Starting phenix.real_space_refine on Thu Feb 13 03:08:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzp_27804/02_2025/8dzp_27804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzp_27804/02_2025/8dzp_27804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzp_27804/02_2025/8dzp_27804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzp_27804/02_2025/8dzp_27804.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzp_27804/02_2025/8dzp_27804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzp_27804/02_2025/8dzp_27804.cif" } resolution = 2.71 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= 0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5524 2.51 5 N 1443 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2160 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 399 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U99': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.62 Number of scatterers: 8657 At special positions: 0 Unit cell: (90.64, 123.2, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1628 8.00 N 1443 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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 1.0 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 36.7% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.008A pdb=" N ILE A 61 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 4.204A pdb=" N PHE A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.516A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.771A pdb=" N GLN A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.588A pdb=" N SER A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 263 through 300 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.506A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.796A pdb=" N ARG A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.800A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.605A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.067A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.838A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.717A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 191 removed outlier: 8.515A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.763A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.908A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.545A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.902A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.596A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.721A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.536A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1251 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: 2.35 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1581 1.33 - 1.45: 2279 1.45 - 1.57: 4883 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8833 Sorted by residual: bond pdb=" N ASP B 200 " pdb=" CA ASP B 200 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.21e-02 6.83e+03 4.16e+00 bond pdb=" N TYR E 223 " pdb=" CA TYR E 223 " ideal model delta sigma weight residual 1.456 1.478 -0.023 1.13e-02 7.83e+03 4.03e+00 bond pdb=" CA THR B 48 " pdb=" C THR B 48 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.33e-02 5.65e+03 3.89e+00 bond pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.80e+00 bond pdb=" C PRO E 224 " pdb=" O PRO E 224 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.30e-02 5.92e+03 3.34e+00 ... (remaining 8828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11655 1.79 - 3.57: 283 3.57 - 5.36: 34 5.36 - 7.14: 17 7.14 - 8.93: 4 Bond angle restraints: 11993 Sorted by residual: angle pdb=" C TYR E 223 " pdb=" CA TYR E 223 " pdb=" CB TYR E 223 " ideal model delta sigma weight residual 110.44 105.08 5.36 9.00e-01 1.23e+00 3.55e+01 angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" CB PRO E 224 " ideal model delta sigma weight residual 103.25 99.25 4.00 1.05e+00 9.07e-01 1.45e+01 angle pdb=" N ASP B 200 " pdb=" CA ASP B 200 " pdb=" CB ASP B 200 " ideal model delta sigma weight residual 110.57 116.19 -5.62 1.57e+00 4.06e-01 1.28e+01 angle pdb=" C ALA A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta sigma weight residual 122.13 128.54 -6.41 1.85e+00 2.92e-01 1.20e+01 angle pdb=" CA ILE A 58 " pdb=" CB ILE A 58 " pdb=" CG2 ILE A 58 " ideal model delta sigma weight residual 110.50 115.95 -5.45 1.70e+00 3.46e-01 1.03e+01 ... (remaining 11988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 5006 24.08 - 48.16: 239 48.16 - 72.24: 25 72.24 - 96.32: 4 96.32 - 120.40: 1 Dihedral angle restraints: 5275 sinusoidal: 2021 harmonic: 3254 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 59.60 120.40 0 5.00e+00 4.00e-02 5.80e+02 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 167.02 -74.02 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA ALA E 229 " pdb=" C ALA E 229 " pdb=" N GLY E 230 " pdb=" CA GLY E 230 " ideal model delta harmonic sigma weight residual -180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1207 0.068 - 0.135: 176 0.135 - 0.203: 11 0.203 - 0.270: 