ALA D 174 " pdb=" C ALA D 174 " pdb=" N GLU D 175 " pdb=" CA GLU D 175 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TRP D 117 " pdb=" C TRP D 117 " pdb=" N MET D 118 " pdb=" CA MET D 118 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ASP F 163 " pdb=" CB ASP F 163 " pdb=" CG ASP F 163 " pdb=" OD1 ASP F 163 " ideal model delta sinusoidal sigma weight residual -30.00 -85.42 55.42 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 10239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1186 0.035 - 0.071: 358 0.071 - 0.106: 101 0.106 - 0.141: 28 0.141 - 0.177: 5 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA MET E 215 " pdb=" N MET E 215 " pdb=" C MET E 215 " pdb=" CB MET E 215 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CG LEU C 202 " pdb=" CB LEU C 202 " pdb=" CD1 LEU C 202 " pdb=" CD2 LEU C 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE E 124 " pdb=" N ILE E 124 " pdb=" C ILE E 124 " pdb=" CB ILE E 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 1675 not shown) Planarity restraints: 3210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 122 " -0.062 5.00e-02 4.00e+02 9.25e-02 1.37e+01 pdb=" N PRO E 123 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 132 " 0.180 9.50e-02 1.11e+02 6.07e-02 5.10e+00 pdb=" NE ARG B 132 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 132 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 132 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 132 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 132 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B 132 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG B 132 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 132 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 100 " -0.189 9.50e-02 1.11e+02 6.35e-02 4.88e+00 pdb=" NE ARG D 100 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 100 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 100 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 100 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG D 100 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG D 100 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 100 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 100 " 0.000 2.00e-02 2.50e+03 ... (remaining 3207 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 3684 2.28 - 2.86: 47946 2.86 - 3.44: 57668 3.44 - 4.02: 72827 4.02 - 4.60: 113226 Nonbonded interactions: 295351 Sorted by model distance: nonbonded pdb=" O GLY F 156 " pdb="HD22 ASN F 195 " model vdw 1.702 1.850 nonbonded pdb="HD22 ASN D 53 " pdb=" O ALA D 105 " model vdw 1.718 1.850 nonbonded pdb=" OE2 GLU B 98 " pdb=" HE ARG B 100 " model vdw 1.720 1.850 nonbonded pdb=" OE1 GLU G 79 " pdb="HH21 ARG G 82 " model vdw 1.720 1.850 nonbonded pdb=" HG1 THR A 210 " pdb=" OE1 GLU A 213 " model vdw 1.722 1.850 ... (remaining 295346 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 12 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 67 through 85 or (resid \ 96 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 97 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 101 through 119 or (resid 120 and ( \ name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 121 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 159 through 161 \ or (resid 162 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 163 through 181 or (resid 182 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 183 through 193)) selection = (chain 'B' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 65 or (resid 66 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 67 through 85 or (resid 96 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 97 through 99 or (res \ id 100 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 101 through 119 or (resid 120 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 \ through 157 or (resid 158 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 159 through 161 or (resid 162 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 163 throu \ gh 193)) selection = (chain 'C' and (resid 12 through 85 or (resid 96 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 97 through 99 or (resid \ 100 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 101 through 119 or (resid 120 and (name N or name CA or name C or nam \ e O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or nam \ e H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 th \ rough 157 or (resid 158 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 159 through 181 or (resid 182 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 183 through \ 186 or (resid 187 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 188 through 193)) selection = (chain 'D' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 61 or (resid 62 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or resid 63 through 65 or \ (resid 66 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 67 through 83 or (resid 84 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) \ or resid 85 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 101 through 119 or (resid 120 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1)) or resid 121 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 159 through 161 \ or (resid 162 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 163 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 183 through 186 or (re \ sid 187 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 188 through 193)) selection = (chain 'E' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 65 or (resid 66 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 67 through 85 or (resid 96 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 97 through 99 or (res \ id 100 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 101 through 119 or (resid 120 and (name N or name CA or name C or \ name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or \ name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 \ through 157 or (resid 158 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 159 through 161 or (resid 162 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 163 throu \ gh 181 or (resid 182 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 183 through 193)) selection = (chain 'F' and (resid 12 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 67 through 119 or (resid \ 120 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name H \ B3 or name HD2 or name