Starting phenix.real_space_refine on Thu Feb 13 10:26:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vih_32009/02_2025/7vih_32009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vih_32009/02_2025/7vih_32009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vih_32009/02_2025/7vih_32009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vih_32009/02_2025/7vih_32009.map" model { file = "/net/cci-nas-00/data/ceres_data/7vih_32009/02_2025/7vih_32009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vih_32009/02_2025/7vih_32009.cif" } resolution = 2.98 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= 0.042 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 5702 2.51 5 N 1510 2.21 5 O 1660 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 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8938 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: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "F" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2237 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain breaks: 2 Chain: "D" Number of atoms: 1826 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1820 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 226, 1820 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 bond proxies already assigned to first conformer: 1843 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: 6.35, per 1000 atoms: 0.71 Number of scatterers: 8938 At special positions: 0 Unit cell: (105.41, 117.03, 131.14, 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 1660 8.00 N 1510 7.00 C 5702 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 1.2 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.5% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 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 removed outlier: 3.604A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.687A 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: 3.792A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.011A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 33 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 110 removed outlier: 3.973A pdb=" N TYR F 110 " --> pdb=" O ALA F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 148 Processing helix chain 'F' and resid 156 through 181 removed outlier: 4.068A pdb=" N LEU F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.502A pdb=" N GLY F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 234 removed outlier: 3.585A pdb=" N ARG F 234 " --> pdb=" O THR F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 282 Proline residue: F 271 - end of helix removed outlier: 4.012A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 314 removed outlier: 3.837A pdb=" N LEU F 297 " --> pdb=" O ALA F 293 " (cutoff:3.500A) Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 315 through 324 removed outlier: 3.545A pdb=" N ARG F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 32 removed outlier: 3.571A 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: 4.624A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 216 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 removed outlier: 4.105A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.578A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.512A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.570A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 5.500A pdb=" N THR A 46 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN A 339 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.631A 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: 6.957A pdb=" N ALA A 72 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A 60 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 70 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 73 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A 78 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 91 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.660A 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: 4.297A pdb=" N GLY A 115 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.190A 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: 6.411A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 5.994A 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: 3.504A pdb=" N GLN A 219 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 211 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS A 217 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.521A pdb=" N CYS A 249 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR A 262 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.519A 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: 3.602A pdb=" N SER A 274 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS A 293 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 306 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 6.546A 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: 5.859A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.281A 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: 3.696A 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: 