Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 09:38:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/07_2023/6xjh_22210_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/07_2023/6xjh_22210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/07_2023/6xjh_22210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/07_2023/6xjh_22210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/07_2023/6xjh_22210_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/07_2023/6xjh_22210_neut_updated.pdb" } resolution = 3.6 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5008 2.51 5 N 1210 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 7596 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2030 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "B" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2030 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "C" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1736 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Chain: "D" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1736 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.17, per 1000 atoms: 0.55 Number of scatterers: 7596 At special positions: 0 Unit cell: (75.98, 100.87, 106.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1334 8.00 N 1210 7.00 C 5008 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: 3.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 6 sheets defined 59.8% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid -3 through 14 Processing helix chain 'A' and resid 18 through 37 Processing helix chain 'A' and resid 51 through 79 removed outlier: 5.133A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 Processing helix chain 'A' and resid 90 through 125 Processing helix chain 'A' and resid 133 through 161 Processing helix chain 'A' and resid 165 through 185 removed outlier: 3.574A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Proline residue: A 179 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 192 through 201 removed outlier: 4.083A pdb=" N ASP A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.653A pdb=" N MET A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 241 Processing helix chain 'B' and resid -3 through 14 Processing helix chain 'B' and resid 18 through 37 Processing helix chain 'B' and resid 51 through 79 removed outlier: 5.133A pdb=" N ASP B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 85 Processing helix chain 'B' and resid 90 through 125 Processing helix chain 'B' and resid 133 through 161 Processing helix chain 'B' and resid 165 through 185 removed outlier: 3.575A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Proline residue: B 179 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 192 through 201 removed outlier: 4.084A pdb=" N ASP B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.653A pdb=" N MET B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 241 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 122 through 136 removed outlier: 4.044A pdb=" N ASN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 removed outlier: 4.068A pdb=" N ASN C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 183 No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 277 through 285 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 122 through 136 removed outlier: 4.044A pdb=" N ASN D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 168 removed outlier: 4.068A pdb=" N ASN D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 183 No H-bonds generated for 'chain 'D' and resid 180 through 183' Processing helix chain 'D' and resid 277 through 285 Processing sheet with id= A, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'C' and resid 197 through 203 removed outlier: 6.765A pdb=" N PHE C 192 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP C 201 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 190 " --> pdb=" O ASP C 201 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE C 173 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU C 31 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 175 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.601A pdb=" N TYR C 10 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL C 14 " --> pdb=" O TYR C 10 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 2 through 4 Processing sheet with id= E, first strand: chain 'D' and resid 197 through 203 removed outlier: 6.772A pdb=" N PHE D 192 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP D 201 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA D 190 " --> pdb=" O ASP D 201 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE D 173 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU D 31 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE D 175 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.600A pdb=" N TYR D 10 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL D 14 " --> pdb=" O TYR D 10 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1254 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: 2.21 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1536 1.32 - 1.47: 2716 1.47 - 1.61: 3434 1.61 - 1.75: 16 1.75 - 1.90: 52 Bond restraints: 7754 Sorted by residual: bond pdb=" C VAL D 199 " pdb=" N GLN D 200 " ideal model delta sigma weight residual 1.330 1.513 -0.183 1.45e-02 4.76e+03 1.59e+02 bond pdb=" C VAL C 199 " pdb=" N GLN C 200 " ideal model delta sigma weight residual 1.330 1.512 -0.182 1.45e-02 4.76e+03 1.58e+02 bond pdb=" CB HIS B 115 " pdb=" CG HIS B 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.11e+01 bond pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.10e+01 bond pdb=" CB GLN B 222 " pdb=" CG GLN B 222 " ideal model delta sigma weight residual 1.520 1.360 0.160 3.00e-02 1.11e+03 2.83e+01 ... (remaining 7749 not shown) Histogram of bond angle deviations from ideal: 96.20 - 103.68: 84 103.68 - 111.16: 2982 111.16 - 118.64: 3243 118.64 - 126.12: 4105 126.12 - 133.60: 68 Bond angle restraints: 10482 Sorted by residual: angle pdb=" N ILE B 167 " pdb=" CA ILE B 167 " pdb=" C ILE B 167 " ideal model delta sigma weight residual 111.58 104.54 7.04 1.06e+00 8.90e-01 4.41e+01 angle pdb=" N ILE A 167 " pdb=" CA ILE A 167 " pdb=" C