Starting phenix.real_space_refine on Tue May 7 09:30:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/05_2024/6xjh_22210_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/05_2024/6xjh_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_22210/05_2024/6xjh_22210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/05_2024/6xjh_22210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/05_2024/6xjh_22210_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjh_22210/05_2024/6xjh_22210_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-dev-5322/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: 4.76, per 1000 atoms: 0.63 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: 3.32 Conformation dependent library (CDL) restraints added in 1.4 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: 1.44 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: 2.09 Time building geometry restraints manager: 3.56 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: 4490 22.45 - 44.89: 100 44.89 - 67.34: 18 67.34 - 89.78: 10 89.78 - 112.23: 2 Dihedral angle restraints: 4620 sinusoidal: 1880 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 4617 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: 0.260 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: 1.170 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.240 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- 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 : 11.428 112.230 2852 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 % Allowed : 0.95 % Favored : 98.57 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.007 TRP A 223 HIS 0.007 0.002 HIS C 178 PHE 0.030 0.006 PHE B 55 TYR 0.069 0.008 TYR B 206 ARG 0.011 0.002 ARG C 189 *********************** 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 : 0.878 Fit side-chains revert: symmetry clash REVERT: A 96 TYR cc_start: 0.8034 (t80) cc_final: 0.7750 (t80) REVERT: A 115 HIS cc_start: 0.8383 (t-90) cc_final: 0.8132 (t-170) REVERT: A 122 VAL cc_start: 0.8548 (t) cc_final: 0.7827 (t) REVERT: A 130 ASN cc_start: 0.6500 (m-40) cc_final: 0.5964 (m-40) REVERT: A 166 MET cc_start: 0.7154 (mmp) cc_final: 0.5945 (ptp) REVERT: A 206 TYR cc_start: 0.7317 (p90) cc_final: 0.7025 (p90) REVERT: A 209 ASP cc_start: 0.7685 (t70) cc_final: 0.7294 (m-30) REVERT: A 220 ASN cc_start: 0.8146 (m-40) cc_final: 0.7893 (m110) REVERT: A 223 TRP cc_start: 0.7890 (t-100) cc_final: 0.7351 (t60) REVERT: A 243 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7856 (mmtt) REVERT: B 42 MET cc_start: 0.4106 (tpt) cc_final: 0.3122 (ptt) REVERT: B 70 VAL cc_start: 0.8394 (t) cc_final: 0.8048 (p) REVERT: B 106 LEU cc_start: 0.8455 (mm) cc_final: 0.8242 (mt) REVERT: B 115 HIS cc_start: 0.8191 (t-90) cc_final: 0.7622 (t-170) REVERT: B 122 VAL cc_start: 0.8676 (t) cc_final: 0.8404 (t) REVERT: B 209 ASP cc_start: 0.8031 (t70) cc_final: 0.7517 (m-30) REVERT: B 211 MET cc_start: 0.8414 (mtp) cc_final: 0.8115 (mtm) REVERT: B 220 ASN cc_start: 0.8351 (m-40) cc_final: 0.8095 (m110) REVERT: B 221 TRP cc_start: 0.8291 (m100) cc_final: 0.7873 (m100) REVERT: B 243 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8027 (mmtt) REVERT: C 3 LEU cc_start: 0.8564 (mt) cc_final: 0.8234 (mt) REVERT: C 43 MET cc_start: 0.8383 (mtm) cc_final: 0.8042 (mtp) REVERT: C 49 ASN cc_start: 0.8163 (m110) cc_final: 0.7928 (m-40) REVERT: C 56 LYS cc_start: 0.7501 (tttt) cc_final: 0.7300 (tptt) REVERT: C 58 ASP cc_start: 0.7504 (t0) cc_final: 0.7233 (t70) REVERT: C 63 ASP cc_start: 0.6664 (m-30) cc_final: 0.6409 (p0) REVERT: C 71 HIS cc_start: 0.7468 (m-70) cc_final: 0.6291 (m-70) REVERT: C 91 LEU cc_start: 0.8556 (mt) cc_final: 0.8300 (mp) REVERT: C 99 TYR cc_start: 0.8282 (t80) cc_final: 0.7900 (t80) REVERT: C 157 ASP cc_start: 0.8631 (m-30) cc_final: 