Starting phenix.real_space_refine on Sat Apr 6 15:22:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxx_36716/04_2024/8jxx_36716_neut_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.104 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 1 4.86 5 C 5446 2.51 5 N 1411 2.21 5 O 1577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 221": "OE1" <-> "OE2" Residue "E GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8493 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2107 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1717 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2518 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1746 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'VCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.00, per 1000 atoms: 0.59 Number of scatterers: 8493 At special positions: 0 Unit cell: (90.2, 123.2, 128.7, 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 1 17.00 S 58 16.00 O 1577 8.00 N 1411 7.00 C 5446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 34.6% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'R' and resid 15 through 42 removed outlier: 3.924A pdb=" N VAL R 36 " --> pdb=" O GLY R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 65 removed outlier: 3.924A pdb=" N PHE R 63 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY R 65 " --> pdb=" O ASP R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 77 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 84 through 117 removed outlier: 4.556A pdb=" N PHE R 89 " --> pdb=" O GLU R 85 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 123 Processing helix chain 'R' and resid 130 through 145 Processing helix chain 'R' and resid 148 through 152 Processing helix chain 'R' and resid 167 through 170 Processing helix chain 'R' and resid 172 through 202 removed outlier: 4.843A pdb=" N ILE R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix Processing helix chain 'R' and resid 294 through 329 Proline residue: R 318 - end of helix removed outlier: 3.701A pdb=" N PHE R 328 " --> pdb=" O ILE R 324 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 361 removed outlier: 4.146A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) Proline residue: R 355 - end of helix removed outlier: 3.542A pdb=" N TYR R 358 " --> pdb=" O ASN R 354 " (cutoff:3.500A) Proline residue: R 359 - end of helix Processing helix chain 'R' and resid 364 through 370 Processing helix chain 'B' and resid 7 through 31 removed outlier: 4.056A pdb=" N ALA B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 310 removed outlier: 4.549A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 350 Processing helix chain 'C' and resid 5 through 24 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 264 through 269 removed outlier: 6.319A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.049A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.074A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 7.130A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.093A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.702A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 7.080A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.690A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 141 through 143 Processing sheet with id= L, first strand: chain 'E' and resid 147 through 149 removed outlier: 7.151A pdb=" N LYS E 245 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1098 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: 2.40 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2671 1.34 - 1.46: 2200 1.46 - 1.59: 3730 1.59 - 1.71: 0 1.71 - 1.83: 85 Bond restraints: 8686 Sorted by residual: bond pdb=" C09 VCL R 401 " pdb=" N10 VCL R 401 " ideal model delta sigma weight residual 1.458 1.305 0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C09 VCL R 401 " pdb=" S11 VCL R 401 " ideal model delta sigma weight residual 1.833 1.714 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CD GLN R 366 " pdb=" OE1 GLN R 366 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.52e+01 bond pdb=" CD GLN R 366 " pdb=" NE2 GLN R 366 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.22e+01 bond pdb=" C15 VCL R 401 " pdb=" N19 VCL R 401 " ideal model delta sigma weight residual 1.315 1.390 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 8681 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.17: 216 107.17 - 113.94: 4845 113.94 - 120.71: 3703 120.71 - 127.48: 2944 127.48 - 134.25: 95 Bond angle restraints: 11803 Sorted