ILE A 167 " ideal model delta sigma weight residual 111.58 104.55 7.03 1.06e+00 8.90e-01 4.40e+01 angle pdb=" CA PHE A 55 " pdb=" CB PHE A 55 " pdb=" CG PHE A 55 " ideal model delta sigma weight residual 113.80 120.37 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" CA PHE B 55 " pdb=" CB PHE B 55 " pdb=" CG PHE B 55 " ideal model delta sigma weight residual 113.80 120.34 -6.54 1.00e+00 1.00e+00 4.28e+01 angle pdb=" C VAL B -4 " pdb=" N PRO B -3 " pdb=" CA PRO B -3 " ideal model delta sigma weight residual 119.56 126.19 -6.63 1.02e+00 9.61e-01 4.23e+01 ... (remaining 10477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 4480 22.45 - 44.89: 88 44.89 - 67.34: 18 67.34 - 89.78: 10 89.78 - 112.23: 2 Dihedral angle restraints: 4598 sinusoidal: 1858 harmonic: 2740 Sorted by residual: dihedral pdb=" O1A AGS C 301 " pdb=" O3A AGS C 301 " pdb=" PA AGS C 301 " pdb=" PB AGS C 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.50 -112.23 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O1A AGS D 301 " pdb=" O3A AGS D 301 " pdb=" PA AGS D 301 " pdb=" PB AGS D 301 " ideal model delta sinusoidal sigma weight residual -67.73 44.46 -112.19 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C ILE B 188 " pdb=" N ILE B 188 " pdb=" CA ILE B 188 " pdb=" CB ILE B 188 " ideal model delta harmonic sigma weight residual -122.00 -130.51 8.51 0 2.50e+00 1.60e-01 1.16e+01 ... (remaining 4595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 673 0.067 - 0.134: 386 0.134 - 0.201: 124 0.201 - 0.268: 36 0.268 - 0.335: 11 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CB VAL D 166 " pdb=" CA VAL D 166 " pdb=" CG1 VAL D 166 " pdb=" CG2 VAL D 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB VAL C 166 " pdb=" CA VAL C 166 " pdb=" CG1 VAL C 166 " pdb=" CG2 VAL C 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG D 189 " pdb=" N ARG D 189 " pdb=" C ARG D 189 " pdb=" CB ARG D 189 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1227 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 206 " -0.069 2.00e-02 2.50e+03 3.63e-02 2.63e+01 pdb=" CG TYR B 206 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 206 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 206 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR B 206 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 206 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 206 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 206 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 206 " 0.068 2.00e-02 2.50e+03 3.61e-02 2.61e+01 pdb=" CG TYR A 206 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 206 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 206 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A 206 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 206 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 206 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 206 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 199 " -0.019 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C VAL C 199 " 0.061 2.00e-02 2.50e+03 pdb=" O VAL C 199 " -0.024 2.00e-02 2.50e+03 pdb=" N GLN C 200 " -0.019 2.00e-02 2.50e+03 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 801 2.72 - 3.26: 8177 3.26 - 3.81: 12835 3.81 - 4.35: 16279 4.35 - 4.90: 26346 Nonbonded interactions: 64438 Sorted by model distance: nonbonded pdb=" O2G AGS D 301 " pdb="MG MG D 302 " model vdw 2.173 2.170 nonbonded pdb=" O2G AGS C 301 " pdb="MG MG C 302 " model vdw 2.173 2.170 nonbonded pdb=" N LYS D 39 " pdb=" O1B AGS D 301 " model vdw 2.257 2.520 nonbonded pdb=" N LYS C 39 " pdb=" O1B AGS C 301 " model vdw 2.258 2.520 nonbonded pdb=" OG1 THR D 40 " pdb="MG MG D 302 " model vdw 2.272 2.170 ... (remaining 64433 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.440 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 22.800 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 0.019 0.183 7754 Z= 1.256 Angle : 1.641 13.306 10482 Z= 1.126 Chirality : 0.095 0.335 1230 Planarity : 0.008 0.036 1264 Dihedral : 11.217 112.230 2830 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer Outliers : 0.48 % 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: 1.10 (0.26), residues: 928 helix: 1.29 (0.20), residues: 558 sheet: 1.10 (0.75), residues: 50 loop : -0.22 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 0.871 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 416 average time/residue: 0.2028 time to fit residues: 111.2256 Evaluate side-chains 218 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 220 ASN B 162 GLN C 126 GLN C 200 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 7754 Z= 0.258 Angle : 0.703 8.818 10482 Z= 0.371 Chirality : 0.047 0.211 1230 Planarity : 0.004 0.039 1264 Dihedral : 9.461 119.820 1018 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 5.23 % 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: 1.60 (0.27), residues: 928 helix: 2.01 (0.21), residues: 550 sheet: 0.77 (0.75), residues: 50 loop : -0.52 (0.34), residues: 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 261 time to evaluate : 0.898 Fit side-chains outliers start: 44 outliers final: 29 residues processed: 290 average time/residue: 0.1676 time to fit residues: 68.2117 Evaluate side-chains 245 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0738 time to fit residues: 5.0371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN C 71 HIS ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7754 Z= 0.257 Angle : 0.639 7.333 10482 Z= 0.337 Chirality : 0.045 0.187 1230 Planarity : 0.004 0.037 1264 Dihedral : 9.146 112.089 1018 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 3.80 % 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: 1.32 (0.27), residues: 928 helix: 1.75 (0.21), residues: 554 sheet: 0.75 (0.76), residues: 50 loop : -0.61 (0.34), residues: 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 238 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 258 average time/residue: 0.1671 time to fit residues: 60.0173 Evaluate side-chains 228 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0762 time to fit residues: 4.4136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 162 GLN B 220 ASN C 71 