Starting phenix.real_space_refine on Thu Mar 13 12:04:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vig_32008/03_2025/7vig_32008.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vig_32008/03_2025/7vig_32008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vig_32008/03_2025/7vig_32008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vig_32008/03_2025/7vig_32008.map" model { file = "/net/cci-nas-00/data/ceres_data/7vig_32008/03_2025/7vig_32008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vig_32008/03_2025/7vig_32008.cif" } resolution = 2.89 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= -0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5692 2.51 5 N 1508 2.21 5 O 1654 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8920 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1804 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "F" Number of atoms: 2245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2245 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 6, 'TRANS': 273} Chain breaks: 2 Chain: "D" Number of atoms: 1804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 bond proxies already assigned to first conformer: 1820 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'7I4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 6.57, per 1000 atoms: 0.74 Number of scatterers: 8920 At special positions: 0 Unit cell: (92.13, 119.52, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 F 1 9.00 O 1654 8.00 N 1508 7.00 C 5692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.40 Conformation dependent library (CDL) restraints added in 1.3 seconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.5% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.013A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.933A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.744A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 removed outlier: 3.779A pdb=" N THR F 32 " --> pdb=" O HIS F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 73 Processing helix chain 'F' and resid 78 through 105 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.824A pdb=" N THR F 109 " --> pdb=" O GLY F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 113 through 148 removed outlier: 3.922A pdb=" N MET F 124 " --> pdb=" O ARG F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 181 removed outlier: 3.832A pdb=" N SER F 171 " --> pdb=" O CYS F 167 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.761A pdb=" N GLY F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 199 through 235 removed outlier: 3.726A pdb=" N LEU F 235 " --> pdb=" O ARG F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 282 Proline residue: F 271 - end of helix removed outlier: 3.890A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 314 Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 315 through 324 removed outlier: 3.515A pdb=" N ARG F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 32 removed outlier: 3.585A pdb=" N ARG D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.743A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 removed outlier: 3.907A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.569A pdb=" N GLU D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.740A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 5.462A pdb=" N THR A 46 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN A 339 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 48 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 61 removed outlier: 3.573A pdb=" N ALA A 59 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A 78 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 91 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104 removed outlier: 4.156A pdb=" N GLY A 115 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.044A pdb=" N THR A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.558A pdb=" N ALA A 207 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A 220 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 209 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.612A pdb=" N CYS A 249 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR A 262 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 251 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277 removed outlier: 3.643A pdb=" N SER A 274 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS A 293 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 306 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 295 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.773A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.157A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.517A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.417A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 185 through 191 removed outlier: 6.625A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1435 1.29 - 1.42: 2399 1.42 - 1.55: 5170 1.55 - 1.68: 3 1.68 - 1.81: 92 Bond restraints: 9099 Sorted by residual: bond pdb=" C16 7I4 F 401 " pdb=" N17 7I4 F 401 " ideal model delta sigma weight residual 1.441 1.155 