0.8243 (t0) REVERT: C 172 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7140 (mmm160) REVERT: C 179 LYS cc_start: 0.8589 (mttt) cc_final: 0.8244 (mtpt) REVERT: D 56 LYS cc_start: 0.7046 (tttt) cc_final: 0.6676 (tppt) REVERT: D 58 ASP cc_start: 0.7536 (t0) cc_final: 0.7330 (m-30) REVERT: D 75 TYR cc_start: 0.7969 (m-80) cc_final: 0.7756 (m-10) REVERT: D 91 LEU cc_start: 0.8503 (mt) cc_final: 0.8190 (mp) REVERT: D 99 TYR cc_start: 0.8610 (t80) cc_final: 0.8218 (t80) REVERT: D 124 MET cc_start: 0.8329 (mtt) cc_final: 0.7843 (mtm) REVERT: D 157 ASP cc_start: 0.8154 (m-30) cc_final: 0.7851 (t0) REVERT: D 165 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mt) REVERT: D 179 LYS cc_start: 0.8586 (mttt) cc_final: 0.8144 (mttp) REVERT: D 183 ILE cc_start: 0.8217 (mt) cc_final: 0.7936 (mt) REVERT: D 185 LEU cc_start: 0.8686 (tp) cc_final: 0.8457 (tt) REVERT: D 194 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7549 (ttp80) outliers start: 4 outliers final: 0 residues processed: 416 average time/residue: 0.2001 time to fit residues: 109.8794 Evaluate side-chains 237 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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: 3.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 162 GLN C 126 GLN C 178 HIS 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 71 HIS D 178 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7754 Z= 0.258 Angle : 0.693 7.456 10482 Z= 0.374 Chirality : 0.046 0.180 1230 Planarity : 0.004 0.035 1264 Dihedral : 10.468 122.748 1040 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.51 % Allowed : 11.88 % Favored : 83.61 % 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: 1.70 (0.27), residues: 928 helix: 2.10 (0.21), residues: 550 sheet: 0.67 (0.74), residues: 50 loop : -0.49 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 223 HIS 0.004 0.001 HIS B 47 PHE 0.018 0.002 PHE C 23 TYR 0.025 0.002 TYR B 206 ARG 0.005 0.001 ARG A -2 *********************** 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 303 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 265 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 15 PHE cc_start: 0.7697 (m-80) cc_final: 0.7479 (m-10) REVERT: A 51 TYR cc_start: 0.7603 (m-10) cc_final: 0.6802 (m-10) REVERT: A 115 HIS cc_start: 0.8159 (t-90) cc_final: 0.7927 (t-170) REVERT: A 122 VAL cc_start: 0.8438 (t) cc_final: 0.7814 (t) REVERT: A 123 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: A 130 ASN cc_start: 0.6233 (m-40) cc_final: 0.4945 (m-40) REVERT: A 141 TRP cc_start: 0.7909 (m100) cc_final: 0.7681 (m100) REVERT: A 166 MET cc_start: 0.6475 (mmp) cc_final: 0.5561 (ptp) REVERT: A 188 ILE cc_start: 0.6201 (mt) cc_final: 0.5830 (mm) REVERT: A 204 PHE cc_start: 0.7161 (m-80) cc_final: 0.6247 (m-80) REVERT: A 209 ASP cc_start: 0.7480 (t70) cc_final: 0.7262 (m-30) REVERT: A 220 ASN cc_start: 0.8211 (m-40) cc_final: 0.7968 (m110) REVERT: A 243 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7847 (mmtt) REVERT: B -2 ARG cc_start: 0.6211 (mtm-85) cc_final: 0.5982 (mmm160) REVERT: B 51 TYR cc_start: 0.7422 (m-80) cc_final: 0.7025 (m-10) REVERT: B 84 GLN cc_start: 0.8493 (tt0) cc_final: 0.8021 (tt0) REVERT: B 87 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7601 (mmm) REVERT: B 115 HIS cc_start: 0.7872 (t-90) cc_final: 0.7598 (t-170) REVERT: B 122 VAL cc_start: 0.8622 (t) cc_final: 0.8066 (t) REVERT: B 152 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8511 (mm) REVERT: B 209 ASP cc_start: 0.7753 (t70) cc_final: 0.7371 (m-30) REVERT: B 222 GLN cc_start: 0.7579 (tt0) cc_final: 0.7218 (mt0) REVERT: B 243 LYS cc_start: 0.8502 (mmtt) cc_final: 0.7974 (mmtt) REVERT: C 4 GLU cc_start: 0.7126 (mp0) cc_final: 0.6817 (mp0) REVERT: C 43 MET cc_start: 0.7975 (mtm) cc_final: 0.7767 (mtt) REVERT: C 49 ASN cc_start: 0.8186 (m110) cc_final: 0.7957 (m-40) REVERT: C 58 ASP cc_start: 0.7239 (t0) cc_final: 0.7025 (t70) REVERT: C 70 GLU cc_start: 0.7802 (tp30) cc_final: 0.7463 (tp30) REVERT: C 71 HIS cc_start: 0.7224 (m-70) cc_final: 0.6941 (m90) REVERT: C 99 TYR cc_start: 0.8234 (t80) cc_final: 0.7940 (t80) REVERT: C 157 ASP cc_start: 0.8592 (m-30) cc_final: 0.8220 (t70) REVERT: D 58 ASP cc_start: 0.7598 (t0) cc_final: 0.7360 (m-30) REVERT: D 64 ASN cc_start: 0.7899 (m-40) cc_final: 0.7569 (m110) REVERT: D 71 HIS cc_start: 0.7701 (m170) cc_final: 0.7456 (m-70) REVERT: D 157 ASP cc_start: 0.8112 (m-30) cc_final: 0.7874 (t0) REVERT: D 181 GLU cc_start: 0.8594 (mp0) cc_final: 0.8161 (pm20) REVERT: D 185 LEU cc_start: 0.8828 (tp) cc_final: 0.8601 (tt) REVERT: D 188 ASP cc_start: 0.6538 (p0) cc_final: 0.6012 (t0) REVERT: D 194 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7568 (ttp80) outliers start: 38 outliers final: 27 residues processed: 292 average time/residue: 0.1775 time to fit residues: 71.5212 Evaluate side-chains 254 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 224 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 200 GLN ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4219 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= 0.222 Angle : 0.616 7.305 10482 Z= 0.328 Chirality : 0.045 0.296 1230 Planarity : 0.004 0.036 1264 Dihedral : 10.319 119.096 1040 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 5.94 % Allowed : 14.73 % Favored : 79.33 % 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: 1.54 (0.27), residues: 928 helix: 1.99 (0.21), residues: 552 sheet: 0.53 (0.67), residues: 58 loop : -0.61 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 223 HIS 0.003 0.001 HIS A 115 PHE 0.024 0.002 PHE A 111 TYR 0.028 0.002 TYR A 206 ARG 0.005 0.001 ARG C 194 *********************** 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 295 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 245 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 115 HIS cc_start: 0.8151 (t-90) cc_final: 0.7945 (t-170) REVERT: A 122 VAL cc_start: 0.8433 (t) cc_final: 0.8232 (t) REVERT: A 123 GLN cc_start: 0.7954 (pp30) cc_final: 0.7370 (tm-30) REVERT: A 141 TRP cc_start: 0.7885 (m100) cc_final: 0.7568 (m100) REVERT: A 166 MET cc_start: 0.6580 (mmp) cc_final: 0.5659 (ttm) REVERT: A 209 ASP cc_start: 0.7596 (t70) cc_final: 0.7209 (m-30) REVERT: A 220 ASN cc_start: 0.8157 (m-40) cc_final: 0.7874 (m110) REVERT: A 233 PHE cc_start: 0.8202 (m-80) cc_final: 0.7974 (m-80) REVERT: A 243 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7865 (mmtt) REVERT: B -2 ARG cc_start: 0.6172 (mtm-85) cc_final: 0.5912 (mmm160) REVERT: B 76 ARG cc_start: 0.6977 (ttm-80) cc_final: 0.6731 (ttp80) REVERT: B 84 GLN cc_start: 0.8489 (tt0) cc_final: 0.8022 (tt0) REVERT: B 87 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7589 (mmm) REVERT: B 115 HIS cc_start: 0.7850 (t-90) cc_final: 0.7555 (t-170) REVERT: B 122 VAL cc_start: 0.8701 (t) cc_final: 0.8221 (t) REVERT: B 152 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8543 (mm) REVERT: B 209 ASP cc_start: 0.7881 (t70) cc_final: 0.7378 (m-30) REVERT: B 243 LYS cc_start: 0.8533 (mmtt) cc_final: 0.7972 (mmtt) REVERT: C 71 HIS cc_start: 0.7230 (m-70) cc_final: 0.6904 (m90) REVERT: C 99 TYR cc_start: 0.8271 (t80) cc_final: 0.8013 (t80) REVERT: C 157 ASP cc_start: 0.8675 (m-30) cc_final: 0.8310 (t70) REVERT: C 200 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7355 (mt0) REVERT: C 281 TYR cc_start: 0.7563 (t80) cc_final: 0.7358 (t80) REVERT: D 64 ASN cc_start: 0.7923 (m-40) cc_final: 0.7579 (m110) REVERT: D 181 GLU cc_start: 0.8581 (mp0) cc_final: 0.8054 (pm20) REVERT: D 185 LEU cc_start: 0.8746 (tp) cc_final: 0.8511 (tt) REVERT: D 188 ASP