Starting phenix.real_space_refine on Wed Mar 12 13:02:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dzr_27806/03_2025/8dzr_27806.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dzr_27806/03_2025/8dzr_27806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2025/8dzr_27806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2025/8dzr_27806.map" model { file = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2025/8dzr_27806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dzr_27806/03_2025/8dzr_27806.cif" } resolution = 2.61 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= 0.020 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 58 5.16 5 Cl 2 4.86 5 C 5092 2.51 5 N 1322 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7944 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1934 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1494 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 4 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2455 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 251 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'U9I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.67 Number of scatterers: 7944 At special positions: 0 Unit cell: (86.24, 121.44, 124.96, 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) Cl 2 17.00 S 58 16.00 O 1470 8.00 N 1322 7.00 C 5092 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=2.04 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.1% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 57 through 80 removed outlier: 4.098A pdb=" N ILE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 110 Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.540A pdb=" N VAL A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 162 removed outlier: 5.024A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.960A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.674A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 298 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 309 through 332 removed outlier: 3.875A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.522A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.718A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 removed outlier: 4.048A pdb=" N THR B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.568A pdb=" N ILE B 285 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS B 286 " --> pdb=" O LEU B 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 286' Processing helix chain 'B' and resid 295 through 305 removed outlier: 3.595A pdb=" N ASN B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 352 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.586A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.072A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.568A pdb=" N GLY A 198 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 211 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 209 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.342A pdb=" N ILE B 221 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA 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: 6.760A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.766A 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: 3.538A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.780A 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: 7.073A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.580A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.295A 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: 7.113A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.547A 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: 6.619A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.799A 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: 5.962A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.537A 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: 5.962A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 3.812A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 427 hydrogen bonds defined for protein. 1203 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: 2.43 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2055 1.33 - 1.45: 1638 1.45 - 1.58: 4322 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 8100 Sorted by residual: bond pdb=" CA SER C 161 " pdb=" CB SER C 161 " ideal model delta sigma weight residual 1.532 1.482 0.050 1.68e-02 3.54e+03 8.86e+00 bond pdb=" N ASP C 170 " pdb=" CA ASP C 170 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.23e-02 6.61e+03 2.65e+00 bond pdb=" C16 U9I A 401 " pdb=" C17 U9I A 401 " ideal model delta sigma weight residual 1.548 1.521 0.027 2.00e-02 2.50e+03 1.82e+00 bond pdb=" C ASP C 170 " pdb=" N ILE C 171 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.26e-02 6.30e+03 1.69e+00 bond pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.42e+00 ... (remaining 8095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10655 1.64 - 3.29: 311 3.29 - 4.93: 40 4.93 - 6.58: 15 6.58 - 8.22: 8 Bond angle restraints: 11029 Sorted by residual: angle pdb=" N PRO A 56 " pdb=" CA