Starting phenix.real_space_refine on Wed Feb 14 03:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2024/7ljd_23391_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2024/7ljd_23391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2024/7ljd_23391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2024/7ljd_23391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2024/7ljd_23391_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ljd_23391/02_2024/7ljd_23391_updated.pdb" } resolution = 3.2 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= -0.000 sd= 0.013 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 56 5.16 5 Cl 2 4.86 5 C 5468 2.51 5 N 1447 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 130": "NH1" <-> "NH2" Residue "R ARG 216": "NH1" <-> "NH2" Residue "R ARG 219": "NH1" <-> "NH2" Residue "R ARG 226": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 266": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N ARG 72": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2269 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 3 Chain: "A" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1987 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 253 Unusual residues: {'CLR': 5, 'G4C': 1, 'LDP': 1, 'PLM': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 LDP R 501 " occ=0.50 ... (9 atoms not shown) pdb=" O2 LDP R 501 " occ=0.50 Time building chain proxies: 5.16, per 1000 atoms: 0.61 Number of scatterers: 8518 At special positions: 0 Unit cell: (95.316, 99.372, 121.68, 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 56 16.00 O 1545 8.00 N 1447 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 3.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 39.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'R' and resid 22 through 49 Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'R' and resid 59 through 76 removed outlier: 3.596A pdb=" N VAL R 68 " --> pdb=" O SER R 65 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER R 69 " --> pdb=" O LEU R 66 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP R 70 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL R 73 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL R 75 " --> pdb=" O LEU R 72 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU R 76 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.753A pdb=" N VAL R 100 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE R 104 " --> pdb=" O ALA R 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET R 105 " --> pdb=" O PHE R 102 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS R 106 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER R 107 " --> pdb=" O ILE R 104 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR R 108 " --> pdb=" O MET R 105 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA R 109 " --> pdb=" O CYS R 106 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU R 112 " --> pdb=" O ALA R 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN R 113 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE R 117 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA R 124 " --> pdb=" O ARG R 121 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE R 125 " --> pdb=" O TYR R 122 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER R 126 " --> pdb=" O TRP R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 removed outlier: 3.676A pdb=" N GLU R 132 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 133 " --> pdb=" O PHE R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 161 removed outlier: 4.784A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 removed outlier: 3.599A pdb=" N ILE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 241 Processing helix chain 'R' and resid 265 through 297 removed outlier: 3.576A pdb=" N LEU R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.145A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 310 through 331 removed outlier: 3.648A pdb=" N TRP R 318 " --> pdb=" O ASP R 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 345 Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.666A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 102' Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.706A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 184 through 204 removed outlier: 3.559A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.662A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.919A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 211 through 214 removed outlier: 7.260A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 41 