by residual: angle pdb=" C LEU C 261 " pdb=" N MET C 262 " pdb=" CA MET C 262 " ideal model delta sigma weight residual 121.75 115.11 6.64 1.73e+00 3.34e-01 1.47e+01 angle pdb=" OE1 GLN R 347 " pdb=" CD GLN R 347 " pdb=" NE2 GLN R 347 " ideal model delta sigma weight residual 122.60 118.84 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" CA PRO R 359 " pdb=" N PRO R 359 " pdb=" CD PRO R 359 " ideal model delta sigma weight residual 112.00 107.02 4.98 1.40e+00 5.10e-01 1.26e+01 angle pdb=" C GLU R 182 " pdb=" CA GLU R 182 " pdb=" CB GLU R 182 " ideal model delta sigma weight residual 109.29 115.72 -6.43 1.82e+00 3.02e-01 1.25e+01 angle pdb=" N GLU R 182 " pdb=" CA GLU R 182 " pdb=" CB GLU R 182 " ideal model delta sigma weight residual 110.53 105.42 5.11 1.47e+00 4.63e-01 1.21e+01 ... (remaining 11798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 4992 35.83 - 71.66: 58 71.66 - 107.49: 6 107.49 - 143.32: 0 143.32 - 179.15: 1 Dihedral angle restraints: 5057 sinusoidal: 1850 harmonic: 3207 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 143.97 -50.97 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA ALA C 305 " pdb=" C ALA C 305 " pdb=" N GLY C 306 " pdb=" CA GLY C 306 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" C14 VCL R 401 " pdb=" C12 VCL R 401 " pdb=" C13 VCL R 401 " pdb=" S11 VCL R 401 " ideal model delta sinusoidal sigma weight residual -110.04 69.11 -179.15 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 969 0.049 - 0.098: 297 0.098 - 0.146: 79 0.146 - 0.195: 1 0.195 - 0.244: 3 Chirality restraints: 1349 Sorted by residual: chirality pdb=" CA TRP R 316 " pdb=" N TRP R 316 " pdb=" C TRP R 316 " pdb=" CB TRP R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA GLN B 306 " pdb=" N GLN B 306 " pdb=" C GLN B 306 " pdb=" CB GLN B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU R 181 " pdb=" CB LEU R 181 " pdb=" CD1 LEU R 181 " pdb=" CD2 LEU R 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 1346 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 VCL R 401 " -0.153 2.00e-02 2.50e+03 1.35e-01 2.28e+02 pdb=" C09 VCL R 401 " 0.051 2.00e-02 2.50e+03 pdb=" N08 VCL R 401 " 0.222 2.00e-02 2.50e+03 pdb=" N10 VCL R 401 " -0.125 2.00e-02 2.50e+03 pdb=" S11 VCL R 401 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 90 " 0.080 2.00e-02 2.50e+03 5.51e-02 7.60e+01 pdb=" CG TRP R 90 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP R 90 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP R 90 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 90 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP R 90 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP R 90 " -0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 90 " 0.082 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 90 " -0.062 2.00e-02 2.50e+03 pdb=" CH2 TRP R 90 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 316 " -0.063 2.00e-02 2.50e+03 3.95e-02 3.91e+01 pdb=" CG TRP R 316 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 316 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP R 316 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 316 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP R 316 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP R 316 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 316 " -0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 316 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP R 316 " -0.001 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 366 2.72 - 3.26: 8019 3.26 - 3.81: 12593 3.81 - 4.35: 15263 4.35 - 4.90: 27063 Nonbonded interactions: 63304 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.173 2.440 nonbonded pdb=" OE1 GLU B 33 " pdb=" NZ LYS B 197 " model vdw 2.243 2.520 nonbonded pdb=" ND2 ASN D 59 " pdb=" O ARG D 62 " model vdw 2.249 2.520 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.252 2.440 nonbonded pdb=" O GLY E 8 " pdb=" NH2 ARG E 18 " model vdw 2.269 2.520 ... (remaining 63299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.900 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: 3.960 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.170 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.007 0.153 8686 Z= 0.429 Angle : 0.808 9.184 11803 Z= 0.467 Chirality : 0.049 0.244 1349 Planarity : 0.007 0.135 1483 Dihedral : 13.253 179.150 2979 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.22 (0.24), residues: 1081 helix: 1.35 (0.27), residues: 361 sheet: 0.43 (0.31), residues: 247 loop : -1.70 