3 0.270 - 0.338: 2 Chirality restraints: 1399 Sorted by residual: chirality pdb=" C22 U99 A 401 " pdb=" C20 U99 A 401 " pdb=" C23 U99 A 401 " pdb=" C8 U99 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -1.89 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1396 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 222 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU E 222 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU E 222 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 223 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO C 236 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 337 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ASP B 337 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP B 337 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 338 " -0.014 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 973 2.75 - 3.29: 8030 3.29 - 3.83: 14569 3.83 - 4.36: 17170 4.36 - 4.90: 30204 Nonbonded interactions: 70946 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.216 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP C 163 " pdb=" OG1 THR C 165 " model vdw 2.283 3.040 nonbonded pdb=" OG SER B 6 " pdb=" OD1 ASP B 9 " model vdw 2.302 3.040 nonbonded pdb=" O THR A 150 " pdb=" OG SER A 153 " model vdw 2.334 3.040 ... (remaining 70941 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=1.00 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.004 0.042 8833 Z= 0.229 Angle : 0.675 8.930 11993 Z= 0.372 Chirality : 0.048 0.338 1399 Planarity : 0.006 0.066 1503 Dihedral : 13.618 120.400 3165 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.46 (0.24), residues: 1100 helix: 0.49 (0.25), residues: 371 sheet: 0.30 (0.29), residues: 285 loop : -1.35 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.011 0.001 HIS C 62 PHE 0.015 0.002 PHE A 143 TYR 0.021 0.002 TYR E 178 ARG 0.013 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.814 Fit side-chains REVERT: B 225 VAL cc_start: 0.8319 (t) cc_final: 0.8118 (t) REVERT: B 269 ASN cc_start: 0.8395 (m110) cc_final: 0.8058 (m110) REVERT: B 275 GLU cc_start: 0.7065 (tt0) cc_final: 0.6770 (tt0) REVERT: B 337 ASP cc_start: 0.7171 (m-30) cc_final: 0.6868 (m-30) REVERT: C 219 ARG cc_start: 0.7254 (mmt90) cc_final: 0.6935 (mmt90) REVERT: C 258 ASP cc_start: 0.6739 (t70) cc_final: 0.6498 (t70) REVERT: E 89 GLU cc_start: 0.7146 (mp0) cc_final: 0.6855 (mp0) outliers start: 1 outliers final: 2 residues processed: 192 average time/residue: 1.1585 time to fit residues: 237.9692 Evaluate side-chains 182 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 88 ASN C 125 ASN C 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112090 restraints weight = 11888.756| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.78 r_work: 0.3332 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8833 Z= 0.201 Angle : 0.522 6.566 11993 Z= 0.281 Chirality : 0.041 0.183 1399 Planarity : 0.004 0.055 1503 Dihedral : 5.239 63.636 1272 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 8.44 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.31 (0.25), residues: 1100 helix: 1.67 (0.27), residues: 371 sheet: 0.51 (0.30), residues: 263 loop : -1.21 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.005 0.001 HIS C 62 PHE 0.013 0.001 PHE B 189 TYR 0.018 0.001 TYR E 178 ARG 0.004 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.783 Fit side-chains REVERT: A 121 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: A 151 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7803 (tmm) REVERT: A 192 SER cc_start: 0.7589 (OUTLIER) cc_final: 0.7290 (m) REVERT: B 275 GLU cc_start: 0.7522 (tt0) cc_final: 0.7125 (tt0) REVERT: C 197 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7704 (mtm-85) REVERT: C 258 ASP cc_start: 0.7448 (t70) cc_final: 0.7117 (t0) REVERT: C 314 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: E 89 GLU cc_start: 0.7795 (mp0) cc_final: 0.7383 (mp0) REVERT: E 93 MET cc_start: 0.8333 (tpp) cc_final: 0.8114 (tpt) outliers start: 17 outliers final: 3 residues processed: 195 average time/residue: 1.0652 time to fit residues: 222.9855 Evaluate side-chains 194 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111429 restraints weight = 12010.481| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.78 r_work: 0.3301 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8833 Z= 0.209 Angle : 0.511 6.426 11993 Z= 0.275 Chirality : 0.042 0.177 1399 Planarity : 0.004 0.054 1503 Dihedral : 5.025 62.106 1270 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.24 % Allowed : 10.04 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.58 (0.25), residues: 1100 helix: 2.03 (0.27), residues: 372 sheet: 0.49 (0.30), residues: 275 loop : -1.10 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.005 0.001 HIS C 62 PHE 0.018 0.001 PHE A 169 TYR 0.021 0.002 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 1.003 Fit side-chains REVERT: A 121 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6765 (ppp) REVERT: A 151 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7885 (tmm) REVERT: A 192 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7272 (m) REVERT: A 329 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7747 (pp) REVERT: B 275 GLU cc_start: 0.7547 (tt0) cc_final: 0.7150 (tt0) REVERT: C 197 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7856 (mtm-85) REVERT: C 217 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7814 (pmt) REVERT: C 258 ASP cc_start: 0.7449 (t70) cc_final: 0.7103 (t0) REVERT: E 89 GLU cc_start: 0.7801 (mp0) cc_final: 0.7371 (mp0) outliers start: 21 outliers final: 8 residues processed: 193 average time/residue: 1.0594 time to fit residues: 219.9114 Evaluate side-chains 200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.132849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110066 restraints weight = 11894.234| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.78 r_work: 0.3279 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8833 Z= 0.271 Angle : 0.538 6.492 11993 Z= 0.290 Chirality : 0.043 0.182 1399 Planarity : 0.004 0.056 1503 Dihedral : 4.886 59.761 1270 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.31 % Allowed : 10.68 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.25), residues: 1100 helix: 2.11 (0.27), residues: 376 sheet: 0.31 (0.29), residues: 296 loop : -1.11 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.004 0.001 HIS C 62 PHE 0.022 0.002 PHE A 169 TYR 0.023 0.002 TYR E 178 ARG 0.009 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.009 Fit side-chains REVERT: A 121 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6845 (ppp) REVERT: A 151 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7807 (tmm) REVERT: A 192 SER cc_start: 0.7616 (OUTLIER) cc_final: 0.7341 (m) REVERT: A 329 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7776 (pp) REVERT: B 275 GLU cc_start: 0.7531 (tt0) cc_final: 0.7129 (tt0) REVERT: B 350 ASP cc_start: 0.7730 (t70) cc_final: 0.7458 (t70) REVERT: C 197 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7916 (mtm-85) REVERT: C 198 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7900 (pt) REVERT: C 217 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7787 (pmt) REVERT: C 258 ASP cc_start: 0.7466 (t70) cc_final: 0.7110 (OUTLIER) REVERT: E 89 GLU cc_start: 0.7837 (mp0) cc_final: 0.7395 (mp0) REVERT: E 223 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7996 (m-80) outliers start: 31 outliers final: 13 residues processed: 190 average time/residue: 1.0199 time to fit residues: 208.7284 Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 HIS E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110462 restraints weight = 11874.738| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.78 r_work: 0.3285 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8833 Z= 0.235 Angle : 0.515 5.949 11993 Z= 0.278 Chirality : 0.042 0.179 1399 Planarity : 0.004 0.055 1503 Dihedral : 4.647 56.977 1270 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.88 % Allowed : 12.07 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 1100 helix: 2.19 (0.27), residues: 377 sheet: 0.32 (0.29), residues: 295 loop : -1.07 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.003 0.001 HIS B 322 PHE 0.018 0.001 PHE A 169 TYR 0.021 0.002 TYR E 178 ARG 0.007 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.939 Fit side-chains REVERT: A 121 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.6797 (ppp) REVERT: A 151 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: A 192 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7336 (m) REVERT: A 329 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7808 (pp) REVERT: B 275 GLU cc_start: 0.7525 (tt0) cc_final: 0.7119 (tt0) REVERT: B 350 ASP cc_start: 0.7722 (t70) cc_final: 0.7481 (t70) REVERT: C 197 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7951 (mtm-85) REVERT: C 198 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7880 (pt) REVERT: C 217 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7774 (pmt) REVERT: C 258 ASP cc_start: 0.7441 (t70) cc_final: 0.7093 (t0) REVERT: E 89 GLU cc_start: 0.7836 (mp0) cc_final: 0.7387 (mp0) REVERT: E 223 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7892 (m-80) outliers start: 27 outliers final: 11 residues processed: 194 average time/residue: 1.0700 time to fit residues: 222.6224 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110266 restraints weight = 11802.121| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.76 r_work: 0.3285 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8833 Z= 0.242 Angle : 0.520 5.977 11993 Z= 0.280 Chirality : 0.042 0.177 1399 Planarity : 0.004 0.055 1503 Dihedral : 4.572 56.802 1267 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.67 % Allowed : 13.03 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.69 (0.25), residues: 1100 helix: 2.23 (0.27), residues: 378 sheet: 0.29 (0.29), residues: 295 loop : -1.06 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.004 0.001 HIS B 188 PHE 0.015 0.001 PHE A 169 TYR 0.021 0.002 