Starting phenix.real_space_refine on Thu Mar 13 12:51:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vih_32009/03_2025/7vih_32009.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vih_32009/03_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_32009/03_2025/7vih_32009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vih_32009/03_2025/7vih_32009.map" model { file = "/net/cci-nas-00/data/ceres_data/7vih_32009/03_2025/7vih_32009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vih_32009/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 6.33, 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: 2.12 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: 1.11 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: 2.91 Time building geometry restraints manager: 2.52 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: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 24.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- 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 : 0.910 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: 1.4157 time to fit residues: 246.1618 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 : 0.924 ------------------------------------------------------------------------------- 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 = 0.115428 restraints weight = 21315.995| |-----------------------------------------------------------------------------| 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: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 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 = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- 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 : 0.919 Fit side-chains REVERT: E 76 LYS cc_start: 0.8702 (ttmp) cc_final: 0.8121 (mptt) REVERT: E 179 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: E 213 THR cc_start: 0.8613 (t) cc_final: 0.8344 (m) REVERT: F 172 LEU cc_start: 0.5901 (mm) cc_final: 0.5521 (mm) REVERT: F 269 TRP cc_start: 0.7329 (OUTLIER) cc_final: 0.7059 (m100) REVERT: D 240 MET cc_start: 0.5388 (ppp) cc_final: 0.5002 (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: 1.1431 time to fit residues: 170.1203 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 : 0.991 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117140 restraints weight = 22763.382| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.87 r_work: 0.3173 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- 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 = 0.42 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: 0.8007 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9118 Z= 0.175 Angle : 0.522 6.323 12340 Z= 0.272 Chirality : 0.041 0.209 1412 Planarity : 0.004 0.059 1544 Dihedral : 7.409 134.501 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.66 % Allowed : 14.11 % 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: 2.41 (0.25), residues: 389 sheet: 0.30 (0.30), residues: 275 loop : -0.50 (0.28), residues: 457 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 0.032 0.001 TYR E 235 ARG 0.005 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 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.065 Fit side-chains REVERT: A 216 MET cc_start: 0.7887 (ppp) cc_final: 0.7617 (pp-130) REVERT: E 43 LYS cc_start: 0.8041 (ptpt) cc_final: 0.6918 (ptmm) REVERT: E 76 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8121 (mptt) REVERT: E 220 GLU cc_start: 0.7495 (tt0) cc_final: 0.6727 (tt0) REVERT: F 110 TYR cc_start: 0.4271 (m-10) cc_final: 0.3864 (m-80) REVERT: F 172 LEU cc_start: 0.6007 (mm) cc_final: 0.5596 (mm) REVERT: F 177 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6440 (tt) REVERT: F 269 TRP cc_start: 0.7358 (OUTLIER) cc_final: 0.7076 (m100) REVERT: D 240 MET cc_start: 0.5510 (ppp) cc_final: 0.5283 (ppp) REVERT: D 247 MET cc_start: 0.8755 (mtp) cc_final: 0.8539 (mtm) outliers start: 26 outliers final: 9 residues processed: 138 average time/residue: 1.2099 time to fit residues: 179.3374 Evaluate side-chains 125 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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: 0.0670 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 E 179 GLN D 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117621 restraints weight = 18893.355| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.87 r_work: 0.3223 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9118 Z= 0.143 Angle : 0.481 6.218 12340 Z= 0.254 Chirality : 0.040 0.199 1412 Planarity : 0.004 0.057 1544 Dihedral : 6.238 112.332 1249 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.27 % Allowed : 15.03 % Favored : 81.70 % 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: 1.23 (0.25), residues: 1121 helix: 2.57 (0.25), residues: 390 sheet: 0.45 (0.31), residues: 269 loop : -0.48 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 117 HIS 0.002 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 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 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 216 MET cc_start: 0.7821 (ppp) cc_final: 0.7545 (pp-130) REVERT: E 43 LYS cc_start: 0.8050 (ptpt) cc_final: 0.6929 (ptmm) REVERT: E 76 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8173 (mptt) REVERT: E 220 GLU cc_start: 0.7507 (tt0) cc_final: 0.6629 (tt0) REVERT: F 110 TYR cc_start: 0.4080 (m-10) cc_final: 0.3666 (m-80) REVERT: F 177 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6227 (tt) REVERT: F 269 TRP cc_start: 0.7256 (OUTLIER) cc_final: 0.6962 (m100) REVERT: D 247 MET cc_start: 0.8683 (mtp) cc_final: 0.8473 (mtm) outliers start: 32 outliers final: 12 residues processed: 142 average time/residue: 1.1714 time to fit residues: 179.2188 Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain E residue 2 VAL 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: 3.