Starting phenix.real_space_refine on Wed Feb 14 05:58:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xji_22211/02_2024/6xji_22211_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xji_22211/02_2024/6xji_22211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xji_22211/02_2024/6xji_22211.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xji_22211/02_2024/6xji_22211.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xji_22211/02_2024/6xji_22211_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xji_22211/02_2024/6xji_22211_neut_updated.pdb" } resolution = 4.0 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= 0.009 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 38 5.16 5 C 5738 2.51 5 N 1404 2.21 5 O 1566 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 GLU 262": "OE1" <-> "OE2" Residue "C ASP 264": "OD1" <-> "OD2" 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 GLU 262": "OE1" <-> "OE2" Residue "D PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8754 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: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2315 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} Chain: "D" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2315 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 283} 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: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8754 At special positions: 0 Unit cell: (75.98, 102.18, 132.31, 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 38 16.00 P 6 15.00 Mg 2 11.99 O 1566 8.00 N 1404 7.00 C 5738 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: 3.74 Conformation dependent library (CDL) restraints added in 1.8 seconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 56.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 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 219 through 232 removed outlier: 5.092A pdb=" N ASP C 223 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 224 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 227 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 254 through 263 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 219 through 232 removed outlier: 5.112A pdb=" N ASP D 223 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 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 269 through 273 removed outlier: 6.479A pdb=" N ASN C 248 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU C 235 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id= D, 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= E, first strand: chain 'D' and resid 2 through 4 Processing sheet with id= F, first strand: chain 'D' and resid 197 through 203 removed outlier: 7.096A pdb=" N PHE D 192 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ASP D 201 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.030A 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= G, first strand: chain 'D' and resid 269 through 273 removed outlier: 3.692A pdb=" N TYR D 269 " --> pdb=" O THR D 216 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 273 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 212 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN D 248 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU D 235 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing sheet with id= H, 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) 483 hydrogen bonds defined for protein. 1350 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: 2.40 Time building geometry restraints manager: 4.01 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: 1753 1.32 - 1.47: 3128 1.47 - 1.61: 3981 1.61 - 1.75: 16 1.75 - 1.90: 56 Bond restraints: 8934 Sorted by residual: 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=" C TYR D 266 " pdb=" N PRO D 267 " ideal model delta sigma weight residual 1.332 1.234 0.098 1.30e-02 5.92e+03 5.67e+01 bond pdb=" C ILE C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 1.331 1.411 -0.080 1.23e-02 6.61e+03 4.20e+01 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 ... (remaining 8929 not shown) Histogram of bond angle deviations from ideal: 96.20 - 104.00: 104 104.00 - 111.80: 4042 111.80 - 119.60: 3818 119.60 - 127.40: 4054 127.40 - 135.20: 