cc_start: 0.6476 (p0) cc_final: 0.6133 (t0) REVERT: D 194 ARG cc_start: 0.7828 (ttp-170) cc_final: 0.7486 (ttp80) outliers start: 50 outliers final: 36 residues processed: 273 average time/residue: 0.1712 time to fit residues: 64.3927 Evaluate side-chains 262 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 88 optimal weight: 0.0270 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 C 89 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4625 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= 0.199 Angle : 0.608 8.924 10482 Z= 0.318 Chirality : 0.044 0.190 1230 Planarity : 0.003 0.034 1264 Dihedral : 10.168 116.347 1040 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.29 % Allowed : 15.68 % Favored : 78.03 % 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: 1.28 (0.27), residues: 928 helix: 1.79 (0.21), residues: 552 sheet: 0.69 (0.69), residues: 58 loop : -0.80 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 60 HIS 0.002 0.001 HIS A 115 PHE 0.030 0.001 PHE B 143 TYR 0.023 0.002 TYR B 206 ARG 0.003 0.000 ARG B 190 *********************** 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 291 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 238 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.8246 (mmmt) cc_final: 0.8015 (mmtt) REVERT: A 51 TYR cc_start: 0.7751 (m-10) cc_final: 0.7503 (m-10) REVERT: A 141 TRP cc_start: 0.7887 (m100) cc_final: 0.7547 (m100) REVERT: A 166 MET cc_start: 0.6477 (mmp) cc_final: 0.5634 (ttm) REVERT: A 206 TYR cc_start: 0.7333 (p90) cc_final: 0.6980 (p90) REVERT: A 209 ASP cc_start: 0.7575 (t70) cc_final: 0.7195 (m-30) REVERT: A 243 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7913 (mmtt) REVERT: B 51 TYR cc_start: 0.7192 (m-10) cc_final: 0.6808 (m-80) REVERT: B 76 ARG cc_start: 0.6955 (ttm-80) cc_final: 0.6715 (ttp80) REVERT: B 84 GLN cc_start: 0.8471 (tt0) cc_final: 0.8003 (tt0) REVERT: B 87 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7494 (mmm) REVERT: B 115 HIS cc_start: 0.7767 (t-90) cc_final: 0.7538 (t-170) REVERT: B 122 VAL cc_start: 0.8343 (t) cc_final: 0.8064 (t) REVERT: B 152 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8489 (mm) REVERT: B 209 ASP cc_start: 0.7912 (t70) cc_final: 0.7359 (m-30) REVERT: B 243 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8070 (mmtt) REVERT: C 70 GLU cc_start: 0.7783 (tp30) cc_final: 0.7493 (tp30) REVERT: C 71 HIS cc_start: 0.7210 (m-70) cc_final: 0.6892 (m90) REVERT: C 99 TYR cc_start: 0.8202 (t80) cc_final: 0.7884 (t80) REVERT: C 157 ASP cc_start: 0.8716 (m-30) cc_final: 0.8331 (t0) REVERT: C 194 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7741 (ttp80) REVERT: C 281 TYR cc_start: 0.7547 (t80) cc_final: 0.7315 (t80) REVERT: D 157 ASP cc_start: 0.8114 (t0) cc_final: 0.7893 (t0) REVERT: D 181 GLU cc_start: 0.8524 (mp0) cc_final: 0.8035 (pm20) REVERT: D 194 ARG cc_start: 0.7757 (ttp-170) cc_final: 0.7386 (ttp80) REVERT: D 204 MET cc_start: 0.6333 (pmm) cc_final: 0.5785 (pmm) outliers start: 53 outliers final: 39 residues processed: 269 average time/residue: 0.1658 time to fit residues: 61.8391 Evaluate side-chains 265 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 162 GLN B 222 GLN ** 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** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7754 Z= 0.189 Angle : 0.589 7.498 10482 Z= 0.309 Chirality : 0.045 0.409 1230 Planarity : 0.003 0.033 1264 Dihedral : 9.975 115.002 1040 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 6.89 % Allowed : 17.10 % Favored : 76.01 % 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: 1.09 (0.27), residues: 928 helix: 1.73 (0.21), residues: 552 sheet: 0.38 (0.74), residues: 50 loop : -0.98 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 60 HIS 0.004 0.001 HIS A 115 PHE 0.017 