Starting phenix.real_space_refine on Wed Feb 14 16:23:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vla_32022/02_2024/7vla_32022_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vla_32022/02_2024/7vla_32022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vla_32022/02_2024/7vla_32022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vla_32022/02_2024/7vla_32022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vla_32022/02_2024/7vla_32022_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vla_32022/02_2024/7vla_32022_updated.pdb" } resolution = 2.7 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 6192 2.51 5 N 1625 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 9675 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 485 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "R" Number of atoms: 2505 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 302, 2493 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Conformer: "B" Number of residues, atoms: 302, 2493 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} bond proxies already assigned to first conformer: 2550 Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR R 291 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR R 291 " occ=0.50 Time building chain proxies: 6.71, per 1000 atoms: 0.69 Number of scatterers: 9675 At special positions: 0 Unit cell: (109.512, 135.876, 131.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1790 8.00 N 1625 7.00 C 6192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 56 " distance=2.03 Simple disulfide: pdb=" SG CYS L 33 " - pdb=" SG CYS L 72 " distance=2.02 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS R 24 " - pdb=" SG CYS R 273 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 3.92 Conformation dependent library (CDL) restraints added in 2.2 seconds 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 15 sheets defined 34.3% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.760A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.515A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.897A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.967A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.607A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'L' and resid 80 through 86 removed outlier: 4.921A pdb=" N LYS L 85 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS L 86 " --> pdb=" O ASP L 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 61 removed outlier: 3.598A pdb=" N GLN R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Proline residue: R 38 - end of helix removed outlier: 4.187A pdb=" N LEU R 43 " --> pdb=" O PRO R 39 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 96 removed outlier: 3.531A pdb=" N LEU R 87 " --> pdb=" O PHE R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 140 through 144 Processing helix chain 'R' and resid 147 through 164 Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 192 through 207 Processing helix chain 'R' and resid 209 through 226 Processing helix chain 'R' and resid 232 through 263 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 265 through 268 No H-bonds generated for 'chain 'R' and resid 265 through 268' Processing helix chain 'R' and resid 276 through 301 removed outlier: 4.134A pdb=" N HIS R 293 " --> pdb=" O ILE R 289 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS R 295 " --> pdb=" O ATYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.550A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.850A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.711A 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: 7.068A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.863A 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: 6.702A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.962A 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: 6.913A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.164A 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: 6.586A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.958A 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: 6.499A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.303A 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: 6.615A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 48 through 51 removed outlier: 3.609A pdb=" N SER L 48 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA L 73 " --> pdb=" O VAL L 61 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 173 through 177 Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 115 through 117 removed outlier: 6.048A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.582A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 155 through 158 Processing sheet with id= O, first strand: chain 'S' and resid 226 through 231 removed outlier: 5.935A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1231 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: 2.90 Time building geometry restraints manager: 4.20 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: 2529 1.33 - 1.45: 1942 1.45 - 1.57: 5320 1.57 - 1.70: 2 1.70 - 1.82: 96 Bond restraints: 9889 Sorted by residual: bond pdb=" N CYS R 273 " pdb=" CA CYS R 273 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.37e+00 