62 Bond angle restraints: 12080 Sorted by residual: angle pdb=" O ILE C 270 " pdb=" C ILE C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 123.00 111.71 11.29 1.10e+00 8.26e-01 1.05e+02 angle pdb=" O VAL C 215 " pdb=" C VAL C 215 " pdb=" N THR C 216 " ideal model delta sigma weight residual 123.10 112.21 10.89 1.17e+00 7.31e-01 8.67e+01 angle pdb=" CA ILE C 270 " pdb=" C ILE C 270 " pdb=" N GLU C 271 " ideal model delta sigma weight residual 115.75 127.43 -11.68 1.28e+00 6.10e-01 8.33e+01 angle pdb=" CA VAL C 215 " pdb=" C VAL C 215 " pdb=" N THR C 216 " ideal model delta sigma weight residual 116.34 127.05 -10.71 1.28e+00 6.10e-01 7.00e+01 angle pdb=" C VAL C 215 " pdb=" N THR C 216 " pdb=" CA THR C 216 " ideal model delta sigma weight residual 123.00 133.79 -10.79 1.38e+00 5.25e-01 6.11e+01 ... (remaining 12075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 5162 22.45 - 44.89: 134 44.89 - 67.34: 32 67.34 - 89.78: 12 89.78 - 112.23: 2 Dihedral angle restraints: 5342 sinusoidal: 2174 harmonic: 3168 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 5339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 808 0.067 - 0.134: 420 0.134 - 0.201: 130 0.201 - 0.268: 40 0.268 - 0.335: 12 Chirality restraints: 1410 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 THR D 272 " pdb=" N THR D 272 " pdb=" C THR D 272 " pdb=" CB THR D 272 " both_signs ideal model delta sigma weight residual False 2.53 2.86 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 1407 not shown) Planarity restraints: 1472 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 THR D 212 " -0.021 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR D 212 " 0.076 2.00e-02 2.50e+03 pdb=" O THR D 212 " -0.029 2.00e-02 2.50e+03 pdb=" N THR D 213 " -0.026 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 854 2.72 - 3.26: 9320 3.26 - 3.81: 14573 3.81 - 4.35: 18671 4.35 - 4.90: 30157 Nonbonded interactions: 73575 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=" CG2 THR D 212 " pdb=" OE1 GLN D 236 " model vdw 2.188 3.460 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 ... (remaining 73570 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: 0.250 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: 0.000 Extract box with map and model: 1.190 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.730 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 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 : 0.018 0.182 8934 Z= 1.178 Angle : 1.602 13.386 12080 Z= 1.098 Chirality : 0.092 0.335 1410 Planarity : 0.008 0.044 1472 Dihedral : 12.076 112.230 3298 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.72 % Allowed : 1.86 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1074 helix: 1.19 (0.19), residues: 606 sheet: 0.91 (0.57), residues: 87 loop : -0.06 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.007 TRP A 223 HIS 0.009 0.003 HIS C 232 PHE 0.030 0.005 PHE B 55 TYR 0.069 0.008 TYR B 206 ARG 0.011 0.001 ARG C 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 385 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7717 (mttt) cc_final: 0.7006 (ttpp) REVERT: A 51 TYR cc_start: 0.7737 (m-80) cc_final: 0.7352 (m-80) REVERT: A 83 ILE cc_start: 0.7062 (tt) cc_final: 0.5957 (tt) REVERT: A 162 GLN cc_start: 0.7683 (mt0) cc_final: 0.7314 (pt0) REVERT: A 166 MET cc_start: 0.6175 (mmp) cc_final: 0.4576 (ttm) REVERT: B 16 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7079 (ttpt) REVERT: B 99 SER cc_start: 0.8641 (t) cc_final: 0.8339 (m) REVERT: B 116 TYR cc_start: 0.6612 (t80) cc_final: 0.5797 (t80) REVERT: B 122 VAL cc_start: 0.8149 (t) cc_final: 0.7750 (t) REVERT: B 142 PHE cc_start: 0.8493 (t80) cc_final: 0.8290 (t80) REVERT: B 166 MET cc_start: 0.6704 (mmp) cc_final: 0.6450 (mmm) REVERT: B 211 MET cc_start: 0.8622 (mtp) cc_final: 0.8337 (ptp) REVERT: C 5 HIS cc_start: 0.5984 (m-70) cc_final: 0.5356 (m90) REVERT: C 13 ASN cc_start: 0.6712 (t0) cc_final: 0.6451 (t0) REVERT: C 18 ASP cc_start: 0.7170 (t0) cc_final: 0.6827 (m-30) REVERT: C 20 ASP cc_start: 0.7347 (m-30) cc_final: 0.6763 (t70) REVERT: C 43 MET cc_start: 0.8065 (mtm) cc_final: 0.7744 (mtp) REVERT: C 58 ASP cc_start: 0.7313 (t0) cc_final: 0.6994 (m-30) REVERT: C 105 ASP cc_start: 0.8347 (m-30) cc_final: 