Starting phenix.real_space_refine on Sat Dec 28 18:10:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vih_32009/12_2024/7vih_32009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vih_32009/12_2024/7vih_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_32009/12_2024/7vih_32009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vih_32009/12_2024/7vih_32009.map" model { file = "/net/cci-nas-00/data/ceres_data/7vih_32009/12_2024/7vih_32009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vih_32009/12_2024/7vih_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.58, per 1000 atoms: 0.74 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 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: 1.02 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: 2.83 Time building geometry restraints manager: 2.84 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.920 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: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- 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 : 0.962 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: 1.3904 time to fit residues: 241.6086 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 : 0.989 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.941 Fit side-chains REVERT: E 76 LYS cc_start: 0.8649 (ttmp) cc_final: 0.8368 (mptt) REVERT: E 186 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: E 213 THR cc_start: 0.8862 (t) cc_final: 0.8607 (m) REVERT: F 172 LEU cc_start: 0.6243 (mm) cc_final: 0.5861 (mm) REVERT: F 269 TRP cc_start: 0.7479 (OUTLIER) cc_final: 0.7241 (m100) REVERT: D 240 MET cc_start: 0.5908 (ppp) cc_final: 0.5553 (ppp) REVERT: D 247 MET cc_start: 0.8859 (mtp) cc_final: 0.8658 (mtm) REVERT: D 280 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7599 (pttp) outliers start: 29 outliers final: 7 residues processed: 139 average time/residue: 1.1942 time to fit residues: 177.7491 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 186 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 Chi-restraints excluded: chain D residue 280 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 39 GLN E 77 ASN E 171 ASN D 188 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1770 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= 0.224 Angle : 0.547 6.618 12340 Z= 0.286 Chirality : 0.042 0.224 1412 Planarity : 0.004 0.060 1544 Dihedral : 7.515 135.178 1250 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.07 % Allowed : 13.50 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1121 helix: 2.28 (0.25), residues: 389 sheet: 0.25 (0.30), residues: 279 loop : -0.52 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.036 0.002 TYR E 235 ARG 0.006 0.000 ARG E 160 *********************** 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 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.172 Fit side-chains REVERT: E 43 LYS cc_start: 0.8129 (ptpt) cc_final: 0.7097 (ptmm) REVERT: E 76 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8360 (mptt) REVERT: E 186 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: E 220 GLU cc_start: 0.7563 (tt0) cc_final: 0.6885 (tt0) REVERT: F 110 TYR cc_start: 0.4271 (m-10) cc_final: 0.3852 (m-80) REVERT: F 177 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6691 (tt) REVERT: F 269 TRP cc_start: 0.7503 (OUTLIER) cc_final: 0.7241 (m100) REVERT: D 240 MET cc_start: 0.6033 (ppp) cc_final: 0.5825 (ppp) outliers start: 30 outliers final: 10 residues processed: 138 average time/residue: 1.2242 time to fit residues: 180.8363 Evaluate side-chains 122 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 186 GLN 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 98 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9118 Z= 0.245 Angle : 0.537 6.674 12340 Z= 0.285 Chirality : 0.042 0.238 1412 Planarity : 0.004 0.055 1544 Dihedral : 6.835 119.258 1249 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.99 % Allowed : 13.91 % Favored : 82.11 % 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: 2.20 (0.25), residues: 389 sheet: 0.21 (0.30), residues: 277 loop : -0.57 (0.28), residues: 455 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 0.011 0.001 PHE D 189 TYR 0.039 0.002 TYR E 235 ARG 0.006 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 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: E 76 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8345 (mptt) REVERT: E 186 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: E 220 GLU cc_start: 0.7688 (tt0) cc_final: 0.6820 (tt0) REVERT: F 110 TYR cc_start: 0.4364 (m-10) cc_final: 0.4022 (m-80) REVERT: F 177 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6710 (tt) REVERT: F 269 TRP cc_start: 0.7531 (OUTLIER) cc_final: 0.7223 (m100) outliers start: 39 outliers final: 16 residues processed: 139 average time/residue: 1.1099 time to fit residues: 166.1595 Evaluate side-chains 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 186 GLN 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 Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 39 GLN E 167 HIS E 171 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.006 0.050 9118 Z= 0.371 Angle : 0.606 7.231 12340 Z= 0.321 Chirality : 0.045 0.270 1412 Planarity : 0.005 0.058 1544 Dihedral : 6.742 108.566 1249 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.37 % Allowed : 15.75 % Favored : 80.88 % 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: 0.60 (0.24), residues: 1121 helix: 1.78 (0.25), residues: 390 sheet: 0.23 (0.31), residues: 275 loop : -0.66 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 117 HIS 0.004 0.001 HIS F 28 PHE 0.012 0.002 PHE D 274 TYR 0.043 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 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.952 Fit side-chains REVERT: E 76 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8344 (mptt) REVERT: F 110 TYR cc_start: 0.4406 (m-10) cc_final: 0.4016 (m-80) REVERT: F 177 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6956 (tt) REVERT: F 269 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.7304 (m100) outliers start: 33 outliers final: 17 residues processed: 135 average time/residue: 1.2011 time to fit residues: 174.0370 Evaluate side-chains 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9118 Z= 0.194 Angle : 0.523 6.663 12340 Z= 0.277 Chirality : 0.042 0.223 1412 Planarity : 0.004 0.054 1544 Dihedral : 5.857 89.167 1249 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.48 % Allowed : 16.67 % Favored : 79.86 % 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: 0.78 (0.25), residues: 1121 helix: 2.02 (0.25), residues: 389 sheet: 0.26 (0.30), residues: 274 loop : -0.59 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 117 HIS 0.001 0.000 HIS E 35 PHE 0.010 0.001 PHE D 189 TYR 0.036 0.001 TYR E 235 ARG 0.007 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 157 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7056 (ptmm) REVERT: E 76 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8309 (mptt) REVERT: E 192 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7969 (ttm) REVERT: F 110 TYR cc_start: 0.4256 (m-10) cc_final: 0.3937 (m-80) REVERT: F 177 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6745 (tt) REVERT: F 235 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.5533 (mt) REVERT: F 292 ARG cc_start: 0.7005 (mpt180) cc_final: 0.5733 (mmm160) outliers start: 34 outliers final: 15 residues processed: 142 average time/residue: 1.1455 time to fit residues: 174.7162 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 : 1.086 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9118 Z= 0.171 Angle : 0.513 6.898 12340 Z= 0.269 Chirality : 0.041 0.211 1412 Planarity : 0.004 0.057 1544 Dihedral : 5.540 78.710 1249 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.66 % Allowed : 18.10 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1121 helix: 2.15 (0.25), residues: 390 sheet: 0.30 (0.30), residues: 274 loop : -0.53 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 117 HIS 0.002 0.000 HIS D 244 PHE 0.010 0.001 PHE D 189 TYR 0.035 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 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.987 Fit side-chains REVERT: E 43 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7045 (ptmm) REVERT: E 76 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8317 (mptt) REVERT: F 110 TYR cc_start: 0.4214 (m-10) cc_final: 0.3894 (m-80) REVERT: F 177 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6633 (tt) REVERT: F 235 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.5506 (mt) outliers start: 26 outliers final: 15 residues processed: 143 average time/residue: 1.0996 time to fit residues: 169.7213 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 177 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2358 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= 0.169 Angle : 0.517 8.118 12340 Z= 0.269 Chirality : 0.041 0.203 1412 Planarity : 0.004 0.056 1544 Dihedral : 5.412 74.819 1249 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.86 % Allowed : 18.40 % Favored : 78.73 % 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: 0.97 (0.25), residues: 1121 helix: 2.20 (0.25), residues: 390 sheet: 0.33 (0.31), residues: 276 loop : -0.50 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 117 HIS 0.002 0.000 HIS E 35 PHE 0.010 0.001 PHE D 189 TYR 0.035 0.001 TYR E 235 ARG 0.006 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 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.904 Fit side-chains REVERT: A 261 MET cc_start: 0.8057 (tpp) cc_final: 0.7655 (ttm) REVERT: E 43 LYS cc_start: 0.8012 (ptpt) cc_final: 0.7027 (ptmm) REVERT: F 110 TYR cc_start: 0.4274 (m-10) cc_final: 0.3937 (m-80) REVERT: F 177 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6834 (tt) REVERT: F 235 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.5519 (mt) REVERT: D 333 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7996 (tp-100) outliers start: 28 outliers final: 17 residues processed: 145 average time/residue: 1.1041 time to fit residues: 172.5905 Evaluate side-chains 139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 177 LEU 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 Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9118 Z= 0.209 Angle : 0.552 9.680 12340 Z= 0.284 Chirality : 0.042 0.214 1412 Planarity : 0.004 0.057 1544 Dihedral : 5.506 74.686 1249 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.66 % Allowed : 19.02 % Favored : 78.32 % 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: 0.90 (0.25), residues: 1121 helix: 2.12 (0.25), residues: 391 sheet: 0.35 (0.31), residues: 274 loop : -0.57 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 117 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE D 189 TYR 0.037 0.001 TYR E 235 ARG 0.010 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 147 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8021 (ptpt) cc_final: 0.7065 (ptmm) REVERT: F 110 TYR cc_start: 0.4345 (m-10) cc_final: 0.4006 (m-80) REVERT: F 177 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6884 (tt) REVERT: F 235 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.5537 (mt) outliers start: 26 outliers final: 20 residues processed: 135 average time/residue: 1.1240 time to fit residues: 163.4277 Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 69 LEU 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 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 64 ILE Chi-restraints excluded: chain F residue 177 LEU 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 Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.0070 chunk 26 optimal weight: 3.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9118 Z= 0.183 Angle : 0.540 9.998 12340 Z= 0.278 Chirality : 0.042 0.206 1412 Planarity : 0.004 0.056 1544 Dihedral : 5.412 71.788 1249 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.35 % Allowed : 19.63 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1121 helix: 2.16 (0.25), residues: 391 sheet: 0.39 (0.31), residues: 274 loop : -0.54 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 117 HIS 0.003 0.000 HIS D 188 PHE 0.010 0.001 PHE D 189 TYR 0.035 0.001 TYR E 235 ARG 0.011 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 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8014 (ptpt) cc_final: 0.7099 (ptmm) REVERT: F 110 TYR cc_start: 0.4290 (m-10) cc_final: 0.4000 (m-80) REVERT: F 235 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.5635 (mt) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 1.1604 time to fit residues: 163.6051 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 : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 69 LEU 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 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 Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3728 r_free = 0.3728 target = 0.146996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113410 restraints weight = 22321.694| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.11 r_work: 0.3167 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2440 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= 0.202 Angle : 0.544 10.029 12340 Z= 0.280 Chirality : 0.042 0.212 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.438 72.282 1249 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.35 % Allowed : 19.63 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1121 helix: 2.14 (0.25), residues: 391 sheet: 0.38 (0.31), residues: 274 loop : -0.54 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 117 HIS 0.002 0.000 HIS D 188 PHE 0.010 0.001 PHE D 189 TYR 0.036 0.001 TYR E 235 ARG 0.003 0.000 ARG F 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3478.52 seconds wall clock time: 63 minutes 19.25 seconds (3799.25 seconds total)