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.007 TRP R 90 HIS 0.006 0.002 HIS C 62 PHE 0.041 0.003 PHE R 183 TYR 0.049 0.004 TYR R 95 ARG 0.007 0.001 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: R 165 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 197 LYS cc_start: 0.8063 (mttp) cc_final: 0.7746 (mttm) REVERT: B 306 GLN cc_start: 0.6852 (mp10) cc_final: 0.6436 (mp10) REVERT: C 46 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7555 (mtp85) REVERT: C 215 GLU cc_start: 0.6978 (mp0) cc_final: 0.6684 (mp0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2087 time to fit residues: 36.3458 Evaluate side-chains 106 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 0.0050 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 366 GLN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8686 Z= 0.206 Angle : 0.577 6.404 11803 Z= 0.308 Chirality : 0.043 0.145 1349 Planarity : 0.004 0.056 1483 Dihedral : 6.228 106.404 1184 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.68 % Allowed : 5.38 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.19 (0.25), residues: 1081 helix: 2.01 (0.28), residues: 363 sheet: 0.46 (0.30), residues: 266 loop : -1.74 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 80 HIS 0.004 0.001 HIS R 75 PHE 0.013 0.001 PHE R 168 TYR 0.016 0.002 TYR B 302 ARG 0.003 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.085 Fit side-chains REVERT: R 30 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7685 (ptm) REVERT: R 75 HIS cc_start: 0.7158 (t-90) cc_final: 0.6935 (t-90) REVERT: R 165 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7899 (mm-30) REVERT: B 197 LYS cc_start: 0.8058 (mttp) cc_final: 0.7844 (mttt) REVERT: C 46 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7543 (mtt-85) REVERT: C 215 GLU cc_start: 0.6703 (mp0) cc_final: 0.6360 (mp0) REVERT: E 87 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.7082 (ptp-170) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.2133 time to fit residues: 37.7161 Evaluate side-chains 124 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN C 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8686 Z= 0.217 Angle : 0.570 6.484 11803 Z= 0.303 Chirality : 0.042 0.145 1349 Planarity : 0.004 0.057 1483 Dihedral : 6.041 101.285 1184 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.58 % Allowed : 8.40 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.33 (0.25), residues: 1081 helix: 2.08 (0.28), residues: 365 sheet: 0.63 (0.31), residues: 254 loop : -1.64 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 90 HIS 0.005 0.001 HIS B 188 PHE 0.014 0.002 PHE C 199 TYR 0.011 0.001 TYR R 173 ARG 0.006 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 30 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7600 (ptp) REVERT: R 165 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7978 (mm-30) REVERT: B 197 LYS cc_start: 0.8088 (mttp) cc_final: 0.7712 (mttm) REVERT: C 46 ARG cc_start: 0.7898 (mtt-85) cc_final: 0.7576 (mtt-85) REVERT: C 215 GLU cc_start: 0.6505 (mp0) cc_final: 0.6258 (mp0) REVERT: E 87 ARG cc_start: 0.7446 (ptp-170) cc_final: 0.7156 (ptp-170) REVERT: E 220 LEU cc_start: 0.8474 (mp) cc_final: 0.8013 (pt) outliers start: 23 outliers final: 18 residues processed: 128 average time/residue: 0.2061 time to fit residues: 36.2669 Evaluate side-chains 131 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.0030 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.0270 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8686 Z= 0.133 Angle : 0.507 6.584 11803 Z= 0.269 Chirality : 0.041 0.140 1349 Planarity : 0.004 0.053 1483 Dihedral : 5.712 91.583 1184 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.13 % Allowed : 10.53 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1081 helix: 2.48 (0.29), residues: 359 sheet: 0.64 (0.31), residues: 263 loop : -1.56 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.003 0.001 HIS R 75 PHE 0.019 0.001 PHE R 352 TYR 0.009 0.001 TYR E 102 ARG 0.004 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7698 (ptm) REVERT: R 165 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8032 (mm-30) REVERT: B 197 LYS cc_start: 0.8112 (mttp) cc_final: 0.7664 (mttm) REVERT: B 269 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8578 (m-40) REVERT: C 130 GLU cc_start: 0.7734 (mp0) cc_final: 0.7365 (mp0) REVERT: C 280 LYS cc_start: 0.7073 (mttm) cc_final: 0.6738 (mttp) REVERT: E 220 LEU cc_start: 0.8567 (mp) cc_final: 0.8115 (pt) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.2070 