bond pdb=" C TYR R 170 " pdb=" N PHE R 171 " ideal model delta sigma weight residual 1.332 1.369 -0.036 1.36e-02 5.41e+03 7.17e+00 bond pdb=" C16 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.554 1.603 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C LEU R 87 " pdb=" O LEU R 87 " ideal model delta sigma weight residual 1.244 1.221 0.023 9.80e-03 1.04e+04 5.42e+00 bond pdb=" C23 CLR R 401 " pdb=" C24 CLR R 401 " ideal model delta sigma weight residual 1.525 1.571 -0.046 2.00e-02 2.50e+03 5.40e+00 ... (remaining 9884 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 235 106.50 - 113.40: 5363 113.40 - 120.29: 3774 120.29 - 127.19: 3914 127.19 - 134.08: 106 Bond angle restraints: 13392 Sorted by residual: angle pdb=" N GLU R 274 " pdb=" CA GLU R 274 " pdb=" C GLU R 274 " ideal model delta sigma weight residual 114.12 104.40 9.72 1.39e+00 5.18e-01 4.89e+01 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.14 119.41 -10.27 1.49e+00 4.50e-01 4.75e+01 angle pdb=" N LYS S 43 " pdb=" CA LYS S 43 " pdb=" C LYS S 43 " ideal model delta sigma weight residual 111.74 118.64 -6.90 1.35e+00 5.49e-01 2.61e+01 angle pdb=" N CYS B 250 " pdb=" CA CYS B 250 " pdb=" C CYS B 250 " ideal model delta sigma weight residual 110.17 102.28 7.89 1.61e+00 3.86e-01 2.40e+01 angle pdb=" N LYS B 209 " pdb=" CA LYS B 209 " pdb=" C LYS B 209 " ideal model delta sigma weight residual 108.34 115.74 -7.40 1.64e+00 3.72e-01 2.04e+01 ... (remaining 13387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 5436 16.67 - 33.34: 399 33.34 - 50.01: 64 50.01 - 66.67: 23 66.67 - 83.34: 10 Dihedral angle restraints: 5932 sinusoidal: 2376 harmonic: 3556 Sorted by residual: dihedral pdb=" CB CYS L 43 " pdb=" SG CYS L 43 " pdb=" SG CYS L 83 " pdb=" CB CYS L 83 " ideal model delta sinusoidal sigma weight residual -86.00 -35.13 -50.87 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CA GLU R 177 " pdb=" C GLU R 177 " pdb=" N PHE R 178 " pdb=" CA PHE R 178 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA PHE B 199 " pdb=" C PHE B 199 " pdb=" N VAL B 200 " pdb=" CA VAL B 200 " ideal model delta harmonic sigma weight residual 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 5929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1334 0.082 - 0.165: 158 0.165 - 0.247: 13 0.247 - 0.330: 6 0.330 - 0.412: 1 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA LYS S 43 " pdb=" N LYS S 43 " pdb=" C LYS S 43 " pdb=" CB LYS S 43 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C17 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C16 CLR R 401 " pdb=" C20 CLR R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.88 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ALA B 248 " pdb=" N ALA B 248 " pdb=" C ALA B 248 " pdb=" CB ALA B 248 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1509 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 176 " 0.029 2.00e-02 2.50e+03 2.52e-02 1.59e+01 pdb=" CG TRP R 176 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP R 176 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP R 176 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 176 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 176 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 176 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 176 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 176 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP R 176 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO S 41 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 13 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C ARG G 13 " -0.034 2.00e-02 2.50e+03 pdb=" O ARG G 13 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS G 14 " 0.012 2.00e-02 2.50e+03 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 10 2.29 - 2.94: 4257 2.94 - 3.59: 13682 3.59 - 4.25: 22709 4.25 - 4.90: 38986 Nonbonded interactions: 79644 Sorted by model distance: nonbonded pdb=" OE2 GLU R 287 " pdb=" OH BTYR R 291 " model vdw 1.634 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.131 2.440 nonbonded pdb=" O ASP R 280 " pdb=" NE2 GLN R 284 " model vdw 2.230 2.520 nonbonded pdb=" O MET S 192 " pdb=" OG SER S 193 " model vdw 2.237 2.440 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.241 2.440 ... (remaining 79639 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: 0.620 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: 3.000 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.830 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9889 Z= 0.367 Angle : 0.866 10.269 13392 Z= 0.507 Chirality : 0.057 0.412 1512 Planarity : 0.005 0.055 1683 Dihedral : 12.463 83.343 3619 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.09 % Allowed : 0.66 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1209 helix: 1.81 (0.26), residues: 405 sheet: 1.12 (0.29), residues: 314 loop : -0.47 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP R 176 HIS 0.007 0.002 HIS A 213 PHE 0.023 0.003 PHE R 316 TYR 0.022 0.002 TYR S 103 ARG 0.012 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 ASP cc_start: 0.6883 (p0) cc_final: 0.6630 (p0) REVERT: B 262 MET cc_start: 0.7591 (tpp) cc_final: 0.7347 (tpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.5042 