3.869A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.683A 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: 6.055A pdb=" N VAL D 34 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE D 199 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU D 36 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE D 221 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N PHE D 267 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE D 223 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN D 269 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 225 " --> pdb=" O ASN D 269 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1309 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: 3.01 Time building geometry restraints manager: 2.73 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: 1440 1.29 - 1.42: 2402 1.42 - 1.55: 5179 1.55 - 1.68: 5 1.68 - 1.81: 92 Bond restraints: 9118 Sorted by residual: bond pdb=" C16 7I4 F 401 " pdb=" N17 7I4 F 401 " ideal model delta sigma weight residual 1.441 1.154 0.287 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C19 7I4 F 401 " pdb=" C23 7I4 F 401 " ideal model delta sigma weight residual 1.537 1.415 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C18 7I4 F 401 " pdb=" C19 7I4 F 401 " ideal model delta sigma weight residual 1.533 1.412 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MET D 240 " pdb=" CA MET D 240 " ideal model delta sigma weight residual 1.457 1.528 -0.072 1.24e-02 6.50e+03 3.34e+01 bond pdb=" C19 7I4 F 401 " pdb=" C20 7I4 F 401 " ideal model delta sigma weight residual 1.538 1.637 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 9113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 12246 3.58 - 7.16: 70 7.16 - 10.74: 18 10.74 - 14.32: 4 14.32 - 17.90: 2 Bond angle restraints: 12340 Sorted by residual: angle pdb=" N VAL D 233 " pdb=" CA VAL D 233 " pdb=" C VAL D 233 " ideal model delta sigma weight residual 110.53 120.89 -10.36 9.40e-01 1.13e+00 1.21e+02 angle pdb=" N THR F 236 " pdb=" CA THR F 236 " pdb=" C THR F 236 " ideal model delta sigma weight residual 109.76 124.56 -14.80 1.59e+00 3.96e-01 8.67e+01 angle pdb=" C THR F 236 " pdb=" CA THR F 236 " pdb=" CB THR F 236 " ideal model delta sigma weight residual 109.84 98.27 11.57 1.63e+00 3.76e-01 5.04e+01 angle pdb=" N GLU D 236 " pdb=" CA GLU D 236 " pdb=" C GLU D 236 " ideal model delta sigma weight residual 111.14 103.92 7.22 1.08e+00 8.57e-01 4.47e+01 angle pdb=" C TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta sigma weight residual 110.79 99.77 11.02 1.66e+00 3.63e-01 4.40e+01 ... (remaining 12335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 5333 35.68 - 71.37: 80 71.37 - 107.05: 9 107.05 - 142.74: 0 142.74 - 178.42: 3 Dihedral angle restraints: 5425 sinusoidal: 2128 harmonic: 3297 Sorted by residual: dihedral pdb=" C TYR F 98 " pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta harmonic sigma weight residual -122.60 -109.85 -12.75 0 2.50e+00 1.60e-01 2.60e+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 -127.90 41.90 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.88 40.12 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 5422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.151: 1411 1.151 - 2.301: 0 2.301 - 3.452: 0 3.452 - 4.603: 0 4.603 - 5.753: 1 Chirality restraints: 1412 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 2.88 -5.75 2.00e-01 2.50e+01 8.28e+02 chirality pdb=" CA LEU F 174 " pdb=" N LEU F 174 " pdb=" C LEU F 174 " pdb=" CB LEU F 174 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL F 96 " pdb=" N VAL F 96 " pdb=" C VAL F 96 " pdb=" CB VAL F 96 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1409 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 307 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO F 308 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO F 308 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 308 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 241 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASN D 241 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 242 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 117 " 0.018 2.00e-02 2.50e+03 1.87e-02 8.75e+00 pdb=" CG TRP F 117 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP F 117 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 117 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 117 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 117 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 117 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP F 117 " 0.001 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 880 2.74 - 3.28: 8878 3.28 - 3.82: 14890 3.82 - 4.36: 18051 4.36 - 4.90: 32056 Nonbonded interactions: 74755 Sorted by model distance: nonbonded pdb=" O GLN A 74 " pdb=" OG SER A 97 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 244 " pdb=" OD1 ASP A 246 " model vdw 2.228 3.040 nonbonded pdb=" O LYS F 283 " pdb=" OG1 THR F 286 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR E 175 " pdb=" OE2 GLU D 8 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR D 290 " pdb=" O SER