time to fit residues: 38.0254 Evaluate side-chains 126 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8686 Z= 0.187 Angle : 0.540 7.153 11803 Z= 0.285 Chirality : 0.042 0.146 1349 Planarity : 0.004 0.054 1483 Dihedral : 5.685 90.720 1184 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.91 % Allowed : 11.20 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.71 (0.26), residues: 1081 helix: 2.61 (0.29), residues: 353 sheet: 0.71 (0.31), residues: 257 loop : -1.42 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.003 0.001 HIS R 75 PHE 0.012 0.001 PHE C 199 TYR 0.010 0.001 TYR R 173 ARG 0.008 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7782 (ptm) REVERT: R 165 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 197 LYS cc_start: 0.8164 (mttp) cc_final: 0.7730 (mttm) REVERT: B 247 MET cc_start: 0.7305 (mtm) cc_final: 0.6927 (mtm) REVERT: B 269 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8546 (m-40) REVERT: C 130 GLU cc_start: 0.7745 (mp0) cc_final: 0.7379 (mp0) REVERT: C 280 LYS cc_start: 0.7179 (mttm) cc_final: 0.6759 (mttp) REVERT: E 220 LEU cc_start: 0.8562 (mp) cc_final: 0.8118 (pt) outliers start: 26 outliers final: 19 residues processed: 131 average time/residue: 0.2106 time to fit residues: 38.0301 Evaluate side-chains 134 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8686 Z= 0.209 Angle : 0.556 7.083 11803 Z= 0.293 Chirality : 0.042 0.146 1349 Planarity : 0.004 0.055 1483 Dihedral : 5.685 88.541 1184 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.25 % Allowed : 11.42 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.68 (0.26), residues: 1081 helix: 2.55 (0.29), residues: 355 sheet: 0.66 (0.31), residues: 257 loop : -1.41 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.003 0.001 HIS R 75 PHE 0.013 0.001 PHE C 199 TYR 0.010 0.001 TYR R 173 ARG 0.006 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: R 30 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7679 (ptp) REVERT: R 75 HIS cc_start: 0.7261 (t-90) cc_final: 0.7055 (t-90) REVERT: R 165 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 197 LYS cc_start: 0.8177 (mttp) cc_final: 0.7759 (mttm) REVERT: B 247 MET cc_start: 0.7306 (mtm) cc_final: 0.6928 (mtm) REVERT: B 269 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8591 (m-40) REVERT: C 130 GLU cc_start: 0.7761 (mp0) cc_final: 0.7399 (mp0) REVERT: E 220 LEU cc_start: 0.8545 (mp) cc_final: 0.8094 (pt) outliers start: 29 outliers final: 22 residues processed: 133 average time/residue: 0.2137 time to fit residues: 38.7620 Evaluate side-chains 136 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 76 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8686 Z= 0.138 Angle : 0.516 7.328 11803 Z= 0.270 Chirality : 0.041 0.145 1349 Planarity : 0.004 0.054 1483 Dihedral : 5.471 82.503 1184 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.80 % Allowed : 11.98 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.81 (0.26), residues: 1081 helix: 2.72 (0.29), residues: 353 sheet: 0.64 (0.31), residues: 257 loop : -1.32 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.002 0.001 HIS R 75 PHE 0.011 0.001 PHE B 189 TYR 0.009 0.001 TYR E 102 ARG 0.005 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 30 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7770 (ptm) REVERT: R 165 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8065 (mm-30) REVERT: B 197 LYS cc_start: 0.8175 (mttp) cc_final: 0.7914 (mttm) REVERT: B 247 MET cc_start: 0.7165 (mtm) cc_final: 0.6777 (mtm) REVERT: B 269 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8699 (m-40) REVERT: C 130 GLU cc_start: 0.7758 (mp0) cc_final: 0.7395 (mp0) REVERT: C 262 MET cc_start: 0.8269 (tpp) cc_final: 0.7953 (tpp) REVERT: E 193 MET cc_start: 0.7490 (tmm) cc_final: 0.7245 (tmm) REVERT: E 220 LEU cc_start: 0.8554 (mp) cc_final: 0.8138 (pt) outliers start: 25 outliers final: 19 residues processed: 134 average time/residue: 0.2085 time to fit residues: 38.5355 Evaluate side-chains 134 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 160 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8686 Z= 0.185 Angle : 0.540 7.736 11803 Z= 0.283 Chirality : 0.041 0.142 1349 Planarity : 0.004 0.054 1483 Dihedral : 5.474 81.806 1184 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.25 % Allowed : 12.21 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1081 helix: 2.67 (0.29), residues: 354 sheet: 0.66 (0.31), residues: 257 loop : -1.34 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.012 