0.001 PHE A 111 TYR 0.024 0.002 TYR B 206 ARG 0.003 0.000 ARG B 190 *********************** 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 292 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 234 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 TRP cc_start: 0.7919 (m100) cc_final: 0.7571 (m100) REVERT: A 166 MET cc_start: 0.6260 (mmp) cc_final: 0.5453 (ttm) REVERT: A 209 ASP cc_start: 0.7311 (t70) cc_final: 0.6976 (m-30) REVERT: A 233 PHE cc_start: 0.8083 (m-80) cc_final: 0.7694 (m-80) REVERT: A 243 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7893 (mmtt) REVERT: B 76 ARG cc_start: 0.6956 (ttm-80) cc_final: 0.6709 (ttp80) REVERT: B 84 GLN cc_start: 0.8486 (tt0) cc_final: 0.8009 (tt0) REVERT: B 87 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7631 (mmm) REVERT: B 115 HIS cc_start: 0.7714 (t-90) cc_final: 0.7455 (t-170) REVERT: B 122 VAL cc_start: 0.8595 (t) cc_final: 0.8379 (t) REVERT: B 152 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8484 (mm) REVERT: B 209 ASP cc_start: 0.7862 (t70) cc_final: 0.7319 (m-30) REVERT: B 243 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8075 (mmtt) REVERT: B 245 ASP cc_start: 0.5941 (m-30) cc_final: 0.5736 (m-30) REVERT: C 70 GLU cc_start: 0.7911 (tp30) cc_final: 0.7641 (tp30) REVERT: C 71 HIS cc_start: 0.7354 (m-70) cc_final: 0.6970 (m90) REVERT: C 99 TYR cc_start: 0.8258 (t80) cc_final: 0.8049 (t80) REVERT: C 157 ASP cc_start: 0.8621 (m-30) cc_final: 0.8240 (t0) REVERT: C 194 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7871 (ttp80) REVERT: D 4 GLU cc_start: 0.7777 (mp0) cc_final: 0.7408 (mp0) REVERT: D 181 GLU cc_start: 0.8486 (mp0) cc_final: 0.8076 (pm20) REVERT: D 194 ARG cc_start: 0.7761 (ttp-170) cc_final: 0.7389 (ttp80) outliers start: 58 outliers final: 44 residues processed: 265 average time/residue: 0.1700 time to fit residues: 62.3696 Evaluate side-chains 260 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7754 Z= 0.208 Angle : 0.582 5.911 10482 Z= 0.305 Chirality : 0.044 0.362 1230 Planarity : 0.003 0.031 1264 Dihedral : 9.912 114.444 1040 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 6.89 % Allowed : 18.17 % Favored : 74.94 % 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: 1.05 (0.27), residues: 928 helix: 1.76 (0.21), residues: 544 sheet: 0.48 (0.74), residues: 50 loop : -1.08 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 60 HIS 0.003 0.001 HIS A 115 PHE 0.017 0.001 PHE A 111 TYR 0.020 0.002 TYR B 136 ARG 0.002 0.000 ARG D 189 *********************** 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 284 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 226 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 31 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 141 TRP cc_start: 0.7923 (m100) cc_final: 0.7577 (m100) REVERT: A 166 MET cc_start: 0.6273 (mmp) cc_final: 0.5484 (ttm) REVERT: A 209 ASP cc_start: 0.7318 (t70) cc_final: 0.6985 (m-30) REVERT: A 233 PHE cc_start: 0.8032 (m-80) cc_final: 0.7672 (m-80) REVERT: A 243 LYS cc_start: 0.8372 (mmtt) cc_final: 0.7875 (mmtt) REVERT: B 51 TYR cc_start: 0.7228 (m-80) cc_final: 0.6718 (m-80) REVERT: B 76 ARG cc_start: 0.6993 (ttm-80) cc_final: 0.6723 (ttp80) REVERT: B 84 GLN cc_start: 0.8520 (tt0) cc_final: 0.8025 (tt0) REVERT: B 87 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7732 (mmm) REVERT: B 115 HIS cc_start: 0.7758 (t-90) cc_final: 0.7494 (t-170) REVERT: B 127 ASN cc_start: 0.5524 (OUTLIER) cc_final: 0.5244 (t0) REVERT: B 152 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8487 (mm) REVERT: B 209 ASP cc_start: 0.7872 (t70) cc_final: 0.7319 (m-30) REVERT: B 245 ASP cc_start: 0.6121 (m-30) cc_final: 0.5902 (m-30) REVERT: C 1 MET cc_start: 0.7039 (tpp) cc_final: 0.6780 (tpt) REVERT: C 70 GLU cc_start: 0.7916 (tp30) cc_final: 