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.211A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.600A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.680A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.006A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.778A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.602A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.779A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.576A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.698A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1014 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: 2.36 Time building geometry restraints manager: 3.58 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: 2114 1.33 - 1.45: 1750 1.45 - 1.58: 4760 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8702 Sorted by residual: bond pdb=" C05 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.355 1.497 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C03 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.460 1.497 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C ILE R 205 " pdb=" N PRO R 206 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.31e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.19e+00 bond pdb=" C5 CLR R 505 " pdb=" C6 CLR R 505 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 8697 not shown) Histogram of bond angle deviations from ideal: 100.03 - 107.05: 225 107.05 - 114.07: 5030 114.07 - 121.08: 3977 121.08 - 128.10: 2488 128.10 - 135.12: 75 Bond angle restraints: 11795 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ILE R 294 " pdb=" N LEU R 295 " pdb=" CA LEU R 295 " ideal model delta sigma weight residual 121.62 127.01 -5.39 1.57e+00 4.06e-01 1.18e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 115.60 -3.00 1.00e+00 1.00e+00 8.97e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.70 -4.30 1.45e+00 4.76e-01 8.78e+00 angle pdb=" N MET R 78 " pdb=" CA MET R 78 " pdb=" C MET R 78 " ideal model delta sigma weight residual 112.75 116.65 -3.90 1.36e+00 5.41e-01 8.23e+00 ... (remaining 11790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5299 17.89 - 35.77: 119 35.77 - 53.65: 24 53.65 - 71.54: 1 71.54 - 89.42: 5 Dihedral angle restraints: 5448 sinusoidal: 2393 harmonic: 3055 Sorted by residual: dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual 93.00 -179.67 -87.33 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 166.82 -73.82 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CA LEU B 198 " pdb=" C LEU B 198 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1173 0.082 - 0.163: 126 0.163 - 0.245: 19 0.245 - 0.327: 6 0.327 - 0.408: 5 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 1326 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 G4C R 502 " -0.215 2.00e-02 2.50e+03 1.50e-01 3.37e+02 pdb=" C05 G4C R 502 " 0.047 2.00e-02 2.50e+03 pdb=" C06 G4C R 502 " -0.169 2.00e-02 2.50e+03 pdb=" C16 G4C R 502 " 0.029 2.00e-02 2.50e+03 pdb=" N04 G4C R 502 " 0.222 2.00e-02 2.50e+03 pdb=" O15 G4C R 502 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 207 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C VAL R 207 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL R 207 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 208 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 93 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 94 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.030 5.00e-02 4.00e+02 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2240 2.82 - 3.34: 7350 3.34 - 3.86: 13173 3.86 - 4.38: 15319 4.38 - 4.90: 27065 Nonbonded interactions: 65147 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.294 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.309 2.440 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.322 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.337 2.440 nonbonded pdb=" OG SER R 198 " pdb=" O2 LDP R 501 " model vdw 2.349 2.440 ... (remaining 65142 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.950 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.530 Find NCS groups from input model: 0.240 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 0.142 8702 Z= 0.267 Angle : 0.853 10.120 11795 Z= 0.463 Chirality : 0.062 0.408 1329 Planarity : 0.007 0.150 1463 Dihedral : 8.668 89.425 3452 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.23), residues: 1030 helix: -1.11 (0.24), residues: 402 sheet: -0.32 (0.34), residues: 218 loop : -2.18 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 133 HIS 0.013 0.003 HIS A 209 PHE 0.032 0.002 PHE A 108 TYR 0.014 0.002 TYR A 243 ARG 0.007 