0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C18 7I4 F 401 " pdb=" C19 7I4 F 401 " ideal model delta sigma weight residual 1.533 1.410 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C19 7I4 F 401 " pdb=" C23 7I4 F 401 " ideal model delta sigma weight residual 1.537 1.417 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C11 7I4 F 401 " pdb=" C12 7I4 F 401 " ideal model delta sigma weight residual 1.462 1.576 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C08 7I4 F 401 " pdb=" C09 7I4 F 401 " ideal model delta sigma weight residual 1.452 1.546 -0.094 2.00e-02 2.50e+03 2.22e+01 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 12217 3.15 - 6.31: 79 6.31 - 9.46: 11 9.46 - 12.61: 4 12.61 - 15.76: 2 Bond angle restraints: 12313 Sorted by residual: angle pdb=" C12 7I4 F 401 " pdb=" C11 7I4 F 401 " pdb=" N10 7I4 F 401 " ideal model delta sigma weight residual 123.31 139.07 -15.76 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C11 7I4 F 401 " pdb=" C12 7I4 F 401 " pdb=" C26 7I4 F 401 " ideal model delta sigma weight residual 119.29 132.36 -13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " pdb=" CG TYR E 235 " ideal model delta sigma weight residual 113.90 106.09 7.81 1.80e+00 3.09e-01 1.88e+01 angle pdb=" C15 7I4 F 401 " pdb=" C16 7I4 F 401 " pdb=" N17 7I4 F 401 " ideal model delta sigma weight residual 110.91 122.57 -11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C08 7I4 F 401 " pdb=" C09 7I4 F 401 " pdb=" N10 7I4 F 401 " ideal model delta sigma weight residual 128.22 138.84 -10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 12308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 4899 16.28 - 32.57: 402 32.57 - 48.85: 90 48.85 - 65.14: 11 65.14 - 81.42: 12 Dihedral angle restraints: 5414 sinusoidal: 2125 harmonic: 3289 Sorted by residual: dihedral pdb=" CA GLU E 234 " pdb=" C GLU E 234 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " ideal model delta harmonic sigma weight residual -180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -126.20 40.20 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA MET D 240 " pdb=" C MET D 240 " pdb=" N ASN D 241 " pdb=" CA ASN D 241 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1386 0.118 - 0.236: 23 0.236 - 0.354: 0 0.354 - 0.472: 0 0.472 - 0.590: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C19 7I4 F 401 " pdb=" C18 7I4 F 401 " pdb=" C20 7I4 F 401 " pdb=" C23 7I4 F 401 " both_signs ideal model delta sigma weight residual False -2.88 -2.29 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CB ILE F 60 " pdb=" CA ILE F 60 " pdb=" CG1 ILE F 60 " pdb=" CG2 ILE F 60 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CG LEU F 136 " pdb=" CB LEU F 136 " pdb=" CD1 LEU F 136 " pdb=" CD2 LEU F 136 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 1407 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 235 " 0.030 2.00e-02 2.50e+03 1.76e-02 6.23e+00 pdb=" CG TYR E 235 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 235 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR E 235 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR E 235 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 235 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 235 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 235 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO E 236 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 113 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO F 114 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " 0.026 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 812 2.74 - 3.28: 8843 3.28 - 3.82: 15048 3.82 - 4.36: 18526 4.36 - 4.90: 32670 Nonbonded interactions: 75899 Sorted by model distance: nonbonded pdb=" O LEU F 174 " pdb=" OH TYR F 202 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASP D 251 " pdb=" ND2 ASN D 255 " model vdw 2.209 3.120 nonbonded pdb=" OE2 GLU D 318 " pdb=" OH TYR D 320 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP A 227 " pdb=" NZ LYS D 209 " model vdw 2.221 3.120 nonbonded pdb=" OG1 THR A 273 " pdb=" O VAL A 314 " model vdw 2.224 3.040 ... (remaining 75894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.600 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.006 0.286 9099 Z= 0.413 Angle : 0.712 15.764 12313 Z= 0.348 Chirality : 0.047 0.590 1410 Planarity : 0.004 0.049 1539 Dihedral : 13.094 81.421 3280 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1116 helix: 1.92 (0.25), residues: 391 sheet: 0.48 (0.31), residues: 274 loop : -0.46 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 81 HIS 0.006 0.001 HIS A 141 PHE 0.014 0.001 PHE D 189 TYR 0.038 0.002 TYR E 235 ARG 0.005 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.907 Fit side-chains REVERT: E 34 MET cc_start: 0.8934 (mmm) cc_final: 0.8672 (mmt) REVERT: D 272 ASP cc_start: 0.7085 (m-30) cc_final: 0.6781 (m-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 1.2462 time to fit residues: 188.9698 Evaluate side-chains 111 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.0170 chunk 100 optimal weight: 0.3980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN F 156 ASN F 303 ASN D 188 HIS