TYR E 178 ARG 0.006 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.990 Fit side-chains REVERT: A 121 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.6808 (ppp) REVERT: A 151 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7775 (tmm) REVERT: A 192 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7368 (m) REVERT: A 325 LEU cc_start: 0.8149 (mm) cc_final: 0.7928 (mt) REVERT: A 329 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7749 (pp) REVERT: B 275 GLU cc_start: 0.7520 (tt0) cc_final: 0.7117 (tt0) REVERT: B 350 ASP cc_start: 0.7686 (t70) cc_final: 0.7471 (t70) REVERT: C 197 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7969 (mtm-85) REVERT: C 198 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7884 (pt) REVERT: C 217 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7765 (pmt) REVERT: C 258 ASP cc_start: 0.7452 (t70) cc_final: 0.7102 (t0) REVERT: E 89 GLU cc_start: 0.7832 (mp0) cc_final: 0.7386 (mp0) REVERT: E 223 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7849 (m-80) outliers start: 25 outliers final: 11 residues processed: 195 average time/residue: 1.0839 time to fit residues: 227.2742 Evaluate side-chains 200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109857 restraints weight = 11775.755| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.74 r_work: 0.3283 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8833 Z= 0.302 Angle : 0.559 9.030 11993 Z= 0.297 Chirality : 0.043 0.186 1399 Planarity : 0.004 0.057 1503 Dihedral : 4.724 57.607 1267 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.88 % Allowed : 13.89 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.63 (0.25), residues: 1100 helix: 2.15 (0.27), residues: 378 sheet: 0.33 (0.29), residues: 293 loop : -1.11 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.004 0.001 HIS B 188 PHE 0.015 0.002 PHE C 151 TYR 0.024 0.002 TYR E 178 ARG 0.005 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.029 Fit side-chains REVERT: A 118 VAL cc_start: 0.6296 (t) cc_final: 0.5743 (t) REVERT: A 121 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6830 (ppp) REVERT: A 151 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7721 (tmm) REVERT: A 192 SER cc_start: 0.7681 (OUTLIER) cc_final: 0.7396 (m) REVERT: A 329 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7815 (pp) REVERT: B 275 GLU cc_start: 0.7567 (tt0) cc_final: 0.7163 (tt0) REVERT: B 350 ASP cc_start: 0.7699 (t70) cc_final: 0.7490 (t70) REVERT: C 197 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7981 (mtm-85) REVERT: C 198 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7927 (pt) REVERT: C 258 ASP cc_start: 0.7519 (t70) cc_final: 0.7131 (OUTLIER) REVERT: E 89 GLU cc_start: 0.7850 (mp0) cc_final: 0.7402 (mp0) outliers start: 27 outliers final: 12 residues processed: 193 average time/residue: 1.1160 time to fit residues: 231.0063 Evaluate side-chains 200 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN E 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.132891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110300 restraints weight = 11965.559| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.76 r_work: 0.3291 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8833 Z= 0.254 Angle : 0.543 8.685 11993 Z= 0.289 Chirality : 0.042 0.179 1399 Planarity : 0.004 0.054 1503 Dihedral : 4.640 55.986 1267 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.56 % Allowed : 14.53 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1100 helix: 2.21 (0.27), residues: 379 sheet: 0.36 (0.29), residues: 295 loop : -1.05 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS B 188 PHE 0.013 0.001 PHE C 151 TYR 0.022 0.002 TYR E 178 ARG 0.005 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.915 Fit side-chains REVERT: A 118 VAL cc_start: 0.6290 (t) cc_final: 0.5768 (t) REVERT: A 121 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6760 (ppp) REVERT: A 151 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7743 (tmm) REVERT: A 192 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7380 (m) REVERT: A 329 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7773 (pp) REVERT: B 269 ASN cc_start: 0.8587 (m-40) cc_final: 0.8265 (m110) REVERT: B 272 ASP cc_start: 0.7395 (p0) cc_final: 0.7157 (p0) REVERT: B 275 GLU cc_start: 0.7538 (tt0) cc_final: 0.7146 (tt0) REVERT: B 350 ASP cc_start: 0.7677 (t70) cc_final: 0.7471 (t70) REVERT: C 197 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7998 (mtm-85) REVERT: C 198 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7909 (pt) REVERT: C 258 ASP cc_start: 0.7489 (t70) cc_final: 0.7128 (t0) REVERT: C 303 ASP cc_start: 0.7799 (m-30) cc_final: 0.7509 (m-30) REVERT: E 89 GLU cc_start: 0.7849 (mp0) cc_final: 0.7399 (mp0) REVERT: E 223 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7892 (m-80) outliers start: 24 outliers final: 11 residues processed: 195 average time/residue: 1.0809 time to fit residues: 226.1754 Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.0000 