0.7459 (tp30) REVERT: C 71 HIS cc_start: 0.7077 (m-70) cc_final: 0.6589 (m90) REVERT: C 157 ASP cc_start: 0.8628 (m-30) cc_final: 0.8247 (t0) REVERT: C 194 ARG cc_start: 0.8193 (ttp-170) cc_final: 0.7830 (ttp80) REVERT: C 204 MET cc_start: 0.6956 (pmm) cc_final: 0.6654 (pmm) REVERT: D 4 GLU cc_start: 0.7788 (mp0) cc_final: 0.7416 (mp0) REVERT: D 194 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7445 (ttp80) REVERT: D 204 MET cc_start: 0.6302 (pmm) cc_final: 0.6083 (pmm) outliers start: 58 outliers final: 47 residues processed: 257 average time/residue: 0.1786 time to fit residues: 64.2929 Evaluate side-chains 265 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 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** A 220 ASN B 162 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 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** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7754 Z= 0.186 Angle : 0.566 6.515 10482 Z= 0.298 Chirality : 0.044 0.317 1230 Planarity : 0.003 0.030 1264 Dihedral : 9.691 112.619 1040 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 6.53 % Allowed : 18.65 % Favored : 74.82 % 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: 0.99 (0.27), residues: 928 helix: 1.76 (0.21), residues: 544 sheet: 0.34 (0.75), residues: 50 loop : -1.16 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 60 HIS 0.003 0.001 HIS A 115 PHE 0.017 0.001 PHE A 111 TYR 0.020 0.001 TYR B 136 ARG 0.004 0.000 ARG C 172 *********************** 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 271 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 216 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7382 (tt) REVERT: A 34 GLN cc_start: 0.8052 (tp40) cc_final: 0.7311 (mp10) REVERT: A 141 TRP cc_start: 0.7881 (m100) cc_final: 0.7550 (m100) REVERT: A 166 MET cc_start: 0.6055 (mmp) cc_final: 0.5371 (ttm) REVERT: A 209 ASP cc_start: 0.7273 (t70) cc_final: 0.6957 (m-30) REVERT: A 233 PHE cc_start: 0.7994 (m-80) cc_final: 0.7698 (m-80) REVERT: B 76 ARG cc_start: 0.6925 (ttm-80) cc_final: 0.6709 (ttp80) REVERT: B 84 GLN cc_start: 0.8453 (tt0) cc_final: 0.7925 (tt0) REVERT: B 87 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7735 (mmm) REVERT: B 127 ASN cc_start: 0.5252 (OUTLIER) cc_final: 0.4983 (t0) REVERT: B 152 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8492 (mm) REVERT: B 209 ASP cc_start: 0.7868 (t70) cc_final: 0.7318 (m-30) REVERT: B 245 ASP cc_start: 0.6247 (m-30) cc_final: 0.6012 (m-30) REVERT: C 70 GLU cc_start: 0.7963 (tp30) cc_final: 0.7563 (tp30) REVERT: C 71 HIS cc_start: 0.7042 (m-70) cc_final: 0.6560 (m90) REVERT: C 157 ASP cc_start: 0.8412 (m-30) cc_final: 0.8124 (t70) REVERT: D 4 GLU cc_start: 0.7721 (mp0) cc_final: 0.7155 (mp0) REVERT: D 124 MET cc_start: 0.7944 (mtm) cc_final: 0.7339 (mtm) REVERT: D 157 ASP cc_start: 0.7978 (t0) cc_final: 0.7667 (t0) REVERT: D 181 GLU cc_start: 0.8469 (mp0) cc_final: 0.7930 (pm20) REVERT: D 194 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7449 (ttp80) outliers start: 55 outliers final: 47 residues processed: 245 average time/residue: 0.1674 time to fit residues: 57.5433 Evaluate side-chains 259 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7754 Z= 0.282 Angle : 0.639 9.234 10482 Z= 0.333 Chirality : 0.045 0.176 1230 Planarity : 0.003 0.028 1264 Dihedral : 9.527 110.275 1040 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 7.36 % Allowed : 18.41 % Favored : 74.23 % 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: 0.90 (0.27), residues: 928 helix: 1.65 (0.21), residues: 552 sheet: 0.16 (0.75), residues: 50 loop : -1.18 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 60 HIS 0.003 0.001 HIS D 197 PHE 0.024 0.002 PHE D 21 TYR 0.023 0.002 TYR C 112 ARG 0.004 0.001 ARG B 190 *********************** 