0.7856 (p0) REVERT: C 118 LYS cc_start: 0.8294 (pttt) cc_final: 0.7879 (tptt) REVERT: C 135 MET cc_start: 0.7637 (mmm) cc_final: 0.7215 (mmt) REVERT: C 195 ASP cc_start: 0.6927 (m-30) cc_final: 0.6680 (m-30) REVERT: D 1 MET cc_start: 0.3952 (tpp) cc_final: 0.3705 (mmm) REVERT: D 56 LYS cc_start: 0.5901 (tttt) cc_final: 0.5669 (tptm) REVERT: D 77 ASN cc_start: 0.8150 (p0) cc_final: 0.7079 (m-40) REVERT: D 165 LEU cc_start: 0.8255 (mt) cc_final: 0.8033 (mt) REVERT: D 181 GLU cc_start: 0.7113 (mp0) cc_final: 0.6607 (tt0) REVERT: D 273 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6499 (ttm110) REVERT: D 281 TYR cc_start: 0.5233 (t80) cc_final: 0.4838 (t80) outliers start: 7 outliers final: 2 residues processed: 388 average time/residue: 0.2155 time to fit residues: 112.7837 Evaluate side-chains 215 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 273 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 HIS C 237 ASN D 5 HIS D 35 ASN ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 203 ASN D 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8934 Z= 0.230 Angle : 0.679 9.956 12080 Z= 0.363 Chirality : 0.046 0.286 1410 Planarity : 0.004 0.034 1472 Dihedral : 10.501 123.542 1205 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.43 % Allowed : 11.03 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1074 helix: 1.94 (0.20), residues: 594 sheet: 0.84 (0.60), residues: 86 loop : -0.40 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 223 HIS 0.006 0.001 HIS C 244 PHE 0.038 0.002 PHE C 107 TYR 0.021 0.002 TYR A 206 ARG 0.004 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 237 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7345 (m-80) cc_final: 0.6978 (m-80) REVERT: A 76 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6707 (ttm170) REVERT: A 162 GLN cc_start: 0.7673 (mt0) cc_final: 0.7374 (pt0) REVERT: A 166 MET cc_start: 0.5638 (mmp) cc_final: 0.4207 (ptm) REVERT: B 16 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7006 (ttpt) REVERT: B 51 TYR cc_start: 0.7088 (m-10) cc_final: 0.6855 (m-10) REVERT: B 68 MET cc_start: 0.8155 (mmm) cc_final: 0.7876 (mmp) REVERT: B 116 TYR cc_start: 0.6921 (t80) cc_final: 0.6422 (t80) REVERT: B 129 LYS cc_start: 0.7307 (tptp) cc_final: 0.7078 (tptp) REVERT: B 142 PHE cc_start: 0.8427 (t80) cc_final: 0.8199 (t80) REVERT: B 239 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8223 (tt) REVERT: C 5 HIS cc_start: 0.5815 (m-70) cc_final: 0.5036 (m90) REVERT: C 18 ASP cc_start: 0.6636 (t0) cc_final: 0.6307 (m-30) REVERT: C 20 ASP cc_start: 0.6751 (m-30) cc_final: 0.6348 (t70) REVERT: C 37 VAL cc_start: 0.8563 (p) cc_final: 0.8250 (m) REVERT: C 54 ASP cc_start: 0.7152 (t0) cc_final: 0.6822 (m-30) REVERT: C 70 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7896 (tp30) REVERT: C 82 TYR cc_start: 0.7699 (t80) cc_final: 0.7492 (t80) REVERT: C 89 GLN cc_start: 0.8077 (mt0) cc_final: 0.7408 (mt0) REVERT: C 118 LYS cc_start: 0.8400 (pttt) cc_final: 0.7844 (tptt) REVERT: C 124 MET cc_start: 0.8425 (mtm) cc_final: 0.8085 (mtm) REVERT: C 187 CYS cc_start: 0.5256 (p) cc_final: 0.4941 (p) REVERT: D 77 ASN cc_start: 0.8004 (p0) cc_final: 0.6907 (m-40) REVERT: D 100 THR cc_start: 0.7643 (m) cc_final: 0.7362 (m) REVERT: D 116 LYS cc_start: 0.7528 (mttt) cc_final: 0.7193 (mtpp) REVERT: D 165 LEU cc_start: 0.8114 (mt) cc_final: 0.7900 (mt) REVERT: D 181 GLU cc_start: 0.6714 (mp0) cc_final: 0.6450 (tt0) outliers start: 43 outliers final: 28 residues processed: 264 average time/residue: 0.1881 time to fit residues: 69.7614 Evaluate side-chains 221 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 0.0000 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.9726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 GLN D 5 HIS D 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8934 Z= 0.212 Angle : 0.615 12.254 12080 Z= 0.322 Chirality : 0.044 0.216 1410 Planarity : 0.003 0.036 1472 Dihedral : 10.145 120.522 1201 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.85 % Allowed : 14.33 % Favored : 80.82 % 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: 1.25 (0.25), residues: 1074 helix: 1.86 (0.20), residues: 594 sheet: -0.10 (0.55), residues: 95 loop : -0.53 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 