0.001 PHE C 199 TYR 0.009 0.001 TYR R 173 ARG 0.005 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 30 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7711 (ptp) REVERT: R 165 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8011 (mm-30) REVERT: B 197 LYS cc_start: 0.8165 (mttp) cc_final: 0.7915 (mttm) REVERT: B 247 MET cc_start: 0.7211 (mtm) cc_final: 0.6811 (mtm) REVERT: B 269 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8298 (m-40) REVERT: C 130 GLU cc_start: 0.7769 (mp0) cc_final: 0.7402 (mp0) REVERT: C 262 MET cc_start: 0.8300 (tpp) cc_final: 0.7958 (tpp) REVERT: E 193 MET cc_start: 0.7530 (tmm) cc_final: 0.7287 (tmm) REVERT: E 220 LEU cc_start: 0.8499 (mp) cc_final: 0.8157 (pt) outliers start: 29 outliers final: 26 residues processed: 130 average time/residue: 0.2044 time to fit residues: 36.8292 Evaluate side-chains 142 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 215 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8686 Z= 0.274 Angle : 0.609 7.697 11803 Z= 0.320 Chirality : 0.043 0.144 1349 Planarity : 0.004 0.055 1483 Dihedral : 5.704 82.706 1184 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.58 % Allowed : 12.21 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.62 (0.25), residues: 1081 helix: 2.48 (0.29), residues: 355 sheet: 0.68 (0.31), residues: 251 loop : -1.43 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 90 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.002 PHE C 199 TYR 0.012 0.002 TYR R 173 ARG 0.004 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: R 165 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 197 LYS cc_start: 0.8149 (mttp) cc_final: 0.7767 (mttm) REVERT: B 247 MET cc_start: 0.7369 (mtm) cc_final: 0.6980 (mtm) REVERT: B 269 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8660 (m-40) REVERT: C 130 GLU cc_start: 0.7797 (mp0) cc_final: 0.7440 (mp0) REVERT: E 220 LEU cc_start: 0.8572 (mp) cc_final: 0.8162 (pt) outliers start: 32 outliers final: 29 residues processed: 130 average time/residue: 0.2135 time to fit residues: 38.4577 Evaluate side-chains 139 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 215 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8686 Z= 0.175 Angle : 0.548 7.711 11803 Z= 0.287 Chirality : 0.041 0.143 1349 Planarity : 0.004 0.053 1483 Dihedral : 5.527 77.667 1184 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.36 % Allowed : 12.77 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.72 (0.26), residues: 1081 helix: 2.61 (0.29), residues: 354 sheet: 0.61 (0.31), residues: 258 loop : -1.36 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 90 HIS 0.004 0.001 HIS R 75 PHE 0.012 0.001 PHE B 189 TYR 0.009 0.001 TYR R 173 ARG 0.008 0.000 ARG E 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 247 MET cc_start: 0.7213 (mtm) cc_final: 0.6813 (mtm) REVERT: B 269 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8709 (m-40) REVERT: C 130 GLU cc_start: 0.7750 (mp0) cc_final: 0.7399 (mp0) REVERT: C 262 MET cc_start: 0.8329 (tpp) cc_final: 0.7950 (tpp) REVERT: E 220 LEU cc_start: 0.8496 (mp) cc_final: 0.8181 (pt) outliers start: 30 outliers final: 27 residues processed: 130 average time/residue: 0.2057 time to fit residues: 37.2381 Evaluate side-chains 139 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 323 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 347 GLN Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 306 GLN Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 160 CYS Chi-restraints excluded: chain E residue 215 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN C 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.166134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120787 restraints weight = 11250.356| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.20 r_work: 0.3319 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.002 0.028 8686 Z= 0.140 Angle : 0.522 7.643 11803 Z= 0.271 Chirality : 0.041 0.138 1349 Planarity : 0.004 0.052 1483 Dihedral : 5.346 74.700 1184 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 13.21 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.86 (0.26), residues: 1081 helix: 2.71 (0.29), residues: 355 sheet: 0.65 (0.31), residues: 263 loop : -1.27 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 90 HIS 0.003 0.001 HIS R 75 PHE 0.012 0.001 PHE B 189 TYR 0.008 0.001 TYR E 102 ARG 0.007 0.000 ARG E 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2045.68 seconds wall clock time: 38 minutes 8.18 seconds (2288.18 seconds total)