D 269 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.105410 restraints weight = 16476.416| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.31 r_work: 0.3052 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9099 Z= 0.183 Angle : 0.575 9.013 12313 Z= 0.292 Chirality : 0.042 0.228 1410 Planarity : 0.004 0.060 1539 Dihedral : 6.274 65.917 1243 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.54 % Allowed : 8.70 % Favored : 89.76 % 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: 1.21 (0.25), residues: 1116 helix: 2.33 (0.25), residues: 386 sheet: 0.70 (0.31), residues: 273 loop : -0.45 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 141 PHE 0.012 0.001 PHE A 233 TYR 0.028 0.001 TYR E 235 ARG 0.006 0.001 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.917 Fit side-chains REVERT: A 21 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7538 (mtt-85) REVERT: A 216 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8238 (ppp) REVERT: A 218 ARG cc_start: 0.8267 (mtp85) cc_final: 0.8059 (mtp85) REVERT: E 186 GLN cc_start: 0.8669 (tt0) cc_final: 0.8401 (tt0) REVERT: E 230 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7730 (ttt) REVERT: D 243 MET cc_start: 0.8249 (tpp) cc_final: 0.8027 (mmm) REVERT: D 272 ASP cc_start: 0.7130 (m-30) cc_final: 0.6813 (m-30) outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 1.0678 time to fit residues: 151.6448 Evaluate side-chains 113 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain F residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 142 GLN E 179 GLN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100023 restraints weight = 25117.800| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.10 r_work: 0.2942 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9099 Z= 0.279 Angle : 0.582 7.715 12313 Z= 0.299 Chirality : 0.043 0.259 1410 Planarity : 0.004 0.058 1539 Dihedral : 5.970 49.668 1243 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.15 % Allowed : 12.90 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1116 helix: 2.22 (0.25), residues: 392 sheet: 0.52 (0.30), residues: 270 loop : -0.64 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.006 0.001 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.042 0.002 TYR E 235 ARG 0.007 0.001 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7288 (mpt180) REVERT: A 216 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8129 (ppp) REVERT: E 186 GLN cc_start: 0.8707 (tt0) cc_final: 0.8467 (tt0) REVERT: E 230 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8041 (ttt) REVERT: F 174 LEU cc_start: 0.7287 (tt) cc_final: 0.7052 (tm) REVERT: D 242 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7481 (mtp85) REVERT: D 272 ASP cc_start: 0.7109 (m-30) cc_final: 0.6676 (m-30) outliers start: 21 outliers final: 9 residues processed: 117 average time/residue: 1.1614 time to fit residues: 145.9459 Evaluate side-chains 114 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN D 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.133077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102804 restraints weight = 17733.165| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.32 r_work: 0.3020 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9099 Z= 0.200 Angle : 0.526 7.274 12313 Z= 0.275 Chirality : 0.042 0.237 1410 Planarity : 0.004 0.058 1539 Dihedral : 5.404 41.370 1243 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.94 % Allowed : 14.33 % Favored : 83.73 % 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: 1.19 (0.25), residues: 1116 helix: 2.46 (0.25), residues: 387 sheet: 0.61 (0.31), residues: 271 loop : -0.56 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 141 PHE 0.015 0.001 PHE D 189 TYR 0.038 0.001 TYR E 235 ARG 0.007 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7621 (mpt-90) REVERT: A 45 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7143 (mpt180) REVERT: E 186 GLN cc_start: 0.8658 (tt0) cc_final: 0.8448 (tt0) REVERT: F 174 LEU cc_start: 0.7177 (tt) cc_final: 0.6931 (tm) REVERT: F 302 LEU cc_start: 0.7763 (mp) cc_final: 0.7424 (mp) REVERT: F 318 MET cc_start: 0.8098 (tpt) cc_final: 0.7875 (tpt) REVERT: D 272 ASP cc_start: 0.7104 (m-30) cc_final: 0.6812 (m-30) outliers start: 19 outliers final: 10 residues processed: 122 average time/residue: 1.2772 time to fit residues: 167.7613 Evaluate side-chains 115 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103277 restraints weight = 27324.237| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.17 r_work: 0.2972 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9099 Z= 0.186 Angle : 0.506 7.412 12313 Z= 0.268 Chirality : 0.041 0.229 1410 Planarity : 0.004 0.057 1539 Dihedral : 5.016 37.937 1243 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.94 % Allowed : 14.74 % Favored : 83.32 % 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: 1.24 (0.25), residues: 1116 helix: 2.53 (0.25), residues: 387 sheet: 0.62 (0.31), residues: 271 loop : -0.55 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 141 PHE 0.013 0.001 PHE D 189 TYR 0.038 0.001 TYR E 235 ARG 0.008 