223 HIS 0.004 0.001 HIS D 244 PHE 0.029 0.002 PHE C 107 TYR 0.021 0.001 TYR C 228 ARG 0.004 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.5795 (m-80) cc_final: 0.5561 (t80) REVERT: A 51 TYR cc_start: 0.7361 (m-80) cc_final: 0.6982 (m-80) REVERT: A 162 GLN cc_start: 0.7811 (mt0) cc_final: 0.7441 (pt0) REVERT: A 166 MET cc_start: 0.5499 (mmp) cc_final: 0.3952 (ttm) REVERT: A 190 ARG cc_start: 0.4276 (mtp180) cc_final: 0.3533 (mmp80) REVERT: B 34 GLN cc_start: 0.6744 (mm-40) cc_final: 0.5869 (tp40) REVERT: B 51 TYR cc_start: 0.7353 (m-10) cc_final: 0.7023 (m-10) REVERT: B 55 PHE cc_start: 0.7583 (t80) cc_final: 0.7358 (t80) REVERT: B 63 LEU cc_start: 0.8145 (mt) cc_final: 0.7912 (tp) REVERT: B 68 MET cc_start: 0.7976 (mmm) cc_final: 0.7759 (mmp) REVERT: B 116 TYR cc_start: 0.7145 (t80) cc_final: 0.6718 (t80) REVERT: B 239 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8250 (tt) REVERT: C 18 ASP cc_start: 0.6808 (t0) cc_final: 0.6276 (m-30) REVERT: C 37 VAL cc_start: 0.8580 (p) cc_final: 0.8293 (m) REVERT: C 43 MET cc_start: 0.7957 (mtm) cc_final: 0.7597 (ttm) REVERT: C 54 ASP cc_start: 0.6892 (t0) cc_final: 0.6624 (m-30) REVERT: C 82 TYR cc_start: 0.7810 (t80) cc_final: 0.7432 (t80) REVERT: C 89 GLN cc_start: 0.8255 (mt0) cc_final: 0.7527 (mt0) REVERT: C 118 LYS cc_start: 0.8428 (pttt) cc_final: 0.7863 (tptt) REVERT: C 124 MET cc_start: 0.8518 (mtm) cc_final: 0.8099 (mtm) REVERT: D 13 ASN cc_start: 0.5512 (t0) cc_final: 0.4658 (p0) REVERT: D 77 ASN cc_start: 0.8077 (p0) cc_final: 0.7153 (m-40) REVERT: D 194 ARG cc_start: 0.6915 (tmt170) cc_final: 0.6451 (tmm-80) outliers start: 47 outliers final: 34 residues processed: 237 average time/residue: 0.1804 time to fit residues: 60.8497 Evaluate side-chains 218 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 239 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 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 5 HIS D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8934 Z= 0.189 Angle : 0.559 5.899 12080 Z= 0.298 Chirality : 0.044 0.358 1410 Planarity : 0.003 0.034 1472 Dihedral : 10.010 119.622 1201 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.46 % Allowed : 15.15 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1074 helix: 1.83 (0.20), residues: 594 sheet: -0.53 (0.54), residues: 95 loop : -0.65 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 223 HIS 0.004 0.001 HIS D 244 PHE 0.031 0.002 PHE C 107 TYR 0.017 0.001 TYR C 228 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 205 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.5883 (m-80) cc_final: 0.5654 (t80) REVERT: A 51 TYR cc_start: 0.7532 (m-80) cc_final: 0.7268 (m-80) REVERT: A 162 GLN cc_start: 0.7824 (mt0) cc_final: 0.7471 (pt0) REVERT: A 166 MET cc_start: 0.5287 (mmp) cc_final: 0.3748 (ttm) REVERT: A 190 ARG cc_start: 0.4119 (mtp180) cc_final: 0.3414 (mmp80) REVERT: B 34 GLN cc_start: 0.6483 (mm-40) cc_final: 0.5758 (tp40) REVERT: B 63 LEU cc_start: 0.8178 (mt) cc_final: 0.7931 (tp) REVERT: B 116 TYR cc_start: 0.7223 (t80) cc_final: 0.6812 (t80) REVERT: B 239 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8056 (tp) REVERT: C 4 GLU cc_start: 0.6419 (tp30) cc_final: 0.5424 (mp0) REVERT: C 18 ASP cc_start: 0.6680 (t0) cc_final: 0.6320 (m-30) REVERT: C 37 VAL cc_start: 0.8588 (p) cc_final: 0.8341 (t) REVERT: C 43 MET cc_start: 0.7912 (mtm) cc_final: 0.7123 (mpp) REVERT: C 54 ASP cc_start: 0.6884 (t0) cc_final: 0.6639 (m-30) REVERT: C 82 TYR cc_start: 0.7829 (t80) cc_final: 0.7378 (t80) REVERT: C 89 GLN cc_start: 0.8289 (mt0) cc_final: 0.7497 (mt0) REVERT: C 118 LYS cc_start: 0.8469 (pttt) cc_final: 0.7900 (tptt) REVERT: C 124 MET cc_start: 0.8522 (mtm) cc_final: 0.8292 (mtm) REVERT: C 135 MET cc_start: 0.7186 (mmp) cc_final: 0.6895 (mmp) REVERT: D 77 ASN cc_start: 0.7917 (p0) cc_final: 0.7266 (m-40) REVERT: D 194 ARG cc_start: 0.6869 (tmt170) cc_final: 0.6195 (tmm-80) REVERT: D 200 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6572 (tm-30) REVERT: D 263 LEU cc_start: 0.5987 (mp) cc_final: 0.5751 (tp) outliers start: 53 outliers final: 40 residues processed: 238 average time/residue: 0.1816 time to fit residues: 61.3855 Evaluate side-chains 217 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 176 