PRO A 56 " pdb=" CB PRO A 56 " ideal model delta sigma weight residual 103.00 110.47 -7.47 1.10e+00 8.26e-01 4.61e+01 angle pdb=" N ASP C 170 " pdb=" CA ASP C 170 " pdb=" C ASP C 170 " ideal model delta sigma weight residual 108.96 101.81 7.15 1.59e+00 3.96e-01 2.02e+01 angle pdb=" N SER C 161 " pdb=" CA SER C 161 " pdb=" C SER C 161 " ideal model delta sigma weight residual 108.74 113.37 -4.63 1.38e+00 5.25e-01 1.13e+01 angle pdb=" N ASP C 170 " pdb=" CA ASP C 170 " pdb=" CB ASP C 170 " ideal model delta sigma weight residual 110.17 115.01 -4.84 1.68e+00 3.54e-01 8.31e+00 angle pdb=" C VAL A 80 " pdb=" N MET A 81 " pdb=" CA MET A 81 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.15e+00 ... (remaining 11024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4361 17.54 - 35.09: 328 35.09 - 52.63: 44 52.63 - 70.18: 6 70.18 - 87.72: 9 Dihedral angle restraints: 4748 sinusoidal: 1639 harmonic: 3109 Sorted by residual: 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 93.00 172.73 -79.73 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CA TYR E 178 " pdb=" C TYR E 178 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1009 0.052 - 0.104: 249 0.104 - 0.156: 57 0.156 - 0.208: 1 0.208 - 0.260: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CB THR E 160 " pdb=" CA THR E 160 " pdb=" OG1 THR E 160 " pdb=" CG2 THR E 160 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP C 170 " pdb=" N ASP C 170 " pdb=" C ASP C 170 " pdb=" CB ASP C 170 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 56 " pdb=" N PRO A 56 " pdb=" C PRO A 56 " pdb=" CB PRO A 56 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1317 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 199 " 0.010 2.00e-02 2.50e+03 1.59e-02 4.43e+00 pdb=" CG PHE B 199 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 199 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 199 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 199 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 199 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 199 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 171 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 172 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO C 236 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.024 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1184 2.76 - 3.29: 7447 3.29 - 3.83: 13291 3.83 - 4.36: 15264 4.36 - 4.90: 27292 Nonbonded interactions: 64478 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.224 3.040 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.268 3.040 nonbonded pdb=" O VAL A 284 " pdb=" OG1 THR A 288 " model vdw 2.286 3.040 nonbonded pdb=" O THR A 111 " pdb=" OH TYR A 320 " model vdw 2.292 3.040 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.293 3.120 ... (remaining 64473 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.210 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 0.050 8100 Z= 0.244 Angle : 0.683 8.223 11029 Z= 0.365 Chirality : 0.048 0.260 1320 Planarity : 0.004 0.044 1374 Dihedral : 12.943 87.720 2730 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.09 (0.25), residues: 1045 helix: 1.15 (0.27), residues: 345 sheet: 0.49 (0.30), residues: 294 loop : -1.56 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.003 0.001 HIS C 142 PHE 0.034 0.002 PHE B 199 TYR 0.023 0.002 TYR C 59 ARG 0.004 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.801 Fit side-chains REVERT: A 288 THR cc_start: 0.7351 (m) cc_final: 0.7091 (m) REVERT: B 18 MET cc_start: 0.7284 (mmm) cc_final: 0.6942 (mmm) REVERT: B 323 MET cc_start: 0.6589 (mpp) cc_final: 0.5984 (mpp) REVERT: E 95 TYR cc_start: 0.8540 (m-80) cc_final: 0.8287 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.8650 time to fit residues: 159.8849 Evaluate side-chains 157 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.0020 chunk 53 optimal weight: 0.0370 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.0470 overall best weight: 0.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN C 237 ASN ** C 259 GLN ** 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 = 0.4097 r_free = 0.4097 target = 0.156022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.136682 restraints weight = 11299.799| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.86 r_work: 0.3764 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8100 Z= 0.136 Angle : 0.511 8.680 11029 Z= 0.270 Chirality : 0.041 0.143 1320 Planarity : 0.003 0.039 1374 Dihedral : 4.394 17.902 1166 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.62 % Allowed : 10.10 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.51 (0.26), residues: 1045 helix: 2.00 (0.28), residues: 346 sheet: 0.69 (0.30), residues: 286 loop : -1.43 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 169 HIS 0.003 0.001 HIS C 142 PHE 0.019 0.001 PHE A 126 TYR 0.016 0.001 TYR E 102 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.777 Fit side-chains REVERT: A 211 SER cc_start: 0.8488 (p) cc_final: 0.8112 (m) REVERT: A 318 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7317 (mp) REVERT: B 199 PHE