Starting phenix.real_space_refine on Thu Mar 14 18:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/03_2024/7bes_12158_updated.pdb" } resolution = 2.85 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 60 5.16 5 C 5870 2.51 5 N 1650 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9446 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1182 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'UDP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'UDP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1704 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1182 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'UDP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'UDP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.56, per 1000 atoms: 0.59 Number of scatterers: 9446 At special positions: 0 Unit cell: (87.316, 116.772, 87.316, 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 60 16.00 P 24 15.00 O 1842 8.00 N 1650 7.00 C 5870 6.00 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 6 sheets defined 43.9% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 93 through 118 removed outlier: 3.716A pdb=" N GLU A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 165 through 176 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 51 through 66 Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 93 through 118 removed outlier: 3.796A pdb=" N GLU B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'B' and resid 165 through 175 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 51 through 66 Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 93 through 118 removed outlier: 3.897A pdb=" N GLU C 118 " --> pdb=" O PHE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'D' and resid 39 through 43 Processing helix chain 'D' and resid 51 through 66 Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.716A pdb=" N GLU D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 51 through 66 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 93 through 118 removed outlier: 3.796A pdb=" N GLU E 118 " --> pdb=" O PHE E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 209 through 215 Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 51 through 66 Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 93 through 118 removed outlier: 3.897A pdb=" N GLU F 118 " --> pdb=" O PHE F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'F' and resid 165 through 176 Processing sheet with id= A, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.024A pdb=" N LEU A 258 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN A 70 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 35 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA A 72 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU A 37 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 74 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 152 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE A 75 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 154 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 206 through 208 removed outlier: 5.977A pdb=" N LEU B 258 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 181 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE B 238 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N MET B 183 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN B 70 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 35 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 72 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU B 37 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 74 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 152 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE B 75 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE B 154 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.354A pdb=" N GLN C 70 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU C 35 " --> pdb=" O GLN C 70 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 72 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU C 37 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL C 74 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 152 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE C 75 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE C 154 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 206 through 208 removed outlier: 6.024A pdb=" N LEU D 258 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN D 70 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU D 35 " --> pdb=" O GLN D 70 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ALA D 72 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU D 37 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL D 74 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 152 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE D 75 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE D 154 " --> pdb=" O ILE D 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 206 through 208 removed outlier: 5.977A pdb=" N LEU E 258 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL E 181 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE E 238 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N MET E 183 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN E 70 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU E 35 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA E 72 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU E 37 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL E 74 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL E 152 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE E 75 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE E 154 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 180 through 183 removed outlier: 6.354A pdb=" N GLN F 70 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU F 35 " --> pdb=" O GLN F 70 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA F 72 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU F 37 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL F 74 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 152 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE F 75 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE F 154 " --> pdb=" O ILE F 75 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1212 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: 2.66 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3186 1.34 - 1.46: 1990 1.46 - 1.59: 4240 1.59 - 1.71: 8 1.71 - 1.84: 136 Bond restraints: 9560 Sorted by residual: bond pdb=" O5' UDP C 301 " pdb=" PA UDP C 301 " ideal model delta sigma weight residual 1.581 1.838 -0.257 1.50e-02 4.44e+03 2.93e+02 bond pdb=" O5' UDP F 301 " pdb=" PA UDP F 301 " ideal model delta sigma weight residual 1.581 1.838 -0.257 1.50e-02 4.44e+03 2.93e+02 bond pdb=" O5' UDP E 301 " pdb=" PA UDP E 301 " ideal model delta sigma weight residual 1.581 1.837 -0.256 1.50e-02 4.44e+03 2.92e+02 bond pdb=" O5' UDP B 301 " pdb=" PA UDP B 301 " ideal model delta sigma weight residual 1.581 1.837 -0.256 1.50e-02 4.44e+03 2.92e+02 bond pdb=" O5' UDP D 301 " pdb=" PA UDP D 301 " ideal model delta sigma weight residual 1.581 1.837 -0.256 1.50e-02 4.44e+03 2.91e+02 ... (remaining 9555 not shown) Histogram of bond angle deviations from ideal: 96.61 - 103.53: 190 103.53 - 110.45: 2112 110.45 - 117.36: 4808 117.36 - 124.28: 5696 124.28 - 131.20: 152 Bond angle restraints: 12958 Sorted by residual: angle pdb=" O2A UDP D 301 " pdb=" PA UDP D 301 " pdb=" O3A UDP D 301 " ideal model delta sigma weight residual 105.97 121.50 -15.53 1.00e+00 1.00e+00 2.41e+02 angle pdb=" O2A UDP A 301 " pdb=" PA UDP A 301 " pdb=" O3A UDP A 301 " ideal model delta sigma weight residual 105.97 121.50 -15.53 1.00e+00 1.00e+00 2.41e+02 angle pdb=" O5' UDP D 301 " pdb=" PA UDP D 301 " pdb=" O2A UDP D 301 " ideal model delta sigma weight residual 110.83 96.61 14.22 1.00e+00 1.00e+00 2.02e+02 angle pdb=" O5' UDP A 301 " pdb=" PA UDP A 301 " pdb=" O2A UDP A 301 " ideal model delta sigma weight residual 110.83 96.61 14.22 1.00e+00 1.00e+00 2.02e+02 angle pdb=" O5' UDP B 301 " pdb=" PA UDP B 301 " pdb=" O2A UDP B 301 " ideal model delta sigma weight residual 110.83 96.63 14.20 1.00e+00 1.00e+00 2.02e+02 ... (remaining 12953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 5300 15.99 - 31.97: 320 31.97 - 47.96: 72 47.96 - 63.94: 68 63.94 - 79.93: 22 Dihedral angle restraints: 5782 sinusoidal: 2390 harmonic: 3392 Sorted by residual: dihedral pdb=" CA LEU D 34 " pdb=" CB LEU D 34 " pdb=" CG LEU D 34 " pdb=" CD1 LEU D 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA LEU A 34 " pdb=" CB LEU A 34 " pdb=" CG LEU A 34 " pdb=" CD1 LEU A 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.01 56.99 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA LEU B 34 " pdb=" CB LEU B 34 " pdb=" CG LEU B 34 " pdb=" CD1 LEU B 34 " ideal model delta sinusoidal sigma weight residual 180.00 123.96 56.04 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 5779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1314 0.062 - 0.125: 174 0.125 - 0.187: 14 0.187 - 0.249: 4 0.249 - 0.312: 10 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C2' UTP E 302 " pdb=" C1' UTP E 302 " pdb=" C3' UTP E 302 " pdb=" O2' UTP E 302 " both_signs ideal model delta sigma weight residual False -2.41 -2.73 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C2' UTP B 302 " pdb=" C1' UTP B 302 " pdb=" C3' UTP B 302 " pdb=" O2' UTP B 302 " both_signs ideal model delta sigma weight residual False -2.41 -2.73 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C2' UTP F 302 " pdb=" C1' UTP F 302 " pdb=" C3' UTP F 302 " pdb=" O2' UTP F 302 " both_signs ideal model delta sigma weight residual False -2.41 -2.71 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1513 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 233 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO B 234 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 233 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO E 234 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 160 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO D 161 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.017 5.00e-02 4.00e+02 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1614 2.77 - 3.30: 9290 3.30 - 3.83: 16687 3.83 - 4.37: 20135 4.37 - 4.90: 33635 Nonbonded interactions: 81361 Sorted by model distance: nonbonded pdb=" O MET A 101 " pdb=" OG1 THR A 104 " model vdw 2.236 2.440 nonbonded pdb=" O MET D 101 " pdb=" OG1 THR D 104 " model vdw 2.236 2.440 nonbonded pdb=" OH TYR F 137 " pdb=" OE1 GLU F 175 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR C 137 " pdb=" OE1 GLU C 175 " model vdw 2.259 2.440 