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.976 Fit side-chains REVERT: R 35 LEU cc_start: 0.7128 (mt) cc_final: 0.6899 (mt) REVERT: R 57 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7800 (mtmt) REVERT: R 193 THR cc_start: 0.8282 (t) cc_final: 0.8063 (m) REVERT: R 197 SER cc_start: 0.8489 (t) cc_final: 0.7878 (m) REVERT: A 124 ASP cc_start: 0.7061 (m-30) cc_final: 0.6732 (m-30) REVERT: A 237 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.7064 (mtt90) REVERT: B 13 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7839 (pp30) REVERT: B 66 ASP cc_start: 0.7119 (p0) cc_final: 0.6493 (t0) REVERT: B 170 ASP cc_start: 0.8247 (t0) cc_final: 0.7929 (t0) REVERT: B 178 THR cc_start: 0.7687 (m) cc_final: 0.7237 (p) REVERT: G 21 MET cc_start: 0.7768 (mtt) cc_final: 0.7549 (ttp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2759 time to fit residues: 74.0502 Evaluate side-chains 137 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 60 ASN R 113 ASN R 242 GLN R 323 ASN A 14 ASN A 82 HIS B 91 HIS B 239 ASN B 268 ASN N 82 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8702 Z= 0.337 Angle : 0.638 7.249 11795 Z= 0.338 Chirality : 0.045 0.168 1329 Planarity : 0.005 0.047 1463 Dihedral : 6.682 86.494 1545 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.33 % Allowed : 7.21 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1030 helix: 0.70 (0.25), residues: 398 sheet: -0.07 (0.34), residues: 226 loop : -1.48 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.010 0.002 HIS A 209 PHE 0.027 0.002 PHE R 129 TYR 0.016 0.002 TYR R 194 ARG 0.005 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.958 Fit side-chains REVERT: R 105 MET cc_start: 0.7801 (ttt) cc_final: 0.7566 (ttt) REVERT: R 333 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6127 (m-10) REVERT: A 34 LYS cc_start: 0.7995 (ttmp) cc_final: 0.7738 (ttmp) REVERT: A 124 ASP cc_start: 0.6881 (m-30) cc_final: 0.6642 (m-30) REVERT: B 66 ASP cc_start: 0.6808 (p0) cc_final: 0.6525 (t0) REVERT: G 21 MET cc_start: 0.8035 (mtt) cc_final: 0.7620 (tmm) REVERT: N 25 SER cc_start: 0.8344 (t) cc_final: 0.7903 (p) outliers start: 12 outliers final: 7 residues processed: 153 average time/residue: 0.2224 time to fit residues: 45.9434 Evaluate side-chains 126 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 323 ASN A 35 GLN A 66 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8702 Z= 0.190 Angle : 0.510 7.322 11795 Z= 0.270 Chirality : 0.041 0.158 1329 Planarity : 0.004 0.048 1463 Dihedral : 6.270 82.586 1545 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.11 % Allowed : 7.77 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1030 helix: 1.36 (0.26), residues: 397 sheet: 0.09 (0.35), residues: 220 loop : -1.26 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.007 0.001 HIS A 82 PHE 0.014 0.001 PHE R 129 TYR 0.014 0.001 TYR N 60 ARG 0.007 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: R 105 MET cc_start: 0.7846 (ttt) cc_final: 0.7554 (ttt) REVERT: R 160 GLN cc_start: 0.6156 (mm-40) cc_final: 0.5950 (mm-40) REVERT: R 226 ARG cc_start: 0.6970 (mtt-85) cc_final: 0.6694 (mtt90) REVERT: R 233 ARG cc_start: 0.6788 (ttm110) cc_final: 0.6097 (mtp85) REVERT: R 333 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: A 124 ASP cc_start: 0.6918 (m-30) cc_final: 0.6653 (m-30) REVERT: A 163 TYR cc_start: 0.7718 (m-80) cc_final: 0.7408 (m-80) REVERT: B 66 ASP cc_start: 0.6660 (p0) cc_final: 0.6341 (t0) REVERT: B 111 TYR cc_start: 0.8545 (m-80) cc_final: 0.8158 (m-80) REVERT: B 154 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7527 (t0) REVERT: G 21 MET cc_start: 0.8008 (mtt) cc_final: 0.7710 (tmm) REVERT: N 25 SER cc_start: 0.8240 (t) cc_final: 0.7947 (p) REVERT: N 71 SER cc_start: 0.7375 (t) cc_final: 0.6991 (p) outliers start: 28 outliers final: 16 residues processed: 149 average time/residue: 0.2126 time to fit residues: 43.6163 Evaluate side-chains 137 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 48 optimal weight: 0.0020 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.9486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8702 Z= 0.171 Angle : 0.499 10.322 11795 Z= 0.260 Chirality : 0.040 0.156 1329 Planarity : 0.004 0.052 1463 Dihedral : 6.030 79.338 1545 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.44 % Allowed : 8.88 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1030 helix: 1.64 (0.26), residues: 400 sheet: 0.07 (0.34), residues: 225 loop : -1.08 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 82 PHE 0.012 0.001 PHE R 333 TYR 0.009 0.001 TYR A 191 ARG 0.005 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 