cc_start: 0.8357 (m-80) cc_final: 0.8100 (m-80) REVERT: B 323 MET cc_start: 0.7173 (mpp) cc_final: 0.6587 (mpp) REVERT: B 327 THR cc_start: 0.7596 (p) cc_final: 0.7296 (p) REVERT: C 49 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7326 (mpp-170) outliers start: 13 outliers final: 4 residues processed: 168 average time/residue: 0.8998 time to fit residues: 162.9976 Evaluate side-chains 166 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 0.9980 chunk 100 optimal weight: 0.0010 chunk 46 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.152667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.132828 restraints weight = 11335.041| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.87 r_work: 0.3707 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8100 Z= 0.248 Angle : 0.559 8.843 11029 Z= 0.293 Chirality : 0.043 0.147 1320 Planarity : 0.003 0.037 1374 Dihedral : 4.600 23.745 1166 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.87 % Allowed : 14.34 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.59 (0.26), residues: 1045 helix: 2.15 (0.28), residues: 347 sheet: 0.80 (0.30), residues: 281 loop : -1.50 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 169 HIS 0.003 0.001 HIS C 225 PHE 0.015 0.001 PHE C 151 TYR 0.025 0.002 TYR E 178 ARG 0.006 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.877 Fit side-chains REVERT: A 107 LEU cc_start: 0.8351 (mp) cc_final: 0.8134 (mp) REVERT: A 211 SER cc_start: 0.8424 (p) cc_final: 0.8169 (m) REVERT: A 318 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7337 (mp) REVERT: B 199 PHE cc_start: 0.8343 (m-80) cc_final: 0.8055 (m-80) REVERT: B 323 MET cc_start: 0.7151 (mpp) cc_final: 0.6537 (mpp) REVERT: B 327 THR cc_start: 0.7602 (p) cc_final: 0.7303 (p) REVERT: C 132 ASN cc_start: 0.8274 (p0) cc_final: 0.7926 (p0) outliers start: 23 outliers final: 13 residues processed: 171 average time/residue: 0.8166 time to fit residues: 151.6582 Evaluate side-chains 176 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 87 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.153163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.133537 restraints weight = 11355.858| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.88 r_work: 0.3716 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8100 Z= 0.188 Angle : 0.526 8.808 11029 Z= 0.277 Chirality : 0.042 0.137 1320 Planarity : 0.003 0.037 1374 Dihedral : 4.385 17.718 1166 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.49 % Allowed : 16.71 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.74 (0.27), residues: 1045 helix: 2.36 (0.28), residues: 346 sheet: 0.84 (0.30), residues: 287 loop : -1.49 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 196 TYR 0.022 0.002 TYR E 178 ARG 0.005 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.769 Fit side-chains REVERT: A 107 LEU cc_start: 0.8340 (mp) cc_final: 0.8094 (mp) REVERT: A 211 SER cc_start: 0.8433 (p) cc_final: 0.8211 (m) REVERT: A 318 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7364 (mp) REVERT: A 328 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6695 (mp) REVERT: B 199 PHE cc_start: 0.8343 (m-80) cc_final: 0.8053 (m-80) REVERT: B 323 MET cc_start: 0.7114 (mpp) cc_final: 0.6498 (mpp) REVERT: B 327 THR cc_start: 0.7595 (p) cc_final: 0.7285 (p) REVERT: C 132 ASN cc_start: 0.8278 (p0) cc_final: 0.7919 (p0) REVERT: C 262 MET cc_start: 0.7645 (ttm) cc_final: 0.7202 (mtt) REVERT: C 323 ASP cc_start: 0.7417 (p0) cc_final: 0.7152 (p0) outliers start: 20 outliers final: 14 residues processed: 177 average time/residue: 0.8076 time to fit residues: 155.3110 Evaluate side-chains 180 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN C 220 GLN C 230 ASN ** C 259 GLN ** 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 = 0.4051 r_free = 0.4051 target = 0.151993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132426 restraints weight = 11289.913| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.84 r_work: 0.3703 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8100 Z= 0.231 Angle : 0.563 9.547 11029 Z= 0.294 Chirality : 0.042 0.139 1320 Planarity : 0.003 0.037 1374 Dihedral : 4.495 20.726 1166 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.24 % Allowed : 17.96 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.26), residues: 1045 helix: 2.38 (0.28), residues: 346 sheet: 0.86 (0.30), residues: 282 loop : -1.57 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 211 HIS 0.003 0.001 HIS C 225 PHE 0.014 0.001 PHE B 196 TYR 0.024 0.002 TYR E 178 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6226 (tm-30) REVERT: A 318 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7324 (mp) REVERT: A 328 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6764 (mp) REVERT: B 199 PHE cc_start: 0.8362 (m-80) cc_final: 0.8110 (m-80) REVERT: B 323 MET cc_start: 0.7190 (mpp) cc_final: 0.6530 (mpp) REVERT: B 327 THR cc_start: 0.7605 (p) cc_final: 0.7299 (p) REVERT: C 76 ASP cc_start: 0.8060 (p0) cc_final: 0.7802 (p0) REVERT: C 132 ASN cc_start: 0.8290 (p0) cc_final: 0.7939 (p0) REVERT: C 323 ASP cc_start: 