nonbonded pdb=" O MET F 101 " pdb=" OG1 THR F 104 " model vdw 2.287 2.440 ... (remaining 81356 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' selection = (chain 'B' and (resid 28 through 261 or resid 301)) selection = chain 'D' selection = (chain 'E' and (resid 28 through 261 or resid 301)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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 individual isotropic 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: 0.600 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: 4.260 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.080 Find NCS groups from input model: 0.550 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:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.257 9560 Z= 0.864 Angle : 1.035 16.023 12958 Z= 0.668 Chirality : 0.050 0.312 1516 Planarity : 0.003 0.031 1652 Dihedral : 13.911 79.928 3638 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 0.85 % Allowed : 4.24 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.24), residues: 1214 helix: 1.82 (0.21), residues: 596 sheet: -1.15 (0.30), residues: 216 loop : -1.33 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 145 PHE 0.006 0.001 PHE A 154 TYR 0.006 0.001 TYR B 98 ARG 0.001 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 276 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.7962 (ttm170) cc_final: 0.7626 (mtt180) REVERT: B 99 MET cc_start: 0.8540 (mtp) cc_final: 0.8268 (mtm) REVERT: C 99 MET cc_start: 0.8800 (mtp) cc_final: 0.8561 (mtp) REVERT: C 141 ARG cc_start: 0.7952 (mmm160) cc_final: 0.7723 (mmt180) REVERT: C 174 LEU cc_start: 0.7031 (mt) cc_final: 0.6739 (pp) REVERT: D 215 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7627 (mtt180) REVERT: E 99 MET cc_start: 0.8538 (mtp) cc_final: 0.8268 (mtm) REVERT: F 99 MET cc_start: 0.8802 (mtp) cc_final: 0.8563 (mtp) REVERT: F 141 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7719 (mmt180) REVERT: F 174 LEU cc_start: 0.7033 (mt) cc_final: 0.6741 (pp) outliers start: 8 outliers final: 0 residues processed: 278 average time/residue: 1.2981 time to fit residues: 382.6034 Evaluate side-chains 182 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 56 GLN A 87 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 112 GLN D 46 GLN D 56 GLN D 87 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9560 Z= 0.191 Angle : 0.463 5.795 12958 Z= 0.233 Chirality : 0.041 0.126 1516 Planarity : 0.003 0.034 1652 Dihedral : 13.538 73.831 1570 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.97 % Allowed : 13.35 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.24), residues: 1214 helix: 1.85 (0.21), residues: 590 sheet: -0.76 (0.30), residues: 220 loop : -1.44 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 145 PHE 0.007 0.001 PHE D 80 TYR 0.009 0.001 TYR D 137 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 210 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: B 99 MET cc_start: 0.8454 (mtp) cc_final: 0.8227 (mtm) REVERT: C 99 MET cc_start: 0.8805 (mtp) cc_final: 0.8533 (mtp) REVERT: C 141 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7769 (mmt180) REVERT: C 147 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: D 118 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: E 99 MET cc_start: 0.8460 (mtp) cc_final: 0.8230 (mtm) REVERT: F 99 MET cc_start: 0.8802 (mtp) cc_final: 0.8534 (mtp) REVERT: F 141 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7769 (mmt180) REVERT: F 147 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7801 (mt-10) outliers start: 28 outliers final: 4 residues processed: 220 average time/residue: 1.4231 time to fit residues: 331.2173 Evaluate side-chains 184 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 147 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 112 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 112 GLN D 46 GLN D 112 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9560 Z= 0.307 Angle : 0.542 8.182 12958 Z= 0.270 Chirality : 0.043 0.127 1516 Planarity : 0.004 0.040 1652 Dihedral : 13.869 77.041 1570 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.39 % Allowed : 16.10 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1214 helix: 1.55 (0.21), residues: 586 sheet: -0.57 (0.30), residues: 220 loop : -1.42 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 145 PHE 0.009 0.001 PHE E 114 TYR 0.011 0.002 TYR B 98 ARG 0.003 0.001 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: B 99 MET cc_start: 0.8506 (mtp) cc_final: 0.8275 (mtm) REVERT: C 117 LYS cc_start: 0.8287 (tppt) cc_final: 0.7693 (ttmt) REVERT: C 141 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7934 (tpt-90) REVERT: C 147 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: D 118 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: E 99 MET cc_start: 0.8509 (mtp) cc_final: 0.8277 (mtm) REVERT: F 117 LYS cc_start: 0.8287 (tppt) cc_final: 0.7693 (ttmt) REVERT: F 141 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7939 (tpt-90) REVERT: F 147 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7917 (mt-10) outliers start: 32 outliers final: 10 residues processed: 210 average time/residue: 1.4088 time to fit residues: 312.7955 Evaluate side-chains 196 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 147 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 87 GLN C 112 GLN D 46 