D 293 " model vdw 2.237 3.040 ... (remaining 74750 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: 2.980 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.287 9118 Z= 0.380 Angle : 0.800 17.898 12340 Z= 0.449 Chirality : 0.161 5.753 1412 Planarity : 0.006 0.135 1544 Dihedral : 13.996 178.421 3287 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.61 % Allowed : 0.41 % Favored : 98.98 % Cbeta Deviations : 0.19 % 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: 0.70 (0.24), residues: 1121 helix: 2.00 (0.25), residues: 389 sheet: 0.08 (0.30), residues: 271 loop : -0.58 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.021 0.001 PHE A 291 TYR 0.039 0.002 TYR F 98 ARG 0.009 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.079 Fit side-chains REVERT: A 28 THR cc_start: 0.8719 (p) cc_final: 0.8423 (t) REVERT: E 34 MET cc_start: 0.8715 (mmm) cc_final: 0.8396 (mmm) REVERT: F 172 LEU cc_start: 0.6014 (mm) cc_final: 0.5746 (mm) REVERT: F 269 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.7239 (m100) outliers start: 6 outliers final: 2 residues processed: 164 average time/residue: 1.4037 time to fit residues: 244.0111 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 174 GLN A 292 ASN E 171 ASN F 116 GLN F 156 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.146602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115427 restraints weight = 21316.002| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.91 r_work: 0.3165 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9118 Z= 0.223 Angle : 0.601 9.037 12340 Z= 0.306 Chirality : 0.043 0.231 1412 Planarity : 0.005 0.078 1544 Dihedral : 7.937 151.124 1252 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.97 % Allowed : 10.43 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1121 helix: 2.19 (0.25), residues: 389 sheet: 0.26 (0.30), residues: 276 loop : -0.54 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.003 0.001 HIS E 167 PHE 0.012 0.001 PHE D 189 TYR 0.034 0.002 TYR E 235 ARG 0.007 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.096 Fit side-chains REVERT: E 76 LYS cc_start: 0.8702 (ttmp) cc_final: 0.8120 (mptt) REVERT: E 179 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: E 213 THR cc_start: 0.8614 (t) cc_final: 0.8345 (m) REVERT: F 172 LEU cc_start: 0.5903 (mm) cc_final: 0.5521 (mm) REVERT: F 269 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.7058 (m100) REVERT: D 240 MET cc_start: 0.5390 (ppp) cc_final: 0.5004 (ppp) REVERT: D 247 MET cc_start: 0.8744 (mtp) cc_final: 0.8525 (mtm) outliers start: 29 outliers final: 7 residues processed: 139 average time/residue: 1.2312 time to fit residues: 183.5219 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 179 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 0.0070 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 292 ASN E 77 ASN E 171 ASN D 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117715 restraints weight = 22762.171| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.93 r_work: 0.3180 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9118 Z= 0.167 Angle : 0.520 6.353 12340 Z= 0.271 Chirality : 0.041 0.209 1412 Planarity : 0.004 0.059 1544 Dihedral : 7.450 135.649 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 14.21 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1121 helix: 2.44 (0.25), residues: 389 sheet: 0.32 (0.30), residues: 268 loop : -0.54 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 117 HIS 0.003 0.000 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.031 0.001 TYR E 235 ARG 0.005 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.104 Fit side-chains REVERT: A 75 ASP cc_start: 0.8785 (p0) cc_final: 0.8582 (p0) REVERT: A 157 VAL cc_start: 0.8907 (t) cc_final: 0.8644 (p) REVERT: A 216 MET cc_start: 0.7850 (ppp) cc_final: 0.7576 (pp-130) REVERT: E 43 LYS cc_start: 0.8033 (ptpt) cc_final: 0.6902 (ptmm) REVERT: E 76 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8110 (mptt) REVERT: E 220 GLU cc_start: 0.7452 (tt0) cc_final: 0.6697 (tt0) REVERT: F 110 TYR cc_start: 0.4302 (m-10) cc_final: 0.3862 (m-80) REVERT: F 172 LEU cc_start: 0.5989 (mm) cc_final: 0.5573 (mm) REVERT: F 177 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6413 (tt) REVERT: F 269 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.7067 (m100) REVERT: D 240 MET cc_start: 0.5484 (ppp) cc_final: 0.5258 (ppp) REVERT: D 247 MET cc_start: 0.8737 (mtp) cc_final: 0.8520 (mtm) outliers start: 25 outliers final: 9 residues processed: 140 average time/residue: 1.1669 time to fit residues: 175.1685 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 103 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN E 39 GLN E 171 ASN ** 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 = 0.3684 r_free = 0.3684 target = 0.144646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112857 restraints weight = 18916.254| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.82 r_work: 0.3143 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9118 Z= 0.243 Angle : 0.538 6.905 12340 Z= 0.283 Chirality : 0.042 0.234 1412 Planarity : 0.004 