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.133533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111057 restraints weight = 11830.867| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.75 r_work: 0.3302 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8833 Z= 0.220 Angle : 0.534 8.526 11993 Z= 0.283 Chirality : 0.042 0.173 1399 Planarity : 0.004 0.054 1503 Dihedral : 4.561 55.479 1267 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.35 % Allowed : 14.96 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1100 helix: 2.25 (0.27), residues: 380 sheet: 0.41 (0.29), residues: 293 loop : -1.04 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS B 188 PHE 0.012 0.001 PHE A 169 TYR 0.019 0.002 TYR E 178 ARG 0.005 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.981 Fit side-chains REVERT: A 118 VAL cc_start: 0.6243 (t) cc_final: 0.5720 (t) REVERT: A 121 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6722 (ppp) REVERT: A 151 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7740 (tmm) REVERT: A 192 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7395 (m) REVERT: A 329 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7785 (pp) REVERT: B 269 ASN cc_start: 0.8571 (m-40) cc_final: 0.8327 (m110) REVERT: B 275 GLU cc_start: 0.7534 (tt0) cc_final: 0.7140 (tt0) REVERT: B 350 ASP cc_start: 0.7689 (t70) cc_final: 0.7489 (t70) REVERT: C 197 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7973 (mtm-85) REVERT: C 198 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7895 (pt) REVERT: C 258 ASP cc_start: 0.7489 (t70) cc_final: 0.7142 (t0) REVERT: C 303 ASP cc_start: 0.7783 (m-30) cc_final: 0.7414 (m-30) REVERT: E 89 GLU cc_start: 0.7850 (mp0) cc_final: 0.7408 (mp0) REVERT: E 223 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7876 (m-80) outliers start: 22 outliers final: 12 residues processed: 194 average time/residue: 1.0748 time to fit residues: 223.6898 Evaluate side-chains 204 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 96 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111062 restraints weight = 11811.870| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.75 r_work: 0.3300 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8833 Z= 0.222 Angle : 0.536 8.838 11993 Z= 0.283 Chirality : 0.042 0.176 1399 Planarity : 0.004 0.054 1503 Dihedral : 4.537 53.991 1267 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.46 % Allowed : 15.49 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.26), residues: 1100 helix: 2.28 (0.27), residues: 380 sheet: 0.42 (0.30), residues: 283 loop : -1.02 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS B 188 PHE 0.012 0.001 PHE C 151 TYR 0.020 0.001 TYR E 178 ARG 0.005 0.000 ARG C 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.994 Fit side-chains REVERT: A 118 VAL cc_start: 0.6240 (t) cc_final: 0.5717 (t) REVERT: A 121 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: A 151 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7761 (tmm) REVERT: A 192 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7398 (m) REVERT: A 329 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7737 (pp) REVERT: B 186 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6749 (tm-30) REVERT: B 269 ASN cc_start: 0.8585 (m-40) cc_final: 0.8340 (m110) REVERT: B 275 GLU cc_start: 0.7554 (tt0) cc_final: 0.7152 (tt0) REVERT: B 350 ASP cc_start: 0.7694 (t70) cc_final: 0.7483 (t70) REVERT: C 197 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7978 (mtm-85) REVERT: C 198 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7884 (pt) REVERT: C 217 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7726 (pmt) REVERT: C 258 ASP cc_start: 0.7506 (t70) cc_final: 0.7143 (t0) REVERT: C 303 ASP cc_start: 0.7788 (m-30) cc_final: 0.7492 (m-30) REVERT: E 89 GLU cc_start: 0.7866 (mp0) cc_final: 0.7421 (mp0) REVERT: E 130 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: E 223 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7889 (m-80) outliers start: 23 outliers final: 12 residues processed: 196 average time/residue: 1.0807 time to fit residues: 227.8495 Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 105 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.133516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110992 restraints weight = 11858.355| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.75 r_work: 0.3300 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8833 Z= 0.235 Angle : 0.548 9.013 11993 Z= 0.290 Chirality : 0.042 0.177 1399 Planarity : 0.004 0.054 1503 Dihedral : 4.567 54.790 1267 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.35 % Allowed : 15.71 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1100 helix: 2.30 (0.27), residues: 379 sheet: 0.39 (0.30), residues: 284 loop : -1.04 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS B 188 PHE 0.012 0.001 PHE C 151 TYR 0.021 0.002 TYR E 178 ARG 0.005 0.000 ARG C 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7252.87 seconds wall clock time: 128 minutes 26.26 seconds (7706.26 seconds total)