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 7754 Z= 0.208 Angle : 0.622 8.397 10482 Z= 0.320 Chirality : 0.047 0.412 1230 Planarity : 0.003 0.034 1264 Dihedral : 8.934 105.368 1018 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 2.38 % 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: 1.13 (0.27), residues: 928 helix: 1.68 (0.21), residues: 556 sheet: 0.69 (0.75), residues: 50 loop : -0.88 (0.34), residues: 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 0.994 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 231 average time/residue: 0.1634 time to fit residues: 52.8489 Evaluate side-chains 218 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0724 time to fit residues: 2.9150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.0010 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN D 35 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7754 Z= 0.179 Angle : 0.596 7.794 10482 Z= 0.309 Chirality : 0.045 0.387 1230 Planarity : 0.003 0.043 1264 Dihedral : 8.690 101.573 1018 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 2.49 % 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: 1.01 (0.27), residues: 928 helix: 1.66 (0.21), residues: 550 sheet: 0.63 (0.74), residues: 50 loop : -1.06 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 240 average time/residue: 0.1705 time to fit residues: 57.0934 Evaluate side-chains 223 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0761 time to fit residues: 3.0966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN C 71 HIS ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 7754 Z= 0.200 Angle : 0.602 13.793 10482 Z= 0.308 Chirality : 0.045 0.383 1230 Planarity : 0.003 0.042 1264 Dihedral : 8.591 99.112 1018 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 2.02 % 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: 1.02 (0.27), residues: 928 helix: 1.64 (0.21), residues: 550 sheet: 0.54 (0.73), residues: 50 loop : -0.96 (0.33), residues: 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 229 average time/residue: 0.1812 time to fit residues: 56.9552 Evaluate side-chains 218 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0816 time to fit residues: 2.6408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 220 ASN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7754 Z= 0.192 Angle : 0.601 11.878 10482 Z= 0.308 Chirality : 0.044 0.322 1230 Planarity : 0.003 0.042 1264 Dihedral : 8.425 96.661 1018 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.31 % 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: 0.97 (0.27), residues: 928 helix: 1.63 (0.21), residues: 548 sheet: 0.46 (0.74), residues: 50 loop : -1.01 (0.33), residues: 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 226 average time/residue: 0.1687 time to fit residues: 53.1028 Evaluate side-chains 212 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0755 time to fit residues: 1.7243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 0.0030 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 222 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7754 Z= 0.193 Angle : 0.608 10.589 10482 Z= 0.311 Chirality : 0.044 0.233 1230 Planarity : 0.003 0.042 1264 Dihedral : 8.289 95.182 1018 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.07 % 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: 0.95 (0.27), residues: 928 helix: 1.63 (0.22), residues: 548 sheet: 0.72 (0.74), residues: 50 loop : -1.10 (0.33), residues: 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 216 time to evaluate : 0.911 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 222 average time/residue: 0.1761 time to fit residues: 53.8280 Evaluate side-chains 211 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0814 time to fit residues: 1.9342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.0060 chunk 49 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.1690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN C 148 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7754 Z= 0.176 Angle : 0.623 15.373 10482 Z= 0.317 Chirality : 0.043 0.243 1230 Planarity : 0.003 0.040 1264 Dihedral : 8.066 92.724 1018 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.36 % 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: 0.92 (0.27), residues: 928 helix: 1.56 (0.22), residues: 548 sheet: 1.04 (0.68), residues: 60 loop : -1.16 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 0.1798 time to fit residues: 55.7664 Evaluate side-chains 207 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0705 time to fit residues: 1.3780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 220 ASN C 200 GLN D 35 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7754 Z= 0.250 Angle : 0.653 9.482 10482 Z= 0.335 Chirality : 0.045 0.270 1230 Planarity : 0.004 0.038 1264 Dihedral : 8.050 91.402 1018 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 1.19 % 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: 0.88 (0.27), residues: 928 helix: 1.57 (0.22), residues: 548 sheet: 0.91 (0.69), residues: 60 loop : -1.23 (0.33), residues: 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 0.896 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 218 average time/residue: 0.1848 time to fit residues: 55.2047 Evaluate side-chains 214 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0785 time to fit residues: 2.4449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093015 restraints weight = 14028.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096222 restraints weight = 7141.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098502 restraints weight = 4645.770| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7754 Z= 0.202 Angle : 0.645 9.733 10482 Z= 0.334 Chirality : 0.045 0.325 1230 Planarity : 0.003 0.035 1264 Dihedral : 7.926 89.324 1018 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.24 % 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: 0.82 (0.27), residues: 928 helix: 1.59 (0.22), residues: 544 sheet: 0.76 (0.77), residues: 50 loop : -1.28 (0.32), residues: 334 =============================================================================== Job complete usr+sys time: 1779.14 seconds wall clock time: 33 minutes 12.42 seconds (1992.42 seconds total)