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9560 Z= 0.345 Angle : 0.557 8.698 12958 Z= 0.278 Chirality : 0.044 0.128 1516 Planarity : 0.004 0.042 1652 Dihedral : 13.892 76.427 1570 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.45 % Allowed : 16.31 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1214 helix: 1.28 (0.20), residues: 590 sheet: -0.52 (0.31), residues: 220 loop : -1.47 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 145 PHE 0.009 0.001 PHE E 114 TYR 0.012 0.002 TYR E 98 ARG 0.003 0.001 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: B 99 MET cc_start: 0.8509 (mtp) cc_final: 0.8296 (mtm) REVERT: C 117 LYS cc_start: 0.8326 (tppt) cc_final: 0.7784 (mtmt) REVERT: C 147 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: C 167 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7905 (t) REVERT: D 118 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: E 99 MET cc_start: 0.8512 (mtp) cc_final: 0.8297 (mtm) REVERT: F 117 LYS cc_start: 0.8325 (tppt) cc_final: 0.7784 (mtmt) REVERT: F 147 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: F 167 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7906 (t) outliers start: 42 outliers final: 18 residues processed: 196 average time/residue: 1.4137 time to fit residues: 293.1742 Evaluate side-chains 194 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 167 THR Chi-restraints excluded: chain F residue 174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.0370 chunk 97 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 112 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN F 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9560 Z= 0.161 Angle : 0.456 5.970 12958 Z= 0.232 Chirality : 0.041 0.127 1516 Planarity : 0.003 0.036 1652 Dihedral : 12.598 75.931 1570 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.60 % Allowed : 18.86 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.24), residues: 1214 helix: 1.67 (0.21), residues: 590 sheet: -0.42 (0.31), residues: 220 loop : -1.24 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 145 PHE 0.005 0.001 PHE F 42 TYR 0.005 0.001 TYR D 98 ARG 0.003 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: B 99 MET cc_start: 0.8361 (mtp) cc_final: 0.8124 (mtm) REVERT: B 112 GLN cc_start: 0.8161 (tt0) cc_final: 0.7918 (tt0) REVERT: C 117 LYS cc_start: 0.8249 (tppt) cc_final: 0.7644 (ttmt) REVERT: D 118 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: E 99 MET cc_start: 0.8364 (mtp) cc_final: 0.8125 (mtm) REVERT: F 117 LYS cc_start: 0.8247 (tppt) cc_final: 0.7643 (ttmt) outliers start: 34 outliers final: 8 residues processed: 213 average time/residue: 1.3983 time to fit residues: 315.4455 Evaluate side-chains 188 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain F residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 87 GLN C 112 GLN D 46 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9560 Z= 0.303 Angle : 0.534 7.803 12958 Z= 0.270 Chirality : 0.043 0.128 1516 Planarity : 0.004 0.041 1652 Dihedral : 13.420 76.065 1570 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.81 % Allowed : 19.07 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.23), residues: 1214 helix: 1.41 (0.21), residues: 590 sheet: -0.52 (0.30), residues: 220 loop : -1.38 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 145 PHE 0.008 0.001 PHE B 114 TYR 0.017 0.002 TYR F 137 ARG 0.003 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.014 Fit side-chains REVERT: A 118 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: B 99 MET cc_start: 0.8496 (mtp) cc_final: 0.8288 (mtm) REVERT: C 117 LYS cc_start: 0.8330 (tppt) cc_final: 0.7751 (ttmt) REVERT: C 167 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7920 (t) REVERT: D 118 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: E 99 MET cc_start: 0.8500 (mtp) cc_final: 0.8290 (mtm) REVERT: F 117 LYS cc_start: 0.8331 (tppt) cc_final: 0.7749 (ttmt) REVERT: F 167 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7969 (t) outliers start: 36 outliers final: 14 residues processed: 201 average time/residue: 1.4539 time to fit residues: 310.3188 Evaluate side-chains 192 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 167 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 56 GLN C 87 GLN C 112 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9560 Z= 0.185 Angle : 0.483 6.238 12958 Z= 0.247 Chirality : 0.042 0.136 1516 Planarity : 0.003 0.037 1652 Dihedral : 12.580 76.449 1570 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.75 % Allowed : 20.34 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1214 helix: 1.64 (0.21), residues: 584 sheet: -0.43 (0.30), residues: 220 loop : -1.31 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 145 PHE 0.005 0.001 PHE E 225 TYR 0.011 0.001 TYR F 137 ARG 0.004 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 199 time to evaluate : 0.954 Fit side-chains REVERT: A 118 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: A 135 GLU cc_start: 0.8011 (pt0) cc_final: 0.7721 (tt0) REVERT: C 117 LYS cc_start: 0.8243 (tppt) cc_final: 0.7659 (ttmt) REVERT: D 118 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: D 135 GLU cc_start: 0.8005 (pt0) cc_final: 0.7708 (tt0) REVERT: F 117 LYS cc_start: 0.8241 (tppt) cc_final: 0.7658 (ttmt) outliers start: 26 outliers final: 10 residues processed: 211 average time/residue: 1.4788 time