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7466 (mpt-90) REVERT: A 45 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7029 (mpt180) REVERT: A 196 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7254 (mmp80) REVERT: C 17 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.6160 (mp0) REVERT: F 174 LEU cc_start: 0.7132 (tt) cc_final: 0.6890 (tm) REVERT: F 302 LEU cc_start: 0.7723 (mp) cc_final: 0.7344 (mp) REVERT: D 272 ASP cc_start: 0.6912 (m-30) cc_final: 0.6618 (m-30) outliers start: 19 outliers final: 11 residues processed: 119 average time/residue: 1.2102 time to fit residues: 154.3352 Evaluate side-chains 117 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.133044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104171 restraints weight = 22488.374| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.66 r_work: 0.2957 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9099 Z= 0.212 Angle : 0.510 6.893 12313 Z= 0.272 Chirality : 0.042 0.229 1410 Planarity : 0.004 0.058 1539 Dihedral : 4.989 35.812 1243 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.25 % Allowed : 14.84 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1116 helix: 2.51 (0.25), residues: 387 sheet: 0.67 (0.31), residues: 277 loop : -0.51 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS A 141 PHE 0.013 0.001 PHE D 189 TYR 0.039 0.001 TYR E 235 ARG 0.008 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7558 (mpt-90) REVERT: A 45 ARG cc_start: 0.7906 (mtp85) cc_final: 0.7084 (mpt180) REVERT: A 196 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7278 (mmp80) REVERT: A 213 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8300 (mmm-85) REVERT: C 17 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: F 135 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7790 (mp) REVERT: F 174 LEU cc_start: 0.7149 (tt) cc_final: 0.6940 (tm) REVERT: F 235 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7629 (pp) REVERT: F 302 LEU cc_start: 0.7820 (mp) cc_final: 0.7448 (mp) REVERT: D 272 ASP cc_start: 0.6926 (m-30) cc_final: 0.6625 (m-30) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 1.1668 time to fit residues: 151.6602 Evaluate side-chains 117 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 0.0030 chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 61 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105122 restraints weight = 18798.542| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.48 r_work: 0.3047 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9099 Z= 0.147 Angle : 0.479 7.940 12313 Z= 0.254 Chirality : 0.041 0.257 1410 Planarity : 0.004 0.056 1539 Dihedral : 4.564 31.397 1243 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.35 % Allowed : 15.66 % Favored : 81.99 % 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: 1.35 (0.25), residues: 1116 helix: 2.61 (0.25), residues: 387 sheet: 0.63 (0.32), residues: 259 loop : -0.40 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 168 HIS 0.002 0.001 HIS A 141 PHE 0.013 0.001 PHE D 189 TYR 0.025 0.001 TYR E 235 ARG 0.010 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7437 (mpt-90) REVERT: A 45 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7146 (mpt180) REVERT: A 196 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7117 (mmp80) REVERT: E 235 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7302 (t80) REVERT: F 135 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7901 (mp) REVERT: F 174 LEU cc_start: 0.7034 (tt) cc_final: 0.6814 (tm) REVERT: F 177 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7731 (mt) REVERT: F 235 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7472 (pp) REVERT: F 292 ARG cc_start: 0.7510 (mpp80) cc_final: 0.6355 (mtm-85) REVERT: F 302 LEU cc_start: 0.7796 (mp) cc_final: 0.7376 (mp) REVERT: D 18 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8113 (ttt) REVERT: D 272 ASP cc_start: 0.7053 (m-30) cc_final: 0.6765 (m-30) outliers start: 23 outliers final: 10 residues processed: 140 average time/residue: 1.1012 time to fit residues: 165.7372 Evaluate side-chains 130 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 87 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 96 optimal weight: 0.0020 chunk 52 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104732 restraints weight = 20127.438| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.65 r_work: 0.3033 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9099 Z= 0.159 Angle : 0.488 7.046 12313 Z= 0.259 Chirality : 0.041 0.265 1410 Planarity : 0.004 0.060 1539 Dihedral : 4.475 29.566 1243 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.05 % Allowed : 16.99 % Favored : 80.96 % 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: 1.39 (0.25), residues: 1116 helix: 2.63 (0.25), residues: 387 sheet: 0.66 (0.32), residues: 259 loop : -0.37 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 141 PHE 0.013 0.001 PHE D 189 TYR 0.026 0.001 TYR E 235 ARG 0.010 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7507 (mpt-90) REVERT: A 45 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7195 (mpt180) REVERT: A 196 ARG cc_start: 0.7914 (mtt-85) cc_final: 0.7183 (mmp80) REVERT: E 235 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7306 (t80) REVERT: F 135 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7992 (mp) REVERT: F 174 LEU cc_start: 0.7067 (tt) cc_final: 0.6835 (tm) REVERT: F 177 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7690 (mt) REVERT: F 235 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7592 (pp) REVERT: F 302 LEU cc_start: 0.7803 (mp) cc_final: 0.7369 (mp) REVERT: D 272 ASP cc_start: 0.7167 (m-30) cc_final: 0.6868 (m-30) outliers start: 20 outliers final: 11 residues processed: 130 average time/residue: 1.4775 time to fit residues: 207.0577 Evaluate side-chains 127 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 76 optimal weight: 0.0030 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.137219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106610 restraints weight = 20216.951| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.62 r_work: 0.3056 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 9099 Z= 0.141 Angle : 0.482 7.183 12313 Z= 0.255 Chirality : 0.040 0.278 1410 Planarity : 0.004 0.059 1539 Dihedral : 4.314 27.059 1243 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.74 % Allowed : 17.30 % Favored : 80.96 % 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: 1.49 (0.25), residues: 1116 helix: 2.68 (0.25), residues: 387 sheet: 0.71 (0.32), residues: 269 loop : -0.30 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.002 0.000 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.025 0.001 TYR E 235 ARG 0.010 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7464 (mpt-90) REVERT: A 45 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7153 (mpt180) REVERT: A 196 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7108 (mmp80) REVERT: E 235 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.7143 (t80) REVERT: F 135 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7902 (mp) REVERT: F 174 LEU cc_start: 0.7041 (tt) cc_final: 0.6809 (tm) REVERT: F 177 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7734 (mt) REVERT: F 292 ARG cc_start: 0.7567 (mpp80) cc_final: 0.6419 (mtm-85) REVERT: F 302 LEU cc_start: 0.7795 (mp) cc_final: 0.7379 (mp) REVERT: D 18 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8146 (ttt) REVERT: D 272 ASP cc_start: 0.7079 (m-30) cc_final: 0.6799 (m-30) outliers start: 17 outliers final: 10 residues processed: 128 average time/residue: 1.1909 time to fit residues: 164.6723 Evaluate side-chains 125 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 104 optimal weight: 0.0020 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN D 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106153 restraints weight = 17583.732| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.32 r_work: 0.3065 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9099 Z= 0.164 Angle : 0.497 9.512 12313 Z= 0.261 Chirality : 0.041 0.291 1410 Planarity : 0.004 0.061 1539 Dihedral : 4.338 26.863 1243 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.84 % Allowed : 17.60 % Favored : 80.55 % 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: 1.52 (0.25), residues: 1116 helix: 2.69 (0.25), residues: 387 sheet: 0.71 (0.31), residues: 274 loop : -0.27 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 168 HIS 0.003 0.001 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.027 0.001 TYR E 235 ARG 0.011 0.000 ARG F 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7567 (mpt-90) REVERT: A 45 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7213 (mpt180) REVERT: A 196 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7188 (mmp80) REVERT: E 235 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.7142 (t80) REVERT: F 174 LEU cc_start: 0.7111 (tt) cc_final: 0.6886 (tm) REVERT: F 177 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7750 (mt) REVERT: F 292 ARG cc_start: 0.7636 (mpp80) cc_final: 0.6495 (mtm-85) REVERT: F 302 LEU cc_start: 0.7851 (mp) cc_final: 0.7429 (mp) REVERT: D 272 ASP cc_start: 0.7144 (m-30) cc_final: 0.6854 (m-30) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 1.2892 time to fit residues: 171.8040 Evaluate side-chains 126 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 97 optimal weight: 0.0170 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106627 restraints weight = 24750.745| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.95 r_work: 0.3027 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 9099 Z= 0.153 Angle : 0.501 10.195 12313 Z= 0.260 Chirality : 0.041 0.285 1410 Planarity : 0.004 0.059 1539 Dihedral : 4.282 25.945 1243 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.54 % Allowed : 17.91 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1116 helix: 2.70 (0.25), residues: 387 sheet: 0.71 (0.31), residues: 274 loop : -0.25 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 168 HIS 0.003 0.001 HIS A 141 PHE 0.012 0.001 PHE D 189 TYR 0.026 0.001 TYR E 235 ARG 0.011 0.000 ARG F 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7298.50 seconds wall clock time: 127 minutes 32.28 seconds (7652.28 seconds total)