0.058 1544 Dihedral : 6.762 118.429 1249 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.58 % Allowed : 14.52 % Favored : 81.90 % 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: 0.98 (0.25), residues: 1121 helix: 2.31 (0.25), residues: 390 sheet: 0.28 (0.30), residues: 282 loop : -0.55 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.012 0.001 PHE D 189 TYR 0.038 0.002 TYR E 235 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8055 (ptpt) cc_final: 0.6898 (ptmm) REVERT: E 76 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8090 (mptt) REVERT: E 220 GLU cc_start: 0.7571 (tt0) cc_final: 0.6670 (tt0) REVERT: F 110 TYR cc_start: 0.4188 (m-10) cc_final: 0.3791 (m-80) REVERT: F 177 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6407 (tt) REVERT: F 269 TRP cc_start: 0.7326 (OUTLIER) cc_final: 0.6988 (m100) REVERT: D 240 MET cc_start: 0.5315 (ppp) cc_final: 0.5110 (ppp) outliers start: 35 outliers final: 14 residues processed: 130 average time/residue: 1.1625 time to fit residues: 162.3399 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 0.0000 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- 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 171 ASN E 179 GLN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112893 restraints weight = 21449.584| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.87 r_work: 0.3137 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9118 Z= 0.256 Angle : 0.534 6.867 12340 Z= 0.285 Chirality : 0.043 0.238 1412 Planarity : 0.004 0.058 1544 Dihedral : 6.269 103.581 1249 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.07 % Allowed : 15.64 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1121 helix: 2.15 (0.25), residues: 390 sheet: 0.27 (0.30), residues: 275 loop : -0.57 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.038 0.002 TYR E 235 ARG 0.006 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7036 (ptmm) REVERT: E 76 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8122 (mptt) REVERT: F 110 TYR cc_start: 0.4353 (m-10) cc_final: 0.3983 (m-80) REVERT: F 177 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6568 (tt) REVERT: F 269 TRP cc_start: 0.7415 (OUTLIER) cc_final: 0.7054 (m100) outliers start: 30 outliers final: 16 residues processed: 135 average time/residue: 1.1832 time to fit residues: 171.8908 Evaluate side-chains 131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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 171 ASN D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112656 restraints weight = 26124.952| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.30 r_work: 0.3116 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9118 Z= 0.233 Angle : 0.527 6.679 12340 Z= 0.281 Chirality : 0.042 0.230 1412 Planarity : 0.004 0.058 1544 Dihedral : 5.842 88.839 1249 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.66 % Allowed : 17.28 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.25), residues: 1121 helix: 2.09 (0.25), residues: 390 sheet: 0.26 (0.30), residues: 275 loop : -0.58 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 117 HIS 0.002 0.001 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.037 0.002 TYR E 235 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8065 (ptpt) cc_final: 0.7014 (ptmm) REVERT: E 76 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8078 (mptt) REVERT: F 110 TYR cc_start: 0.4301 (m-10) cc_final: 0.3943 (m-80) REVERT: F 177 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6557 (tt) REVERT: F 269 TRP cc_start: 0.7421 (OUTLIER) cc_final: 0.7060 (m100) outliers start: 26 outliers final: 18 residues processed: 137 average time/residue: 1.1724 time to fit residues: 172.6272 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113925 restraints weight = 25888.969| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.27 r_work: 0.3119 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9118 Z= 0.209 Angle : 0.526 6.816 12340 Z= 0.277 Chirality : 0.042 0.219 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.643 79.973 1249 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.17 % Allowed : 17.48 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1121 helix: 2.13 (0.25), residues: 390 sheet: 0.29 (0.30), residues: 274 loop : -0.56 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.036 0.001 TYR E 235 ARG 0.009 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8053 (ptpt) cc_final: 0.7057 (ptmm) REVERT: E 76 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8070 (mptt) REVERT: E 186 GLN cc_start: 0.8557 (tt0) cc_final: 0.8223 (tt0) REVERT: F 110 TYR cc_start: 0.4263 (m-10) cc_final: 0.3903 (m-80) REVERT: F 235 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5114 (mt) REVERT: F 269 TRP cc_start: 0.7405 (OUTLIER) cc_final: 0.7065 (m100) REVERT: D 298 GLU cc_start: 0.6187 (mt-10) cc_final: 0.5921 (tp30) outliers start: 31 outliers final: 18 residues processed: 139 average time/residue: 1.1685 time to fit residues: 174.5809 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114843 restraints weight = 26252.656| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.34 