333 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6136 (m-10) REVERT: A 124 ASP cc_start: 0.6907 (m-30) cc_final: 0.6638 (m-30) REVERT: A 163 TYR cc_start: 0.7885 (m-80) cc_final: 0.7533 (m-80) REVERT: B 66 ASP cc_start: 0.6652 (p0) cc_final: 0.6331 (t0) REVERT: B 111 TYR cc_start: 0.8528 (m-80) cc_final: 0.8240 (m-80) REVERT: N 25 SER cc_start: 0.8213 (t) cc_final: 0.8012 (p) REVERT: N 71 SER cc_start: 0.7716 (t) cc_final: 0.7416 (p) outliers start: 22 outliers final: 16 residues processed: 130 average time/residue: 0.2100 time to fit residues: 37.8260 Evaluate side-chains 124 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 176 GLN B 266 HIS B 295 ASN G 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8702 Z= 0.465 Angle : 0.686 10.285 11795 Z= 0.359 Chirality : 0.046 0.194 1329 Planarity : 0.005 0.066 1463 Dihedral : 6.932 71.925 1545 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.66 % Allowed : 9.43 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1030 helix: 0.97 (0.25), residues: 405 sheet: -0.14 (0.35), residues: 205 loop : -1.22 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.010 0.002 HIS A 209 PHE 0.025 0.003 PHE R 333 TYR 0.021 0.002 TYR N 94 ARG 0.009 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 0.930 Fit side-chains REVERT: R 333 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7136 (m-10) REVERT: A 40 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8303 (t) REVERT: A 124 ASP cc_start: 0.6981 (m-30) cc_final: 0.6711 (m-30) REVERT: A 163 TYR cc_start: 0.7867 (m-80) cc_final: 0.7580 (m-80) REVERT: A 202 THR cc_start: 0.7104 (m) cc_final: 0.6875 (p) REVERT: B 153 ASP cc_start: 0.7979 (p0) cc_final: 0.7518 (p0) REVERT: B 156 GLN cc_start: 0.7851 (mt0) cc_final: 0.7200 (mp10) REVERT: B 197 ARG cc_start: 0.8515 (ttm110) cc_final: 0.8224 (mtp85) REVERT: B 234 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8729 (m-80) REVERT: N 25 SER cc_start: 0.8427 (t) cc_final: 0.8143 (p) REVERT: N 33 LYS cc_start: 0.8010 (tttt) cc_final: 0.7802 (tttp) REVERT: N 71 SER cc_start: 0.8007 (t) cc_final: 0.7745 (p) outliers start: 33 outliers final: 26 residues processed: 144 average time/residue: 0.2264 time to fit residues: 44.3571 Evaluate side-chains 143 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8702 Z= 0.257 Angle : 0.566 8.380 11795 Z= 0.296 Chirality : 0.042 0.174 1329 Planarity : 0.004 0.058 1463 Dihedral : 6.438 68.833 1545 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.22 % Allowed : 10.65 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1030 helix: 1.32 (0.25), residues: 403 sheet: -0.20 (0.35), residues: 205 loop : -1.13 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.019 0.002 PHE N 108 TYR 0.018 0.001 TYR N 60 ARG 0.007 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.947 Fit side-chains REVERT: R 233 ARG cc_start: 0.6782 (ttm-80) cc_final: 0.6118 (mtp85) REVERT: A 124 ASP cc_start: 0.6916 (m-30) cc_final: 0.6650 (m-30) REVERT: A 163 TYR cc_start: 0.7774 (m-80) cc_final: 0.7571 (m-80) REVERT: A 202 THR cc_start: 0.7003 (m) cc_final: 0.6704 (p) REVERT: B 66 ASP cc_start: 0.6449 (p0) cc_final: 0.6039 (t0) REVERT: B 153 ASP cc_start: 0.7848 (p0) cc_final: 0.7511 (p0) REVERT: B 156 GLN cc_start: 0.7805 (mt0) cc_final: 0.7268 (mp10) REVERT: B 197 ARG cc_start: 0.8551 (ttm110) cc_final: 0.8080 (mtp85) REVERT: B 234 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: N 25 SER cc_start: 0.8455 (t) cc_final: 0.8169 (p) REVERT: N 71 SER cc_start: 0.7979 (t) cc_final: 0.7742 (p) outliers start: 29 outliers final: 24 residues processed: 137 average time/residue: 0.2133 time to fit residues: 40.0990 Evaluate side-chains 133 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS B 156 GLN G 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8702 Z= 0.181 Angle : 0.506 8.035 11795 Z= 0.264 Chirality : 0.040 0.216 1329 Planarity : 0.004 0.057 1463 Dihedral : 5.889 66.298 1545 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.89 % Allowed : 11.21 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1030 helix: 1.57 (0.26), residues: 405 sheet: -0.20 (0.34), residues: 210 loop : -1.03 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.015 0.001 PHE N 108 TYR 0.018 0.001 TYR N 60 ARG 0.006 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: R 233 ARG cc_start: 0.6810 (ttm-80) cc_final: 0.6152 (mtp85) REVERT: A 35 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6845 (mm-40) REVERT: A 124 ASP cc_start: 0.6949 (m-30) cc_final: 0.6665 (m-30) REVERT: B 66 ASP cc_start: 0.6422 (p0) cc_final: 0.6026 (t0) REVERT: B 197 