HE1)) or resid 121 through 161 or (resid 162 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 163 t \ hrough 193)) selection = (chain 'G' and (resid 12 through 85 or (resid 96 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 97 through 119 or (resid \ 120 and (name N or name CA or name C or name O or name CB or name CG or name ND \ 1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name H \ B3 or name HD2 or name HE1)) or resid 121 through 161 or (resid 162 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 163 t \ hrough 193)) } 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=1.00 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.310 Extract box with map and model: 10.140 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 67.630 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 0.045 11015 Z= 0.276 Angle : 0.739 13.102 14969 Z= 0.358 Chirality : 0.039 0.177 1678 Planarity : 0.006 0.093 1941 Dihedral : 16.670 87.445 4132 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.17 % Allowed : 14.80 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 1.92 (0.23), residues: 1351 helix: 1.79 (0.17), residues: 989 sheet: -2.96 (1.11), residues: 9 loop : 0.02 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 184 HIS 0.005 0.001 HIS E 120 PHE 0.035 0.002 PHE B 168 TYR 0.022 0.002 TYR E 145 ARG 0.017 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 MET cc_start: 0.7304 (mtm) cc_final: 0.7082 (mtm) outliers start: 2 outliers final: 2 residues processed: 154 average time/residue: 0.5998 time to fit residues: 124.8854 Evaluate side-chains 138 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 171 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.0040 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN C 139 ASN C 176 GLN F 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11015 Z= 0.182 Angle : 0.494 7.716 14969 Z= 0.252 Chirality : 0.035 0.156 1678 Planarity : 0.004 0.060 1941 Dihedral : 3.896 24.392 1463 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.20 % Allowed : 15.06 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.24 (0.23), residues: 1351 helix: 2.05 (0.17), residues: 987 sheet: -3.04 (1.23), residues: 9 loop : 0.07 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 184 HIS 0.002 0.001 HIS D 62 PHE 0.007 0.001 PHE A 32 TYR 0.008 0.001 TYR D 169 ARG 0.004 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.812 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: C 214 MET cc_start: 0.7851 (mtm) cc_final: 0.7453 (mtm) REVERT: D 215 MET cc_start: 0.6433 (mtm) cc_final: 0.6059 (mtm) outliers start: 14 outliers final: 8 residues processed: 148 average time/residue: 0.5287 time to fit residues: 110.9285 Evaluate side-chains 137 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 119 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS F 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11015 Z= 0.192 Angle : 0.496 6.367 14969 Z= 0.251 Chirality : 0.035 0.138 1678 Planarity : 0.004 0.053 1941 Dihedral : 3.736 15.189 1460 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.55 % Allowed : 15.06 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.33 (0.23), residues: 1351 helix: 2.13 (0.16), residues: 988 sheet: -3.23 (1.27), residues: 9 loop : 0.08 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 HIS 0.003 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.010 0.001 TYR D 169 ARG 0.003 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.933 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: C 214 MET cc_start: 0.8089 (mtm) cc_final: 0.7731 (mtm) REVERT: D 215 MET cc_start: 0.6627 (mtm) cc_final: 0.6384 (mtm) REVERT: E 28 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6870 (mp0) outliers start: 18 outliers final: 13 residues processed: 149 average time/residue: 0.5424 time to fit residues: 112.6588 Evaluate side-chains 145 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 163 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 63 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11015 Z= 0.202 Angle : 0.487 5.200 14969 Z= 0.249 Chirality : 0.035 0.135 1678 Planarity : 0.004 0.047 1941 Dihedral : 3.725 14.918 1460 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.98 % Allowed : 14.63 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.33 (0.23), residues: 1351 helix: 2.13 (0.16), residues: 992 sheet: -3.37 (1.35), residues: 9 loop : 0.04 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 HIS 0.004 0.001 HIS A 84 PHE 0.009 0.001 PHE B 168 TYR 0.010 0.001 TYR D 169 ARG 0.003 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.805 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: C 214 MET cc_start: 0.8104 (mtm) cc_final: 0.7761 (mtm) REVERT: D 215 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6455 (mtm) REVERT: E 28 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6891 (mp0) outliers start: 23 outliers final: 16 residues processed: 148 average time/residue: 0.5375 time to fit residues: 111.1449 Evaluate side-chains 146 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 163 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11015 Z= 0.209 Angle : 0.487 4.782 14969 Z= 0.251 Chirality : 0.036 0.136 1678 Planarity : 0.004 0.039 1941 Dihedral : 3.721 14.469 1460 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 14.89 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.33 (0.23), residues: 1351 helix: 2.13 (0.16), residues: 992 sheet: -3.36 (1.35), residues: 9 loop : 0.03 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 184 HIS 0.004 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.014 0.001 TYR E 145 ARG 0.003 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.745 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: C 214 MET cc_start: 0.8127 (mtm) cc_final: 0.7779 (mtm) REVERT: D 215 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6429 (mtm) REVERT: E 28 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6947 (mp0) outliers start: 22 outliers final: 18 residues processed: 148 average time/residue: 0.5521 time to fit residues: 115.3185 Evaluate side-chains 148 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 163 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11015 Z= 0.171 Angle : 0.473 5.200 14969 Z= 0.240 Chirality : 0.035 0.135 1678 Planarity : 0.004 0.038 1941 Dihedral : 3.660 14.043 1460 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.72 % Allowed : 15.49 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.48 (0.23), residues: 1351 helix: 2.24 (0.16), residues: 992 sheet: -3.18 (1.37), residues: 9 loop : 0.10 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.002 0.001 HIS E 120 PHE 0.008 0.001 PHE A 32 TYR 0.013 0.001 TYR E 145 ARG 0.003 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.656 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: C 214 MET cc_start: 0.7969 (mtm) cc_final: 0.7609 (mtm) REVERT: D 215 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6454 (mtm) REVERT: E 28 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6930 (mp0) outliers start: 20 outliers final: 15 residues processed: 152 average time/residue: 0.5249 time to fit residues: 111.2815 Evaluate side-chains 148 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11015 Z= 0.149 Angle : 0.470 6.439 14969 Z= 0.236 Chirality : 0.035 0.142 1678 Planarity : 0.004 0.039 1941 Dihedral : 3.585 13.914 1460 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.46 % Allowed : 16.09 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.63 (0.23), residues: 1351 helix: 2.34 (0.16), residues: 992 sheet: -3.06 (1.38), residues: 9 loop : 0.15 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 133 HIS 0.005 0.001 HIS E 120 PHE 0.008 0.001 PHE B 168 TYR 0.011 0.001 TYR D 164 ARG 0.002 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.757 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: B 96 MET cc_start: 0.4523 (ppp) cc_final: 0.4274 (ppp) REVERT: C 214 MET cc_start: 0.7956 (mtm) cc_final: 0.7661 (mtm) REVERT: E 28 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6919 (mp0) outliers start: 17 outliers final: 14 residues processed: 152 average time/residue: 0.5291 time to fit residues: 112.3690 Evaluate side-chains 148 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11015 Z= 0.178 Angle : 0.477 4.629 14969 Z= 0.243 Chirality : 0.035 0.138 1678 Planarity : 0.004 0.057 1941 Dihedral : 3.595 13.896 1460 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.81 % Allowed : 16.09 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.57 (0.23), residues: 1351 helix: 2.30 (0.16), residues: 991 sheet: -3.11 (1.41), residues: 9 loop : 0.14 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 133 HIS 0.004 0.001 HIS E 120 PHE 0.007 0.001 PHE A 32 TYR 0.018 0.001 TYR E 145 ARG 0.007 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 1.775 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: B 96 MET cc_start: 0.4471 (ppp) cc_final: 0.4216 (ppp) REVERT: C 214 MET cc_start: 0.7983 (mtm) cc_final: 0.7677 (mtm) REVERT: E 28 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: E 145 TYR cc_start: 0.6828 (m-80) cc_final: 0.6627 (m-80) REVERT: F 55 MET cc_start: 0.5728 (ttm) cc_final: 0.5198 (mtp) REVERT: F 166 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7144 (m-30) outliers start: 21 outliers final: 18 residues processed: 149 average time/residue: 0.5479 time to fit residues: 112.1908 Evaluate side-chains 152 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 166 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11015 Z= 0.165 Angle : 0.478 5.795 14969 Z= 0.241 Chirality : 0.035 0.137 1678 Planarity : 0.004 0.077 1941 Dihedral : 3.566 14.012 1460 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.89 % Allowed : 16.01 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.65 (0.23), residues: 1351 helix: 2.33 (0.16), residues: 995 sheet: -3.03 (1.43), residues: 9 loop : 0.22 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 184 HIS 0.005 0.001 HIS E 120 PHE 0.009 0.001 PHE G 161 TYR 0.012 0.001 TYR D 164 ARG 0.007 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 1.806 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: B 96 MET cc_start: 0.4487 (ppp) cc_final: 0.4201 (ppp) REVERT: C 214 MET cc_start: 0.7988 (mtm) cc_final: 0.7676 (mtm) REVERT: E 28 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: F 166 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7198 (m-30) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.5340 time to fit residues: 112.9604 Evaluate side-chains 152 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 166 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 87 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11015 Z= 0.152 Angle : 0.480 7.705 14969 Z= 0.240 Chirality : 0.035 0.136 1678 Planarity : 0.004 0.057 1941 Dihedral : 3.516 13.979 1460 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.81 % Allowed : 16.09 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.73 (0.23), residues: 1351 helix: 2.40 (0.16), residues: 995 sheet: -2.93 (1.44), residues: 9 loop : 0.25 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.005 0.000 HIS E 120 PHE 0.008 0.001 PHE B 168 TYR 0.012 0.001 TYR D 164 ARG 0.010 0.000 ARG G 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 66 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 66 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 MET cc_start: 0.4437 (ppp) cc_final: 0.4163 (ppp) REVERT: C 214 MET cc_start: 0.7983 (mtm) cc_final: 0.7730 (mtm) REVERT: E 28 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: F 166 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7179 (m-30) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.5597 time to fit residues: 122.3374 Evaluate side-chains 153 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 166 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.0670 chunk 97 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.078276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060547 restraints weight = 112076.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062998 restraints weight = 46509.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064546 restraints weight = 28326.450| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11015 Z= 0.183 Angle : 0.498 7.832 14969 Z= 0.251 Chirality : 0.035 0.139 1678 Planarity : 0.004 0.058 1941 Dihedral : 3.548 13.873 1460 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.64 % Allowed : 16.27 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.66 (0.23), residues: 1351 helix: 2.34 (0.16), residues: 995 sheet: -2.95 (1.45), residues: 9 loop : 0.24 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 184 HIS 0.005 0.001 HIS E 120 PHE 0.008 0.001 PHE G 161 TYR 0.013 0.001 TYR D 164 ARG 0.008 0.000 ARG G 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4213.73 seconds wall clock time: 75 minutes 41.57 seconds (4541.57 seconds total)