0.7439 (p0) cc_final: 0.7166 (p0) outliers start: 26 outliers final: 16 residues processed: 175 average time/residue: 0.8662 time to fit residues: 163.7975 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.152375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132727 restraints weight = 11268.458| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.85 r_work: 0.3708 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8100 Z= 0.210 Angle : 0.557 9.170 11029 Z= 0.289 Chirality : 0.042 0.215 1320 Planarity : 0.003 0.037 1374 Dihedral : 4.416 18.466 1166 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.24 % Allowed : 18.70 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.74 (0.26), residues: 1045 helix: 2.45 (0.28), residues: 347 sheet: 0.80 (0.30), residues: 288 loop : -1.55 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 196 TYR 0.023 0.002 TYR E 178 ARG 0.002 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.767 Fit side-chains REVERT: A 211 SER cc_start: 0.8489 (p) cc_final: 0.8248 (m) REVERT: A 226 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6409 (tpp) REVERT: A 318 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7370 (mp) REVERT: A 328 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6761 (mp) REVERT: B 199 PHE cc_start: 0.8369 (m-80) cc_final: 0.7996 (m-80) REVERT: B 323 MET cc_start: 0.7166 (mpp) cc_final: 0.6499 (mpp) REVERT: B 327 THR cc_start: 0.7607 (p) cc_final: 0.7307 (p) REVERT: C 99 TRP cc_start: 0.8679 (m100) cc_final: 0.8407 (m100) REVERT: C 132 ASN cc_start: 0.8281 (p0) cc_final: 0.7918 (p0) REVERT: C 315 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7656 (t) REVERT: C 323 ASP cc_start: 0.7434 (p0) cc_final: 0.7177 (p0) outliers start: 26 outliers final: 15 residues processed: 178 average time/residue: 0.8205 time to fit residues: 158.2570 Evaluate side-chains 184 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 100 optimal weight: 0.0010 chunk 23 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.152652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.132976 restraints weight = 11317.377| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.85 r_work: 0.3709 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8100 Z= 0.202 Angle : 0.552 9.223 11029 Z= 0.287 Chirality : 0.042 0.184 1320 Planarity : 0.003 0.036 1374 Dihedral : 4.373 18.780 1166 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.99 % Allowed : 19.83 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1045 helix: 2.48 (0.28), residues: 347 sheet: 0.91 (0.30), residues: 281 loop : -1.56 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 196 TYR 0.023 0.002 TYR E 178 ARG 0.003 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6242 (tm-30) REVERT: A 226 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.6399 (tpp) REVERT: A 318 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7332 (mp) REVERT: A 328 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6772 (mp) REVERT: B 199 PHE cc_start: 0.8369 (m-80) cc_final: 0.8099 (m-80) REVERT: B 323 MET cc_start: 0.7182 (mpp) cc_final: 0.6503 (mpp) REVERT: B 327 THR cc_start: 0.7604 (p) cc_final: 0.7304 (p) REVERT: C 132 ASN cc_start: 0.8279 (p0) cc_final: 0.7917 (p0) REVERT: C 315 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7663 (t) REVERT: C 323 ASP cc_start: 0.7442 (p0) cc_final: 0.7180 (p0) outliers start: 24 outliers final: 14 residues processed: 182 average time/residue: 0.8467 time to fit residues: 167.1580 Evaluate side-chains 182 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.151387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131526 restraints weight = 11282.842| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.88 r_work: 0.3690 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8100 Z= 0.254 Angle : 0.589 9.751 11029 Z= 0.305 Chirality : 0.043 0.204 1320 Planarity : 0.003 0.036 1374 Dihedral : 4.556 21.834 1166 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.99 % Allowed : 19.95 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.69 (0.26), residues: 1045 helix: 2.31 (0.28), residues: 352 sheet: 0.86 (0.30), residues: 282 loop : -1.58 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 211 HIS 0.003 0.001 HIS C 225 PHE 0.016 0.001 PHE B 196 TYR 0.027 0.002 TYR E 178 ARG 0.003 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 96 ILE cc_start: 0.8260 (mt) cc_final: 0.8046 (mt) REVERT: A 107 LEU cc_start: 0.8354 (mp) cc_final: 0.8112 (mp) REVERT: A 200 LYS cc_start: 0.8141 (mppt) cc_final: 0.7933 (mppt) REVERT: A 209 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6261 (tm-30) REVERT: A 226 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.6418 (tpp) REVERT: A 250 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7806 (mp) REVERT: A 318 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7351 (mp) REVERT: A 328 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6875 (mp) REVERT: B 199 PHE cc_start: 0.8383 (m-80) cc_final: 0.8103 (m-80) REVERT: B 323 MET cc_start: 0.7241 (mpp) cc_final: 0.6561 (mpp) REVERT: B 327 THR cc_start: 0.7624 (p) cc_final: 0.7320 (p) REVERT: C 132 ASN cc_start: 0.8295 (p0) cc_final: 0.7934 (p0) REVERT: C 314 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7756 (ptm160) REVERT: C 315 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7747 (t) REVERT: C 323 ASP cc_start: 0.7462 (p0) cc_final: 0.7207 (p0) outliers start: 24 outliers final: 14 residues processed: 183 average time/residue: 0.7999 time to fit residues: 158.7168 Evaluate side-chains 185 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 48 optimal weight: 0.0040 chunk 14 optimal weight: 4.