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 281 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 219 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7434 (tt) REVERT: A 34 GLN cc_start: 0.8073 (tp40) cc_final: 0.7317 (mp10) REVERT: A 141 TRP cc_start: 0.7880 (m100) cc_final: 0.7543 (m100) REVERT: A 166 MET cc_start: 0.6072 (mmp) cc_final: 0.5374 (ttm) REVERT: A 209 ASP cc_start: 0.7341 (t70) cc_final: 0.6991 (m-30) REVERT: A 233 PHE cc_start: 0.7980 (m-80) cc_final: 0.7665 (m-80) REVERT: B 76 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6959 (ttp80) REVERT: B 84 GLN cc_start: 0.8511 (tt0) cc_final: 0.7965 (tt0) REVERT: B 87 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7790 (mmm) REVERT: B 127 ASN cc_start: 0.5243 (OUTLIER) cc_final: 0.4997 (t0) REVERT: B 209 ASP cc_start: 0.7748 (t70) cc_final: 0.7172 (m-30) REVERT: B 245 ASP cc_start: 0.6129 (m-30) cc_final: 0.5871 (m-30) REVERT: C 70 GLU cc_start: 0.7946 (tp30) cc_final: 0.7584 (tp30) REVERT: C 71 HIS cc_start: 0.7112 (m-70) cc_final: 0.6565 (m90) REVERT: C 157 ASP cc_start: 0.8351 (m-30) cc_final: 0.8128 (t70) REVERT: D 157 ASP cc_start: 0.7994 (t0) cc_final: 0.7701 (t0) REVERT: D 181 GLU cc_start: 0.8433 (mp0) cc_final: 0.8006 (pm20) REVERT: D 194 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7468 (ttp80) outliers start: 62 outliers final: 48 residues processed: 255 average time/residue: 0.1696 time to fit residues: 60.0230 Evaluate side-chains 261 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** 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: 0.7397 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7754 Z= 0.218 Angle : 0.613 7.789 10482 Z= 0.322 Chirality : 0.045 0.374 1230 Planarity : 0.003 0.027 1264 Dihedral : 9.356 107.907 1040 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.65 % Allowed : 19.71 % Favored : 73.63 % 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: 1.63 (0.21), residues: 550 sheet: 0.28 (0.76), residues: 50 loop : -1.19 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 60 HIS 0.003 0.001 HIS A 115 PHE 0.018 0.001 PHE A 111 TYR 0.025 0.002 TYR C 99 ARG 0.008 0.001 ARG C 172 *********************** 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 270 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 214 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7327 (tt) REVERT: A 34 GLN cc_start: 0.8164 (tp40) cc_final: 0.7377 (mp10) REVERT: A 38 MET cc_start: 0.6074 (mmm) cc_final: 0.5753 (tpt) REVERT: A 141 TRP cc_start: 0.7867 (m100) cc_final: 0.7550 (m100) REVERT: A 166 MET cc_start: 0.6025 (mmp) cc_final: 0.5327 (ttm) REVERT: A 209 ASP cc_start: 0.7299 (t70) cc_final: 0.6977 (m-30) REVERT: A 233 PHE cc_start: 0.7973 (m-80) cc_final: 0.7660 (m-80) REVERT: B 76 ARG cc_start: 0.6998 (ttm-80) cc_final: 0.6670 (ttp80) REVERT: B 84 GLN cc_start: 0.8474 (tt0) cc_final: 0.7940 (tt0) REVERT: B 87 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: B 127 ASN cc_start: 0.5101 (OUTLIER) cc_final: 0.4870 (t0) REVERT: B 209 ASP cc_start: 0.7721 (t70) cc_final: 0.7160 (m-30) REVERT: B 245 ASP cc_start: 0.6187 (m-30) cc_final: 0.5896 (m-30) REVERT: C 70 GLU cc_start: 0.7942 (tp30) cc_final: 0.7610 (tp30) REVERT: C 71 HIS cc_start: 0.7098 (m-70) cc_final: 0.6567 (m90) REVERT: C 157 ASP cc_start: 0.8355 (m-30) cc_final: 0.8132 (t70) REVERT: D 4 GLU cc_start: 0.7524 (mp0) cc_final: 0.6954 (mp0) REVERT: D 157 ASP cc_start: 0.8003 (t0) cc_final: 0.7705 (t0) REVERT: D 181 GLU cc_start: 0.8386 (mp0) cc_final: 0.7914 (pm20) REVERT: D 194 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7456 (ttp80) outliers start: 56 outliers final: 49 residues processed: 244 average time/residue: 0.1629 time to fit residues: 55.9987 Evaluate side-chains 262 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 