to fit residues: 328.9739 Evaluate side-chains 194 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 89 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 56 GLN C 87 GLN C 112 GLN D 46 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9560 Z= 0.287 Angle : 0.547 7.603 12958 Z= 0.276 Chirality : 0.043 0.136 1516 Planarity : 0.004 0.042 1652 Dihedral : 12.952 77.074 1570 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.13 % Allowed : 19.60 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.23), residues: 1214 helix: 1.45 (0.21), residues: 584 sheet: -0.43 (0.30), residues: 220 loop : -1.42 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 145 PHE 0.007 0.001 PHE E 225 TYR 0.021 0.002 TYR F 137 ARG 0.004 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 0.938 Fit side-chains REVERT: A 118 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: C 117 LYS cc_start: 0.8290 (tppt) cc_final: 0.7712 (ttmt) REVERT: C 167 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7943 (t) REVERT: D 118 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6706 (mp0) REVERT: F 117 LYS cc_start: 0.8287 (tppt) cc_final: 0.7712 (ttmt) REVERT: F 167 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8031 (t) outliers start: 39 outliers final: 18 residues processed: 201 average time/residue: 1.4792 time to fit residues: 314.1465 Evaluate side-chains 195 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 167 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 87 GLN C 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9560 Z= 0.192 Angle : 0.496 6.319 12958 Z= 0.252 Chirality : 0.042 0.142 1516 Planarity : 0.003 0.039 1652 Dihedral : 12.111 77.514 1570 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.28 % Allowed : 20.55 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.23), residues: 1214 helix: 1.64 (0.21), residues: 584 sheet: -0.37 (0.31), residues: 220 loop : -1.33 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 145 PHE 0.005 0.001 PHE B 225 TYR 0.024 0.001 TYR F 137 ARG 0.003 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 0.947 Fit side-chains REVERT: A 118 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: A 135 GLU cc_start: 0.8006 (pt0) cc_final: 0.7729 (tt0) REVERT: B 141 ARG cc_start: 0.8155 (ttm170) cc_final: 0.7684 (ttm170) REVERT: C 117 LYS cc_start: 0.8223 (tppt) cc_final: 0.7643 (ttmt) REVERT: C 167 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7918 (t) REVERT: D 118 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: D 135 GLU cc_start: 0.8003 (pt0) cc_final: 0.7744 (tt0) REVERT: F 117 LYS cc_start: 0.8218 (tppt) cc_final: 0.7639 (ttmt) REVERT: F 167 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7951 (t) outliers start: 31 outliers final: 14 residues processed: 203 average time/residue: 1.4337 time to fit residues: 307.4914 Evaluate side-chains 193 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 245 ASN Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.0070 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 56 GLN C 87 GLN C 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9560 Z= 0.178 Angle : 0.499 5.871 12958 Z= 0.253 Chirality : 0.041 0.139 1516 Planarity : 0.003 0.036 1652 Dihedral : 10.635 68.128 1570 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.54 % Allowed : 22.88 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.23), residues: 1214 helix: 1.68 (0.21), residues: 582 sheet: -0.33 (0.31), residues: 220 loop : -1.24 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 145 PHE 0.005 0.001 PHE B 225 TYR 0.024 0.001 TYR F 137 ARG 0.003 0.000 ARG F 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.027 Fit side-chains REVERT: A 118 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: A 135 GLU cc_start: 0.7927 (pt0) cc_final: 0.7657 (tt0) REVERT: B 99 MET cc_start: 0.8379 (mtp) cc_final: 0.8146 (mtm) REVERT: B 141 ARG cc_start: 0.8153 (ttm170) cc_final: 0.7692 (ttm170) REVERT: C 117 LYS cc_start: 0.8211 (tppt) cc_final: 0.7624 (ttmt) REVERT: D 118 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: D 135 GLU cc_start: 0.7927 (pt0) cc_final: 0.7671 (tt0) REVERT: E 99 MET cc_start: 0.8383 (mtp) cc_final: 0.8154 (mtm) REVERT: F 117 LYS cc_start: 0.8207 (tppt) cc_final: 0.7621 (ttmt) outliers start: 24 outliers final: 12 residues processed: 190 average time/residue: 1.4514 time to fit residues: 291.2721 Evaluate side-chains 187 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 87 GLN C 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 87 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115192 restraints weight = 10947.275| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.70 r_work: 0.3230 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9560 Z= 0.200 Angle : 0.506 5.989 12958 Z= 0.256 Chirality : 0.042 0.138 1516 Planarity : 0.003 0.038 1652 Dihedral : 10.514 68.678 1570 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.65 % Allowed : 22.67 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.23), residues: 1214 helix: 1.62 (0.21), residues: 582 sheet: -0.30 (0.31), residues: 220 loop : -1.24 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 145 PHE 0.006 0.001 PHE B 225 TYR 0.023 0.001 TYR F 137 ARG 0.002 0.000 ARG E 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.23 seconds wall clock time: 84 minutes 25.33 seconds (5065.33 seconds total)