ARG cc_start: 0.8516 (ttm110) cc_final: 0.8041 (mtp85) REVERT: N 25 SER cc_start: 0.8405 (t) cc_final: 0.8188 (p) REVERT: N 71 SER cc_start: 0.7981 (t) cc_final: 0.7775 (p) outliers start: 26 outliers final: 25 residues processed: 132 average time/residue: 0.2320 time to fit residues: 41.5520 Evaluate side-chains 129 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8702 Z= 0.209 Angle : 0.528 7.913 11795 Z= 0.275 Chirality : 0.041 0.194 1329 Planarity : 0.004 0.057 1463 Dihedral : 5.814 63.215 1545 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.44 % Allowed : 10.99 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1030 helix: 1.53 (0.26), residues: 406 sheet: -0.18 (0.34), residues: 210 loop : -1.05 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.016 0.001 PHE N 108 TYR 0.017 0.001 TYR N 60 ARG 0.007 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 124 ASP cc_start: 0.6942 (m-30) cc_final: 0.6657 (m-30) REVERT: B 66 ASP cc_start: 0.6330 (p0) cc_final: 0.5973 (t0) REVERT: B 111 TYR cc_start: 0.8553 (m-80) cc_final: 0.8291 (m-80) REVERT: B 197 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8201 (mtp85) outliers start: 31 outliers final: 30 residues processed: 127 average time/residue: 0.2129 time to fit residues: 37.2100 Evaluate side-chains 135 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8702 Z= 0.267 Angle : 0.555 8.076 11795 Z= 0.290 Chirality : 0.042 0.192 1329 Planarity : 0.004 0.057 1463 Dihedral : 5.891 57.918 1545 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.22 % Allowed : 11.65 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1030 helix: 1.45 (0.26), residues: 405 sheet: -0.19 (0.34), residues: 210 loop : -1.09 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.018 0.002 PHE N 108 TYR 0.016 0.002 TYR A 163 ARG 0.007 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: R 233 ARG cc_start: 0.6813 (ttm-80) cc_final: 0.6150 (mtp85) REVERT: A 117 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8510 (mtp180) REVERT: A 124 ASP cc_start: 0.6868 (m-30) cc_final: 0.6595 (m-30) REVERT: A 163 TYR cc_start: 0.7802 (m-80) cc_final: 0.7563 (m-80) REVERT: A 202 THR cc_start: 0.6932 (m) cc_final: 0.6658 (p) REVERT: B 197 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8124 (mtp85) outliers start: 29 outliers final: 27 residues processed: 129 average time/residue: 0.2163 time to fit residues: 38.2036 Evaluate side-chains 134 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8702 Z= 0.179 Angle : 0.518 8.195 11795 Z= 0.268 Chirality : 0.040 0.184 1329 Planarity : 0.004 0.055 1463 Dihedral : 5.630 55.219 1545 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.00 % Allowed : 12.10 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1030 helix: 1.52 (0.26), residues: 412 sheet: -0.11 (0.34), residues: 210 loop : -1.03 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.014 0.001 PHE N 108 TYR 0.016 0.001 TYR N 60 ARG 0.007 0.000 ARG R 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 0.938 Fit side-chains REVERT: R 85 GLU cc_start: 0.6018 (tp30) cc_final: 0.5486 (mm-30) REVERT: A 24 LYS cc_start: 0.7106 (mmmt) cc_final: 0.6792 (mmmt) REVERT: A 117 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8462 (mtp180) REVERT: A 124 ASP cc_start: 0.6944 (m-30) cc_final: 0.6649 (m-30) REVERT: A 163 TYR cc_start: 0.7837 (m-80) cc_final: 0.7551 (m-80) REVERT: B 66 ASP cc_start: 0.6234 (p0) cc_final: 0.5850 (t0) REVERT: B 111 TYR cc_start: 0.8515 (m-80) cc_final: 0.8285 (m-80) REVERT: B 197 ARG cc_start: 0.8497 (ttm110) cc_final: 0.8127 (mtp85) outliers start: 27 outliers final: 24 residues processed: 128 average time/residue: 0.2171 time to fit residues: 37.9108 Evaluate side-chains 127 residues out of total 901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.174292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132222 restraints weight = 8946.641| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.82 r_work: 0.3260 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8702 Z= 0.159 Angle : 0.499 8.149 11795 Z= 0.257 Chirality : 0.040 0.175 1329 Planarity : 0.004 0.055 1463 Dihedral : 5.398 56.159 1545 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.55 % Allowed : 12.21 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1030 helix: 1.64 (0.26), residues: 412 sheet: 0.13 (0.35), residues: 204 loop : -1.00 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 PHE 0.013 0.001 PHE N 108 TYR 0.016 0.001 TYR N 60 ARG 0.007 0.000 ARG R 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.36 seconds wall clock time: 38 minutes 33.92 seconds (2313.92 seconds total)