210 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7754 Z= 0.277 Angle : 0.643 8.235 10482 Z= 0.335 Chirality : 0.045 0.165 1230 Planarity : 0.004 0.030 1264 Dihedral : 9.282 106.257 1040 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 6.65 % Allowed : 20.07 % Favored : 73.28 % 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: 0.77 (0.27), residues: 928 helix: 1.57 (0.21), residues: 550 sheet: 0.17 (0.78), residues: 50 loop : -1.28 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 60 HIS 0.003 0.001 HIS C 178 PHE 0.027 0.002 PHE A 187 TYR 0.023 0.002 TYR C 112 ARG 0.005 0.001 ARG C 172 ********************** 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 267 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 0.814 Fit side-chains REVERT: A 6 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7368 (tt) REVERT: A 34 GLN cc_start: 0.8160 (tp40) cc_final: 0.7386 (mp10) REVERT: A 38 MET cc_start: 0.6257 (mmm) cc_final: 0.5748 (tpt) REVERT: A 141 TRP cc_start: 0.7883 (m100) cc_final: 0.7564 (m100) REVERT: A 166 MET cc_start: 0.6218 (mmp) cc_final: 0.5506 (ttm) REVERT: A 209 ASP cc_start: 0.7324 (t70) cc_final: 0.6992 (m-30) REVERT: A 233 PHE cc_start: 0.7925 (m-80) cc_final: 0.7618 (m-80) REVERT: B 76 ARG cc_start: 0.7259 (ttm-80) cc_final: 0.6894 (ttp80) REVERT: B 84 GLN cc_start: 0.8454 (tt0) cc_final: 0.7884 (tt0) REVERT: B 87 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7871 (mmm) REVERT: B 115 HIS cc_start: 0.7709 (t-90) cc_final: 0.7408 (t-170) REVERT: B 127 ASN cc_start: 0.5124 (OUTLIER) cc_final: 0.4879 (t0) REVERT: B 209 ASP cc_start: 0.7739 (t70) cc_final: 0.7171 (m-30) REVERT: B 245 ASP cc_start: 0.6352 (m-30) cc_final: 0.6070 (m-30) REVERT: C 70 GLU cc_start: 0.7944 (tp30) cc_final: 0.7590 (tp30) REVERT: C 71 HIS cc_start: 0.7118 (m-70) cc_final: 0.6560 (m90) REVERT: D 4 GLU cc_start: 0.7638 (mp0) cc_final: 0.7048 (mp0) REVERT: D 157 ASP cc_start: 0.8145 (t0) cc_final: 0.7827 (t0) REVERT: D 181 GLU cc_start: 0.8306 (mp0) cc_final: 0.7841 (pm20) REVERT: D 194 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7426 (ttp80) outliers start: 56 outliers final: 48 residues processed: 244 average time/residue: 0.1667 time to fit residues: 56.9308 Evaluate side-chains 258 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 207 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 276 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.0070 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 0.0670 chunk 13 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.3294 ------------------------------------------------------------------------------- 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 162 GLN C 148 ASN ** C 200 GLN ** 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** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094012 restraints weight = 13870.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097297 restraints weight = 7100.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.099596 restraints weight = 4622.477| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7754 Z= 0.176 Angle : 0.593 8.457 10482 Z= 0.309 Chirality : 0.043 0.193 1230 Planarity : 0.003 0.028 1264 Dihedral : 8.994 104.357 1040 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.97 % Allowed : 23.16 % Favored : 73.87 % 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: 0.83 (0.27), residues: 928 helix: 1.62 (0.21), residues: 550 sheet: 0.32 (0.80), residues: 50 loop : -1.30 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 60 HIS 0.003 0.001 HIS A 115 PHE 0.027 0.001 PHE B 218 TYR 0.028 0.001 TYR C 99 ARG 0.005 0.000 ARG C 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1947.52 seconds wall clock time: 36 minutes 15.17 seconds (2175.17 seconds total)