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN E 39 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 = 0.3696 r_free = 0.3696 target = 0.145560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114935 restraints weight = 21453.124| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.73 r_work: 0.3158 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9118 Z= 0.225 Angle : 0.518 6.766 12340 Z= 0.276 Chirality : 0.042 0.223 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.911 98.251 1249 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.97 % Allowed : 15.54 % Favored : 81.49 % 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: 1.06 (0.25), residues: 1121 helix: 2.35 (0.25), residues: 390 sheet: 0.33 (0.30), residues: 279 loop : -0.49 (0.29), residues: 452 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 0.012 0.001 PHE D 189 TYR 0.037 0.002 TYR E 235 ARG 0.004 0.000 ARG E 38 *********************** 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 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.048 Fit side-chains REVERT: E 76 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8186 (mptt) REVERT: F 110 TYR cc_start: 0.4279 (m-10) cc_final: 0.3879 (m-80) REVERT: F 177 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6431 (tt) REVERT: F 269 TRP cc_start: 0.7405 (OUTLIER) cc_final: 0.7091 (m100) outliers start: 29 outliers final: 15 residues processed: 130 average time/residue: 1.2354 time to fit residues: 172.8192 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.0050 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN E 39 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 = 0.3715 r_free = 0.3715 target = 0.147190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117085 restraints weight = 26106.565| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.33 r_work: 0.3145 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9118 Z= 0.171 Angle : 0.498 6.692 12340 Z= 0.264 Chirality : 0.041 0.214 1412 Planarity : 0.004 0.058 1544 Dihedral : 5.566 86.021 1249 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.45 % Allowed : 16.56 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1121 helix: 2.37 (0.25), residues: 390 sheet: 0.30 (0.30), residues: 275 loop : -0.49 (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 0.034 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 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 261 MET cc_start: 0.8589 (tpp) cc_final: 0.8270 (ttm) REVERT: E 43 LYS cc_start: 0.7995 (ptpt) cc_final: 0.6844 (ptmm) REVERT: E 76 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8143 (mptt) REVERT: E 186 GLN cc_start: 0.8539 (tt0) cc_final: 0.8295 (tt0) REVERT: F 110 TYR cc_start: 0.4236 (m-10) cc_final: 0.3844 (m-80) REVERT: F 177 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6366 (tt) REVERT: F 269 TRP cc_start: 0.7366 (OUTLIER) cc_final: 0.7033 (m100) outliers start: 24 outliers final: 15 residues processed: 131 average time/residue: 1.1811 time to fit residues: 165.6967 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 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 = 0.3700 r_free = 0.3700 target = 0.145671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114855 restraints weight = 25780.263| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.30 r_work: 0.3131 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9118 Z= 0.199 Angle : 0.515 6.751 12340 Z= 0.272 Chirality : 0.041 0.215 1412 Planarity : 0.004 0.060 1544 Dihedral : 5.531 80.641 1249 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.76 % Allowed : 17.38 % 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: 1.03 (0.25), residues: 1121 helix: 2.28 (0.25), residues: 391 sheet: 0.34 (0.30), residues: 280 loop : -0.49 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 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 0.006 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 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8034 (ptpt) cc_final: 0.6895 (ptmm) REVERT: E 76 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8194 (mptt) REVERT: E 186 GLN cc_start: 0.8568 (tt0) cc_final: 0.8257 (tt0) REVERT: F 110 TYR cc_start: 0.4311 (m-10) cc_final: 0.3907 (m-80) REVERT: F 235 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5198 (mt) REVERT: F 269 TRP cc_start: 0.7437 (OUTLIER) cc_final: 0.7111 (m100) outliers start: 27 outliers final: 18 residues processed: 131 average time/residue: 1.1880 time to fit residues: 167.0255 Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 91 THR 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 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: 8.9990 chunk 104 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN 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 = 0.3679 r_free = 0.3679 target = 0.143940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112453 restraints weight = 26249.506| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.30 r_work: 0.3113 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2291 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= 0.257 Angle : 0.550 6.852 12340 Z= 0.289 Chirality : 0.043 0.235 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.677 81.453 1249 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.07 % Allowed : 17.28 % Favored : 79.65 % 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: 2.08 (0.25), residues: 391 sheet: 0.28 (0.30), residues: 276 loop : -0.59 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 117 HIS 0.002 0.001 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.039 0.002 TYR E 235 ARG 0.009 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: 30 poor density : 119 time to evaluate : 0.936 Fit side-chains REVERT: A 211 ASP cc_start: 0.7842 (t70) cc_final: 0.7333 (t70) REVERT: E 43 LYS cc_start: 0.8028 (ptpt) cc_final: 0.6916 (ptmm) REVERT: E 76 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8081 (mptt) REVERT: E 186 GLN cc_start: 0.8546 (tt0) cc_final: 0.8227 (tt0) REVERT: F 110 TYR cc_start: 0.4299 (m-10) cc_final: 0.3953 (m-80) REVERT: F 235 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.5213 (mt) REVERT: F 269 TRP cc_start: 0.7423 (OUTLIER) cc_final: 0.7108 (m100) outliers start: 30 outliers final: 17 residues processed: 138 average time/residue: 1.1350 time to fit residues: 168.9827 Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 44 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 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 = 0.3706 r_free = 0.3706 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115507 restraints weight = 21245.854| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.88 r_work: 0.3167 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9118 Z= 0.183 Angle : 0.524 7.294 12340 Z= 0.275 Chirality : 0.042 0.213 1412 Planarity : 0.004 0.059 1544 Dihedral : 5.459 75.694 1249 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.66 % Allowed : 18.40 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1121 helix: 2.17 (0.25), residues: 391 sheet: 0.30 (0.30), residues: 275 loop : -0.55 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 117 HIS 0.002 0.000 HIS D 188 PHE 0.011 0.001 PHE D 189 TYR 0.035 0.001 TYR E 235 ARG 0.011 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 : 0.916 Fit side-chains revert: symmetry clash REVERT: E 43 LYS cc_start: 0.7905 (ptpt) cc_final: 0.6817 (ptmm) REVERT: E 76 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8190 (mptt) REVERT: E 160 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7226 (mtp85) REVERT: E 186 GLN cc_start: 0.8539 (tt0) cc_final: 0.8059 (pt0) REVERT: F 110 TYR cc_start: 0.4287 (m-10) cc_final: 0.3930 (m-80) REVERT: F 172 LEU cc_start: 0.6015 (mm) cc_final: 0.5563 (mm) REVERT: F 235 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.5166 (mt) REVERT: D 298 GLU cc_start: 0.6183 (mt-10) cc_final: 0.5937 (tp30) outliers start: 26 outliers final: 16 residues processed: 135 average time/residue: 1.2996 time to fit residues: 189.3687 Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110051 restraints weight = 22324.558| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.00 r_work: 0.3105 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9118 Z= 0.351 Angle : 0.614 8.052 12340 Z= 0.320 Chirality : 0.045 0.252 1412 Planarity : 0.005 0.061 1544 Dihedral : 5.937 84.115 1249 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.15 % Allowed : 19.12 % 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: 0.67 (0.25), residues: 1121 helix: 1.83 (0.25), residues: 391 sheet: 0.31 (0.31), residues: 276 loop : -0.66 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 117 HIS 0.004 0.001 HIS A 310 PHE 0.012 0.002 PHE D 189 TYR 0.042 0.002 TYR E 235 ARG 0.010 0.001 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 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: E 43 LYS cc_start: 0.8052 (ptpt) cc_final: 0.7048 (ptmm) REVERT: E 76 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8079 (mptt) REVERT: E 137 ASP cc_start: 0.7406 (p0) cc_final: 0.7163 (p0) REVERT: E 186 GLN cc_start: 0.8520 (tt0) cc_final: 0.8018 (pt0) REVERT: E 192 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (ttm) REVERT: F 110 TYR cc_start: 0.4332 (m-10) cc_final: 0.3976 (m-80) REVERT: F 172 LEU cc_start: 0.6005 (mm) cc_final: 0.5522 (mm) REVERT: F 235 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.5255 (mt) REVERT: F 269 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.7101 (m100) outliers start: 21 outliers final: 14 residues processed: 129 average time/residue: 1.1642 time to fit residues: 161.3283 Evaluate side-chains 135 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 233 PHE 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 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 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3698 r_free = 0.3698 target = 0.145737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112779 restraints weight = 23703.685| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.02 r_work: 0.3162 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2452 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= 0.190 Angle : 0.551 9.392 12340 Z= 0.285 Chirality : 0.042 0.218 1412 Planarity : 0.004 0.058 1544 Dihedral : 5.574 75.381 1249 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.45 % Allowed : 19.02 % Favored : 78.53 % 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: 0.85 (0.25), residues: 1121 helix: 2.07 (0.25), residues: 391 sheet: 0.35 (0.31), residues: 274 loop : -0.60 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 117 HIS 0.002 0.001 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.037 0.001 TYR E 235 ARG 0.012 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7239.40 seconds wall clock time: 126 minutes 6.92 seconds (7566.92 seconds total)