r_work: 0.3146 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9118 Z= 0.184 Angle : 0.521 7.075 12340 Z= 0.272 Chirality : 0.041 0.213 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.510 75.861 1249 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.76 % Allowed : 18.10 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1121 helix: 2.19 (0.25), residues: 390 sheet: 0.30 (0.30), residues: 275 loop : -0.55 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 117 HIS 0.002 0.000 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.036 0.001 TYR E 235 ARG 0.010 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8056 (ptpt) cc_final: 0.7089 (ptmm) REVERT: E 76 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8091 (mptt) REVERT: E 186 GLN cc_start: 0.8557 (tt0) cc_final: 0.8058 (pt0) REVERT: F 110 TYR cc_start: 0.4275 (m-10) cc_final: 0.3903 (m-80) REVERT: F 235 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5087 (mt) REVERT: F 269 TRP cc_start: 0.7439 (OUTLIER) cc_final: 0.7112 (m100) REVERT: D 298 GLU cc_start: 0.6214 (mt-10) cc_final: 0.5958 (tp30) outliers start: 27 outliers final: 17 residues processed: 136 average time/residue: 1.1585 time to fit residues: 169.4007 Evaluate side-chains 138 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.116632 restraints weight = 21201.035| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.90 r_work: 0.3187 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9118 Z= 0.159 Angle : 0.509 8.117 12340 Z= 0.265 Chirality : 0.041 0.197 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.318 71.463 1249 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.56 % Allowed : 18.81 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1121 helix: 2.26 (0.25), residues: 391 sheet: 0.35 (0.30), residues: 275 loop : -0.53 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 117 HIS 0.002 0.000 HIS E 167 PHE 0.010 0.001 PHE D 189 TYR 0.033 0.001 TYR E 235 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8426 (tpp) cc_final: 0.8174 (ttm) REVERT: E 43 LYS cc_start: 0.8000 (ptpt) cc_final: 0.6910 (ptmm) REVERT: E 76 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8201 (mptt) REVERT: E 186 GLN cc_start: 0.8538 (tt0) cc_final: 0.8066 (pt0) REVERT: F 110 TYR cc_start: 0.4241 (m-10) cc_final: 0.3849 (m-80) REVERT: F 235 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5107 (mt) REVERT: D 298 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5946 (tp30) outliers start: 25 outliers final: 17 residues processed: 141 average time/residue: 1.1052 time to fit residues: 168.1556 Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 0.0670 chunk 39 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 258 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116039 restraints weight = 22194.822| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.00 r_work: 0.3179 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9118 Z= 0.173 Angle : 0.537 10.228 12340 Z= 0.276 Chirality : 0.041 0.200 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.351 71.411 1249 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 19.73 % Favored : 77.81 % 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: 1.04 (0.25), residues: 1121 helix: 2.26 (0.25), residues: 391 sheet: 0.38 (0.30), residues: 279 loop : -0.48 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 117 HIS 0.002 0.000 HIS E 167 PHE 0.010 0.001 PHE D 189 TYR 0.034 0.001 TYR E 235 ARG 0.008 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7026 (ptmm) REVERT: E 76 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8211 (mptt) REVERT: E 186 GLN cc_start: 0.8535 (tt0) cc_final: 0.8077 (pt0) REVERT: F 110 TYR cc_start: 0.4240 (m-10) cc_final: 0.3845 (m-80) REVERT: F 235 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5142 (mt) REVERT: F 269 TRP cc_start: 0.7386 (OUTLIER) cc_final: 0.7049 (m100) REVERT: D 296 TYR cc_start: 0.7002 (t80) cc_final: 0.6702 (t80) REVERT: D 298 GLU cc_start: 0.6177 (mt-10) cc_final: 0.5938 (tp30) outliers start: 24 outliers final: 16 residues processed: 131 average time/residue: 1.1872 time to fit residues: 166.9864 Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 0.0370 chunk 2 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114794 restraints weight = 23665.101| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.04 r_work: 0.3183 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9118 Z= 0.161 Angle : 0.526 10.588 12340 Z= 0.272 Chirality : 0.041 0.196 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.298 69.358 1249 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.56 % Allowed : 19.63 % Favored : 77.81 % 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: 1.07 (0.25), residues: 1121 helix: 2.31 (0.26), residues: 391 sheet: 0.42 (0.31), residues: 274 loop : -0.49 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 117 HIS 0.003 0.000 HIS D 188 PHE 0.011 0.001 PHE A 291 TYR 0.033 0.001 TYR E 235 ARG 0.008 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6651.57 seconds wall clock time: 118 minutes 14.91 seconds (7094.91 seconds total)