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN D 35 ASN ** 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: 0.6342 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8934 Z= 0.378 Angle : 0.730 9.488 12080 Z= 0.379 Chirality : 0.046 0.166 1410 Planarity : 0.005 0.043 1472 Dihedral : 10.046 114.873 1201 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.91 % Allowed : 17.42 % Favored : 75.67 % 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: 0.47 (0.25), residues: 1074 helix: 1.38 (0.20), residues: 592 sheet: -1.01 (0.51), residues: 95 loop : -0.97 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 223 HIS 0.009 0.001 HIS D 244 PHE 0.046 0.002 PHE C 107 TYR 0.022 0.002 TYR D 112 ARG 0.004 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 192 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 21 TYR cc_start: 0.7498 (m-10) cc_final: 0.7241 (m-10) REVERT: A 51 TYR cc_start: 0.7735 (m-80) cc_final: 0.7432 (m-80) REVERT: A 76 ARG cc_start: 0.6928 (ttm-80) cc_final: 0.6408 (ttm-80) REVERT: A 166 MET cc_start: 0.5353 (mmp) cc_final: 0.3766 (ttm) REVERT: A 190 ARG cc_start: 0.4354 (mtp180) cc_final: 0.3646 (mmp80) REVERT: B -2 ARG cc_start: 0.4278 (mtt180) cc_final: 0.3978 (mtt-85) REVERT: B 2 ARG cc_start: 0.6497 (mtm-85) cc_final: 0.5422 (tmt170) REVERT: B 34 GLN cc_start: 0.6456 (mm-40) cc_final: 0.5916 (tp40) REVERT: B 38 MET cc_start: 0.4153 (pmm) cc_final: 0.2684 (pmm) REVERT: B 63 LEU cc_start: 0.8104 (mt) cc_final: 0.7855 (tp) REVERT: B 116 TYR cc_start: 0.7211 (t80) cc_final: 0.6820 (t80) REVERT: B 239 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8104 (tp) REVERT: C 18 ASP cc_start: 0.6666 (t0) cc_final: 0.6064 (m-30) REVERT: C 43 MET cc_start: 0.7885 (mtm) cc_final: 0.7211 (mpp) REVERT: C 54 ASP cc_start: 0.7072 (t0) cc_final: 0.6798 (m-30) REVERT: C 82 TYR cc_start: 0.7951 (t80) cc_final: 0.7419 (t80) REVERT: C 89 GLN cc_start: 0.8446 (mt0) cc_final: 0.8038 (mt0) REVERT: C 118 LYS cc_start: 0.8429 (pttt) cc_final: 0.7927 (tptt) REVERT: C 124 MET cc_start: 0.8843 (mtm) cc_final: 0.8615 (mtm) REVERT: C 284 ILE cc_start: 0.8423 (mm) cc_final: 0.8195 (mm) REVERT: D 77 ASN cc_start: 0.8032 (p0) cc_final: 0.7435 (m-40) REVERT: D 150 MET cc_start: 0.8167 (mmm) cc_final: 0.7312 (mmm) REVERT: D 165 LEU cc_start: 0.8205 (mm) cc_final: 0.7764 (mt) REVERT: D 200 GLN cc_start: 0.7456 (tm-30) cc_final: 0.6819 (tm-30) REVERT: D 232 HIS cc_start: 0.3790 (m90) cc_final: 0.3179 (m-70) REVERT: D 246 MET cc_start: 0.7333 (mpp) cc_final: 0.6792 (mpp) REVERT: D 278 ARG cc_start: 0.7638 (ttt90) cc_final: 0.6903 (ttm-80) outliers start: 67 outliers final: 48 residues processed: 233 average time/residue: 0.1925 time to fit residues: 63.9203 Evaluate side-chains 222 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU 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 54 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** 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: 0.6282 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8934 Z= 0.186 Angle : 0.587 13.117 12080 Z= 0.308 Chirality : 0.043 0.229 1410 Planarity : 0.003 0.034 1472 Dihedral : 9.346 112.592 1198 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.43 % Allowed : 21.03 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1074 helix: 1.62 (0.20), residues: 595 sheet: -0.85 (0.50), residues: 101 loop : -0.97 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 223 HIS 0.005 0.001 HIS D 244 PHE 0.033 0.002 PHE C 107 TYR 0.020 0.001 TYR D 112 ARG 0.003 0.000 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 15 PHE cc_start: 0.5782 (t80) cc_final: 0.5401 (t80) REVERT: A 38 MET cc_start: 0.7035 (mpp) cc_final: 0.6453 (mmm) REVERT: A 141 TRP cc_start: 0.7248 (m100) cc_final: 0.6922 (m-10) REVERT: A 166 MET cc_start: 0.5273 (mmp) cc_final: 0.3750 (ttm) REVERT: A 190 ARG cc_start: 0.4162 (mtp180) cc_final: 0.3506 (mmp80) REVERT: B -2 ARG cc_start: 0.4335 (mtt180) cc_final: 0.4015 (mtt-85) REVERT: B 2 ARG cc_start: 0.6233 (mtm-85) cc_final: 0.5681 (ptm-80) REVERT: B 34 GLN cc_start: 0.6426 (mm-40) cc_final: 0.5749 (tp40) REVERT: B 63 LEU cc_start: 0.8263 (mt) cc_final: 0.7954 (tp) REVERT: B 116 TYR cc_start: 0.7136 (t80) cc_final: 0.6834 (t80) REVERT: B 239 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8025 (tp) REVERT: C 18 ASP cc_start: 0.6399 (t0) cc_final: 0.6035 (m-30) REVERT: C 43 MET cc_start: 0.7740 (mtm) cc_final: 0.7270 (mpp) REVERT: C 54 ASP cc_start: 0.7095 (t0) cc_final: 0.6815 (m-30) REVERT: C 82 TYR cc_start: 0.7818 (t80) cc_final: 0.7202 (t80) REVERT: C 89 GLN cc_start: 0.8374 (mt0) cc_final: 0.7891 (mt0) REVERT: C 118 LYS cc_start: 0.8317 (pttt) cc_final: 0.7831 (tptt) REVERT: C 124 MET cc_start: 0.8800 (mtm) cc_final: 0.8576 (mtm) REVERT: C 187 CYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5741 (p) REVERT: C 270 ILE cc_start: 0.6622 (tt) cc_final: 0.6196 (mt) REVERT: C 284 ILE cc_start: 0.8390 (mm) cc_final: 0.8155 (mm) REVERT: D 77 ASN cc_start: 0.8075 (p0) cc_final: 0.7509 (m-40) REVERT: D 101 ASP cc_start: 0.8109 (p0) cc_final: 0.7070 (t0) REVERT: D 135 MET cc_start: 0.8493 (mmt) cc_final: 0.8197 (mmm) REVERT: D 150 MET cc_start: 0.8037 (mmm) cc_final: 0.7059 (mmm) REVERT: D 165 LEU cc_start: 0.8134 (mm) cc_final: 0.7695 (mt) REVERT: D 200 GLN cc_start: 0.7482 (tm-30) cc_final: 0.6888 (tm-30) REVERT: D 232 HIS cc_start: 0.3643 (m90) cc_final: 0.3147 (m-70) REVERT: D 278 ARG cc_start: 0.7595 (ttt90) cc_final: 0.6829 (ttm-80) outliers start: 43 outliers final: 32 residues processed: 212 average time/residue: 0.1771 time to fit residues: 53.9635 Evaluate side-chains 209 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU 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 73 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8934 Z= 0.175 Angle : 0.578 11.717 12080 Z= 0.301 Chirality : 0.043 0.321 1410 Planarity : 0.003 0.032 1472 Dihedral : 9.210 112.857 1198 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.02 % Allowed : 22.27 % Favored : 73.71 % 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 (0.25), residues: 1074 helix: 1.68 (0.20), residues: 595 sheet: -0.84 (0.49), residues: 101 loop : -0.97 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 223 HIS 0.006 0.001 HIS D 244 PHE 0.024 0.001 PHE C 107 TYR 0.024 0.001 TYR D 112 ARG 0.004 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 15 PHE cc_start: 0.5792 (t80) cc_final: 0.5398 (t80) REVERT: A 38 MET cc_start: 0.7239 (mpp) cc_final: 0.6581 (mmp) REVERT: A 141 TRP cc_start: 0.7116 (m100) cc_final: 0.6832 (m-10) REVERT: A 166 MET cc_start: 0.5253 (mmp) cc_final: 0.3765 (ttm) REVERT: A 190 ARG cc_start: 0.4098 (mtp180) cc_final: 0.3491 (mmp80) REVERT: B -2 ARG cc_start: 0.4363 (mtt180) cc_final: 0.3882 (mtt-85) REVERT: B 2 ARG cc_start: 0.6213 (mtm-85) cc_final: 0.5680 (ptm-80) REVERT: B 34 GLN cc_start: 0.6422 (mm-40) cc_final: 0.5810 (tp40) REVERT: B 80 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7236 (mp10) REVERT: B 116 TYR cc_start: 0.7138 (t80) cc_final: 0.6835 (t80) REVERT: B 239 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8036 (tp) REVERT: C 18 ASP cc_start: 0.6367 (t0) cc_final: 0.5981 (m-30) REVERT: C 43 MET cc_start: 0.7906 (mtm) cc_final: 0.7425 (mpp) REVERT: C 54 ASP cc_start: 0.7076 (t0) cc_final: 0.6805 (m-30) REVERT: C 82 TYR cc_start: 0.7859 (t80) cc_final: 0.7246 (t80) REVERT: C 89 GLN cc_start: 0.8383 (mt0) cc_final: 0.7876 (mt0) REVERT: C 118 LYS cc_start: 0.8140 (pttt) cc_final: 0.7609 (tptt) REVERT: C 124 MET cc_start: 0.8795 (mtm) cc_final: 0.8568 (mtm) REVERT: C 270 ILE cc_start: 0.6609 (tt) cc_final: 0.6177 (mt) REVERT: C 284 ILE cc_start: 0.8371 (mm) cc_final: 0.8158 (mm) REVERT: D 77 ASN cc_start: 0.8096 (p0) cc_final: 0.7552 (m-40) REVERT: D 101 ASP cc_start: 0.8049 (p0) cc_final: 0.7179 (t0) REVERT: D 135 MET cc_start: 0.8458 (mmt) cc_final: 0.8134 (mmm) REVERT: D 150 MET cc_start: 0.8014 (mmm) cc_final: 0.7543 (mmm) REVERT: D 165 LEU cc_start: 0.8137 (mm) cc_final: 0.7696 (mt) REVERT: D 200 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7028 (tm-30) REVERT: D 232 HIS cc_start: 0.3592 (m90) cc_final: 0.3101 (m-70) REVERT: D 278 ARG cc_start: 0.7536 (ttt90) cc_final: 0.6785 (ttm-80) outliers start: 39 outliers final: 33 residues processed: 213 average time/residue: 0.1718 time to fit residues: 52.7275 Evaluate side-chains 210 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU 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 99 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN D 35 ASN ** 