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.152751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.132909 restraints weight = 11438.748| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.90 r_work: 0.3708 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8100 Z= 0.190 Angle : 0.562 9.434 11029 Z= 0.292 Chirality : 0.042 0.191 1320 Planarity : 0.003 0.037 1374 Dihedral : 4.350 17.843 1166 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 20.95 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.77 (0.26), residues: 1045 helix: 2.42 (0.28), residues: 352 sheet: 0.87 (0.31), residues: 282 loop : -1.56 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 80 TYR 0.022 0.002 TYR E 178 ARG 0.002 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8314 (mp) cc_final: 0.8052 (mp) REVERT: A 111 THR cc_start: 0.8083 (m) cc_final: 0.7806 (t) REVERT: A 209 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: A 318 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7315 (mp) REVERT: A 328 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6833 (mp) REVERT: B 18 MET cc_start: 0.8220 (mmm) cc_final: 0.8019 (mmm) REVERT: B 199 PHE cc_start: 0.8367 (m-80) cc_final: 0.8033 (m-80) REVERT: B 323 MET cc_start: 0.7188 (mpp) cc_final: 0.6499 (mpp) REVERT: B 327 THR cc_start: 0.7627 (p) cc_final: 0.7330 (p) REVERT: C 132 ASN cc_start: 0.8273 (p0) cc_final: 0.7911 (p0) REVERT: C 315 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7675 (t) REVERT: C 323 ASP cc_start: 0.7457 (p0) cc_final: 0.7204 (p0) outliers start: 20 outliers final: 14 residues processed: 184 average time/residue: 0.8156 time to fit residues: 162.6434 Evaluate side-chains 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.151792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132220 restraints weight = 11249.840| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.84 r_work: 0.3700 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8100 Z= 0.235 Angle : 0.592 9.904 11029 Z= 0.307 Chirality : 0.043 0.217 1320 Planarity : 0.003 0.036 1374 Dihedral : 4.489 20.649 1166 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.49 % Allowed : 21.20 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.73 (0.26), residues: 1045 helix: 2.40 (0.28), residues: 350 sheet: 0.86 (0.31), residues: 282 loop : -1.59 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.003 0.001 HIS C 225 PHE 0.014 0.001 PHE B 196 TYR 0.025 0.002 TYR E 178 ARG 0.001 0.000 ARG E 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8326 (mp) cc_final: 0.8067 (mp) REVERT: A 111 THR cc_start: 0.8131 (m) cc_final: 0.7850 (t) REVERT: A 209 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6198 (tm-30) REVERT: A 318 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7323 (mp) REVERT: A 328 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6874 (mp) REVERT: B 18 MET cc_start: 0.8217 (mmm) cc_final: 0.8015 (mmm) REVERT: B 199 PHE cc_start: 0.8374 (m-80) cc_final: 0.7966 (m-80) REVERT: B 323 MET cc_start: 0.7221 (mpp) cc_final: 0.6533 (mpp) REVERT: B 327 THR cc_start: 0.7633 (p) cc_final: 0.7341 (p) REVERT: C 45 MET cc_start: 0.8023 (mtt) cc_final: 0.7818 (mtm) REVERT: C 132 ASN cc_start: 0.8285 (p0) cc_final: 0.7917 (p0) REVERT: C 315 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7753 (t) REVERT: C 323 ASP cc_start: 0.7463 (p0) cc_final: 0.7217 (p0) outliers start: 20 outliers final: 16 residues processed: 179 average time/residue: 0.8345 time to fit residues: 161.8410 Evaluate side-chains 189 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 135 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 0.0270 chunk 87 optimal weight: 0.0670 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.156687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136744 restraints weight = 11250.103| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.89 r_work: 0.3708 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8100 Z= 0.198 Angle : 0.577 9.697 11029 Z= 0.299 Chirality : 0.042 0.201 1320 Planarity : 0.004 0.050 1374 Dihedral : 4.402 18.404 1166 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.37 % Allowed : 21.32 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.75 (0.26), residues: 1045 helix: 2.42 (0.28), residues: 352 sheet: 0.86 (0.31), residues: 282 loop : -1.59 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 80 TYR 0.022 0.002 TYR E 178 ARG 0.010 0.000 ARG C 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6983.07 seconds wall clock time: 119 minutes 29.11 seconds (7169.11 seconds total)