Starting phenix.real_space_refine (version: dev) on Sun Feb 19 06:13:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_12158_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_12158.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_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_12158/02_2023/7bes_12158_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_12158_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_12158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_12158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_12158_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bes_12158/02_2023/7bes_12158_updated.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 5.81, per 1000 atoms: 0.62 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: 3.71 Conformation dependent library (CDL) restraints added in 1.6 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: 0.98 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: 2.59 Time building geometry restraints manager: 3.97 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 - 13.23: 5108 13.23 - 26.46: 346 26.46 - 39.69: 82 39.69 - 52.92: 16 52.92 - 66.15: 10 Dihedral angle restraints: 5562 sinusoidal: 2170 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 5559 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 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. 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: 0.770 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: 4.700 Check model and map are aligned: 0.130 Process input model: 27.330 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 10.011 66.148 3418 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 % 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 *********************** 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 : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 278 average time/residue: 1.3264 time to fit residues: 390.7785 Evaluate side-chains 182 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4205 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9180 ------------------------------------------------------------------------------- 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: 0.8268 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 9560 Z= 0.189 Angle : 0.463 5.847 12958 Z= 0.233 Chirality : 0.041 0.127 1516 Planarity : 0.003 0.035 1652 Dihedral : 5.033 51.351 1350 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer Outliers : 3.39 % 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: 1.84 (0.21), residues: 590 sheet: -0.76 (0.30), residues: 220 loop : -1.43 (0.29), residues: 404 *********************** 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 236 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 4 residues processed: 214 average time/residue: 1.5369 time to fit residues: 349.4173 Evaluate side-chains 174 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.4430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8362 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 9560 Z= 0.389 Angle : 0.589 9.320 12958 Z= 0.293 Chirality : 0.045 0.130 1516 Planarity : 0.004 0.042 1652 Dihedral : 5.792 56.371 1350 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 3.18 % 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: 0.05 (0.23), residues: 1214 helix: 1.38 (0.20), residues: 586 sheet: -0.64 (0.30), residues: 220 loop : -1.55 (0.29), residues: 408 *********************** 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 218 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 204 average time/residue: 1.5491 time to fit residues: 333.4077 Evaluate side-chains 187 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.1376 time to fit residues: 2.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 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 46 GLN A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 46 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2711 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= 0.188 Angle : 0.469 6.538 12958 Z= 0.236 Chirality : 0.041 0.126 1516 Planarity : 0.003 0.041 1652 Dihedral : 5.374 53.835 1350 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 3.18 % 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: 1.67 (0.21), residues: 588 sheet: -0.41 (0.31), residues: 220 loop : -1.41 (0.29), residues: 406 *********************** 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 232 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 210 average time/residue: 1.5417 time to fit residues: 341.7015 Evaluate side-chains 196 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 184 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.1563 time to fit residues: 2.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.0270 chunk 97 optimal weight: 0.4980 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN C 112 GLN D 46 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9560 Z= 0.163 Angle : 0.456 6.648 12958 Z= 0.230 Chirality : 0.041 0.127 1516 Planarity : 0.003 0.038 1652 Dihedral : 5.173 53.720 1350 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 3.60 % 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: 0.50 (0.24), residues: 1214 helix: 1.73 (0.21), residues: 588 sheet: -0.40 (0.31), residues: 220 loop : -1.32 (0.30), residues: 406 *********************** 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 242 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 228 average time/residue: 1.5223 time to fit residues: 366.8441 Evaluate side-chains 202 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.1854 time to fit residues: 2.6271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 0.0870 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.3560 ------------------------------------------------------------------------------- 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** C 112 GLN D 46 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 9560 Z= 0.260 Angle : 0.505 6.940 12958 Z= 0.255 Chirality : 0.042 0.132 1516 Planarity : 0.003 0.041 1652 Dihedral : 5.358 57.856 1350 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 4.03 % 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: 0.39 (0.23), residues: 1214 helix: 1.61 (0.21), residues: 588 sheet: -0.45 (0.30), residues: 220 loop : -1.32 (0.29), residues: 406 *********************** 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 229 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 1.106 Fit side-chains outliers start: 38 outliers final: 20 residues processed: 211 average time/residue: 1.4697 time to fit residues: 328.0038 Evaluate side-chains 191 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 171 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.4563 time to fit residues: 4.5327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** C 56 GLN C 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9560 Z= 0.228 Angle : 0.506 6.886 12958 Z= 0.258 Chirality : 0.042 0.125 1516 Planarity : 0.003 0.038 1652 Dihedral : 5.353 59.977 1350 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer Outliers : 3.18 % 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: 0.40 (0.23), residues: 1214 helix: 1.63 (0.21), residues: 584 sheet: -0.42 (0.30), residues: 220 loop : -1.33 (0.29), residues: 410 *********************** 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 215 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 206 average time/residue: 1.6689 time to fit residues: 363.2721 Evaluate side-chains 204 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.6721 time to fit residues: 4.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 0.0670 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 56 GLN F 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9560 Z= 0.182 Angle : 0.489 6.095 12958 Z= 0.249 Chirality : 0.041 0.130 1516 Planarity : 0.003 0.035 1652 Dihedral : 5.168 57.887 1350 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 3.07 % 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: 0.51 (0.23), residues: 1214 helix: 1.72 (0.21), residues: 584 sheet: -0.36 (0.30), residues: 220 loop : -1.27 (0.29), residues: 410 *********************** 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 221 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 206 average time/residue: 1.5114 time to fit residues: 329.0894 Evaluate side-chains 190 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.043 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.6306 time to fit residues: 4.3135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 112 GLN D 56 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3196 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= 0.175 Angle : 0.480 6.446 12958 Z= 0.246 Chirality : 0.041 0.132 1516 Planarity : 0.003 0.035 1652 Dihedral : 5.053 56.730 1350 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 2.97 % 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: 0.57 (0.23), residues: 1214 helix: 1.75 (0.21), residues: 582 sheet: -0.28 (0.30), residues: 220 loop : -1.22 (0.29), residues: 412 *********************** 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 201 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 192 average time/residue: 1.4672 time to fit residues: 298.1268 Evaluate side-chains 182 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.2164 time to fit residues: 1.9980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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** C 56 GLN C 112 GLN D 46 GLN D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN F 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9560 Z= 0.176 Angle : 0.502 8.328 12958 Z= 0.254 Chirality : 0.041 0.132 1516 Planarity : 0.003 0.035 1652 Dihedral : 4.969 55.427 1350 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 1.69 % 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: 0.62 (0.23), residues: 1214 helix: 1.78 (0.21), residues: 580 sheet: -0.22 (0.31), residues: 220 loop : -1.19 (0.29), residues: 414 ********************** 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 191 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 189 average time/residue: 1.4501 time to fit residues: 290.0411 Evaluate side-chains 182 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 46 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114391 restraints weight = 10967.228| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.73 r_work: 0.3210 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 9560 Z= 0.261 Angle : 0.530 6.594 12958 Z= 0.270 Chirality : 0.043 0.139 1516 Planarity : 0.003 0.038 1652 Dihedral : 5.144 52.971 1350 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 2.12 % 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: 0.46 (0.23), residues: 1214 helix: 1.63 (0.21), residues: 578 sheet: -0.27 (0.30), residues: 220 loop : -1.25 (0.29), residues: 416 =============================================================================== Job complete usr+sys time: 4876.14 seconds wall clock time: 86 minutes 58.47 seconds (5218.47 seconds total)