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: 0.6345 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8934 Z= 0.297 Angle : 0.668 12.247 12080 Z= 0.344 Chirality : 0.045 0.292 1410 Planarity : 0.004 0.033 1472 Dihedral : 9.366 112.993 1198 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.46 % Allowed : 21.65 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1074 helix: 1.43 (0.20), residues: 592 sheet: -1.05 (0.48), residues: 101 loop : -1.23 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 223 HIS 0.008 0.001 HIS D 244 PHE 0.021 0.002 PHE C 107 TYR 0.019 0.002 TYR D 112 ARG 0.004 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7164 (mpp) cc_final: 0.6325 (mmp) REVERT: A 141 TRP cc_start: 0.7265 (m100) cc_final: 0.6948 (m-10) REVERT: A 166 MET cc_start: 0.5219 (mmp) cc_final: 0.3778 (ttm) REVERT: A 190 ARG cc_start: 0.4177 (mtp180) cc_final: 0.3575 (mmp80) REVERT: B -2 ARG cc_start: 0.4419 (mtt180) cc_final: 0.3911 (mtt-85) REVERT: B 2 ARG cc_start: 0.6423 (mtm-85) cc_final: 0.5445 (tmt170) REVERT: B 34 GLN cc_start: 0.6425 (mm-40) cc_final: 0.6041 (tt0) REVERT: B 63 LEU cc_start: 0.8298 (mt) cc_final: 0.7966 (tp) REVERT: B 116 TYR cc_start: 0.7279 (t80) cc_final: 0.6818 (t80) REVERT: B 239 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7918 (tp) REVERT: C 18 ASP cc_start: 0.6596 (t0) cc_final: 0.6075 (m-30) REVERT: C 43 MET cc_start: 0.7857 (mtm) cc_final: 0.7518 (mpp) REVERT: C 54 ASP cc_start: 0.7084 (t0) cc_final: 0.6810 (m-30) REVERT: C 82 TYR cc_start: 0.7887 (t80) cc_final: 0.7171 (t80) REVERT: C 89 GLN cc_start: 0.8428 (mt0) cc_final: 0.7943 (mt0) REVERT: C 118 LYS cc_start: 0.8122 (pttt) cc_final: 0.7590 (tptt) REVERT: C 124 MET cc_start: 0.8850 (mtm) cc_final: 0.8606 (mtm) REVERT: D 77 ASN cc_start: 0.8083 (p0) cc_final: 0.7665 (m-40) REVERT: D 101 ASP cc_start: 0.8103 (p0) cc_final: 0.7226 (t0) REVERT: D 150 MET cc_start: 0.7939 (mmm) cc_final: 0.7403 (mmm) REVERT: D 165 LEU cc_start: 0.8191 (mm) cc_final: 0.7737 (mt) REVERT: D 200 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7134 (tm-30) REVERT: D 232 HIS cc_start: 0.3721 (m90) cc_final: 0.3068 (m-70) REVERT: D 278 ARG cc_start: 0.7352 (ttt90) cc_final: 0.6754 (ttm-80) outliers start: 53 outliers final: 44 residues processed: 221 average time/residue: 0.1757 time to fit residues: 56.0265 Evaluate side-chains 228 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU 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 70 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8934 Z= 0.185 Angle : 0.600 11.702 12080 Z= 0.314 Chirality : 0.043 0.342 1410 Planarity : 0.003 0.033 1472 Dihedral : 9.159 115.233 1198 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.92 % Allowed : 23.51 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1074 helix: 1.54 (0.21), residues: 590 sheet: -1.02 (0.48), residues: 101 loop : -1.08 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 223 HIS 0.006 0.001 HIS D 244 PHE 0.030 0.001 PHE C 107 TYR 0.023 0.001 TYR D 112 ARG 0.003 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.6897 (mpp) cc_final: 0.6244 (mmp) REVERT: A 141 TRP cc_start: 0.7234 (m100) cc_final: 0.6946 (m-10) REVERT: A 166 MET cc_start: 0.5177 (mmp) cc_final: 0.3737 (ttm) REVERT: A 190 ARG cc_start: 0.4039 (mtp180) cc_final: 0.3468 (mmp80) REVERT: B -2 ARG cc_start: 0.4386 (mtt180) cc_final: 0.3912 (mtt-85) REVERT: B 2 ARG cc_start: 0.6293 (mtm-85) cc_final: 0.5438 (tmt170) REVERT: B 34 GLN cc_start: 0.6312 (mm-40) cc_final: 0.5904 (tt0) REVERT: B 80 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7434 (mp10) REVERT: B 116 TYR cc_start: 0.7183 (t80) cc_final: 0.6743 (t80) REVERT: B 239 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8020 (tp) REVERT: C 18 ASP cc_start: 0.6344 (t0) cc_final: 0.5891 (m-30) REVERT: C 54 ASP cc_start: 0.7346 (t0) cc_final: 0.6969 (m-30) REVERT: C 82 TYR cc_start: 0.7899 (t80) cc_final: 0.7229 (t80) REVERT: C 89 GLN cc_start: 0.8382 (mt0) cc_final: 0.7859 (mt0) REVERT: C 118 LYS cc_start: 0.8142 (pttt) cc_final: 0.7564 (tptt) REVERT: C 201 ASP cc_start: 0.6736 (t70) cc_final: 0.6512 (t70) REVERT: C 270 ILE cc_start: 0.6576 (tt) cc_final: 0.6146 (mt) REVERT: C 284 ILE cc_start: 0.8191 (mm) cc_final: 0.7668 (tp) REVERT: D 77 ASN cc_start: 0.8080 (p0) cc_final: 0.7701 (m-40) REVERT: D 101 ASP cc_start: 0.8072 (p0) cc_final: 0.7282 (t0) REVERT: D 150 MET cc_start: 0.7839 (mmm) cc_final: 0.7316 (mmm) REVERT: D 165 LEU cc_start: 0.8112 (mm) cc_final: 0.7645 (mt) REVERT: D 200 GLN cc_start: 0.7610 (tm-30) cc_final: 0.7113 (tm-30) REVERT: D 232 HIS cc_start: 0.3603 (m90) cc_final: 0.3088 (m-70) REVERT: D 278 ARG cc_start: 0.7303 (ttt90) cc_final: 0.6735 (ttm-80) outliers start: 38 outliers final: 34 residues processed: 217 average time/residue: 0.1821 time to fit residues: 56.8188 Evaluate side-chains 220 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8934 Z= 0.199 Angle : 0.600 11.737 12080 Z= 0.311 Chirality : 0.044 0.303 1410 Planarity : 0.003 0.031 1472 Dihedral : 9.042 118.337 1198 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.51 % Allowed : 23.81 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1074 helix: 1.48 (0.21), residues: 590 sheet: -0.95 (0.48), residues: 101 loop : -1.06 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 223 HIS 0.006 0.001 HIS D 244 PHE 0.030 0.001 PHE C 107 TYR 0.021 0.001 TYR D 112 ARG 0.002 0.000 ARG C 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.6763 (mpp) cc_final: 0.6254 (mmp) REVERT: A 141 TRP cc_start: 0.7225 (m100) cc_final: 0.6908 (m-10) REVERT: A 166 MET cc_start: 0.5207 (mmp) cc_final: 0.3663 (ttm) REVERT: A 190 ARG cc_start: 0.4060 (mtp180) cc_final: 0.3469 (mmp80) REVERT: B -2 ARG cc_start: 0.4365 (mtt180) cc_final: 0.3873 (mtt-85) REVERT: B 2 ARG cc_start: 0.6346 (mtm-85) cc_final: 0.5392 (tmt170) REVERT: B 9 TYR cc_start: 0.7506 (m-80) cc_final: 0.6936 (t80) REVERT: B 63 LEU cc_start: 0.8273 (mt) cc_final: 0.7956 (tp) REVERT: B 80 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7401 (mp10) REVERT: B 116 TYR cc_start: 0.7190 (t80) cc_final: 0.6733 (t80) REVERT: B 239 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7916 (tp) REVERT: C 18 ASP cc_start: 0.6393 (t0) cc_final: 0.5935 (m-30) REVERT: C 54 ASP cc_start: 0.7328 (t0) cc_final: 0.6940 (m-30) REVERT: C 82 TYR cc_start: 0.7910 (t80) cc_final: 0.7240 (t80) REVERT: C 89 GLN cc_start: 0.8395 (mt0) cc_final: 0.7879 (mt0) REVERT: C 118 LYS cc_start: 0.8138 (pttt) cc_final: 0.7547 (tptt) REVERT: C 124 MET cc_start: 0.8652 (mtm) cc_final: 0.8374 (ttm) REVERT: C 201 ASP cc_start: 0.6779 (t70) cc_final: 0.6562 (t70) REVERT: C 270 ILE cc_start: 0.6571 (tt) cc_final: 0.6161 (mt) REVERT: C 284 ILE cc_start: 0.8150 (mm) cc_final: 0.7640 (tp) REVERT: D 77 ASN cc_start: 0.8185 (p0) cc_final: 0.7755 (m110) REVERT: D 101 ASP cc_start: 0.8069 (p0) cc_final: 0.7261 (t0) REVERT: D 150 MET cc_start: 0.7754 (mmm) cc_final: 0.7195 (mmm) REVERT: D 165 LEU cc_start: 0.8098 (mm) cc_final: 0.7648 (mt) REVERT: D 200 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7110 (tm-30) REVERT: D 232 HIS cc_start: 0.3416 (m90) cc_final: 0.2867 (m-70) REVERT: D 278 ARG cc_start: 0.7238 (ttt90) cc_final: 0.6661 (ttm-80) outliers start: 34 outliers final: 29 residues processed: 203 average time/residue: 0.1709 time to fit residues: 50.5085 Evaluate side-chains 207 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 135 MET Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 136 ASN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.154138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132428 restraints weight = 13060.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.134632 restraints weight = 9107.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135875 restraints weight = 6978.843| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8934 Z= 0.258 Angle : 0.640 11.956 12080 Z= 0.332 Chirality : 0.045 0.330 1410 Planarity : 0.004 0.031 1472 Dihedral : 9.149 120.764 1198 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.23 % Allowed : 23.30 % Favored : 72.47 % 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: 0.36 (0.25), residues: 1074 helix: 1.40 (0.21), residues: 586 sheet: -0.96 (0.49), residues: 101 loop : -1.20 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 223 HIS 0.007 0.001 HIS D 244 PHE 0.025 0.002 PHE C 107 TYR 0.021 0.002 TYR D 75 ARG 0.002 0.000 ARG C 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.40 seconds wall clock time: 36 minutes 1.72 seconds (2161.72 seconds total)