time to fit residues: 280.0070 Evaluate side-chains 139 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 48 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 108 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: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 176 GLN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9889 Z= 0.228 Angle : 0.600 9.560 13392 Z= 0.319 Chirality : 0.044 0.182 1512 Planarity : 0.004 0.043 1683 Dihedral : 5.948 57.686 1389 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.51 % Allowed : 8.41 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1209 helix: 2.20 (0.25), residues: 406 sheet: 1.03 (0.29), residues: 311 loop : -0.51 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 176 HIS 0.004 0.001 HIS A 213 PHE 0.024 0.002 PHE R 85 TYR 0.022 0.002 TYR A 296 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7474 (tp30) cc_final: 0.7263 (tp30) REVERT: B 262 MET cc_start: 0.7463 (tpp) cc_final: 0.7233 (tpp) REVERT: B 280 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7967 (tttt) outliers start: 16 outliers final: 6 residues processed: 152 average time/residue: 1.4645 time to fit residues: 235.7389 Evaluate side-chains 142 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain S residue 62 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 340 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9889 Z= 0.285 Angle : 0.600 7.186 13392 Z= 0.323 Chirality : 0.045 0.182 1512 Planarity : 0.005 0.055 1683 Dihedral : 5.775 51.805 1389 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.89 % Allowed : 9.07 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1209 helix: 2.23 (0.25), residues: 406 sheet: 0.90 (0.29), residues: 313 loop : -0.56 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 176 HIS 0.005 0.001 HIS A 213 PHE 0.019 0.002 PHE R 101 TYR 0.023 0.002 TYR A 296 ARG 0.005 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: B 75 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7252 (mm110) REVERT: B 96 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7668 (mtt-85) REVERT: B 197 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7037 (mtt90) outliers start: 20 outliers final: 10 residues processed: 152 average time/residue: 1.4822 time to fit residues: 239.3299 Evaluate side-chains 153 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain S residue 85 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 32 GLN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9889 Z= 0.154 Angle : 0.513 7.343 13392 Z= 0.274 Chirality : 0.041 0.180 1512 Planarity : 0.004 0.045 1683 Dihedral : 5.305 48.065 1389 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.27 % Allowed : 10.40 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1209 helix: 2.49 (0.26), residues: 406 sheet: 0.95 (0.29), residues: 306 loop : -0.55 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 176 HIS 0.003 0.001 HIS R 186 PHE 0.014 0.001 PHE R 85 TYR 0.016 0.001 TYR R 62 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: B 197 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7255 (mpt180) REVERT: B 214 ARG cc_start: 0.7234 (mmt-90) cc_final: 0.6918 (mmt180) REVERT: R 239 ARG cc_start: 0.6979 (mtm180) cc_final: 0.6657 (ptp-110) REVERT: S 234 GLU cc_start: 0.7960 (pt0) cc_final: 0.7704 (pt0) outliers start: 24 outliers final: 9 residues processed: 157 average time/residue: 1.4099 time to fit residues: 235.3711 Evaluate side-chains 150 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 32 GLN B 176 GLN B 340 ASN G 5 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 284 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9889 Z= 0.158 Angle : 0.508 8.582 13392 Z= 0.270 Chirality : 0.041 0.175 1512 Planarity : 0.004 0.045 1683 Dihedral : 5.128 45.114 1389 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 11.15 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1209 helix: 2.56 (0.25), residues: 407 sheet: 0.95 (0.29), residues: 307 loop : -0.50 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 176 HIS 0.003 0.001 HIS R 180 PHE 0.019 0.001 PHE R 101 TYR 0.012 0.001 TYR R 62 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6935 (mtt90) REVERT: S 234 GLU cc_start: 0.7962 (pt0) cc_final: 0.7696 (pt0) outliers start: 21 outliers final: 11 residues processed: 151 average time/residue: 1.3492 time to fit residues: 217.1140 Evaluate side-chains 146 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 chunk 111 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 32 GLN B 176 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9889 Z= 0.147 Angle : 0.504 10.382 13392 Z= 0.266 Chirality : 0.040 0.171 1512 Planarity : 0.003 0.042 1683 Dihedral : 4.980 43.468 1389 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.46 % Allowed : 11.72 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1209 helix: 2.66 (0.25), residues: 406 sheet: 0.97 (0.29), residues: 302 loop : -0.50 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 176 HIS 0.003 0.001 HIS R 180 PHE 0.013 0.001 PHE A 189 TYR 0.011 0.001 TYR R 62 ARG 0.007 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: A 195 HIS cc_start: 0.7610 (m-70) cc_final: 0.7379 (m90) REVERT: B 197 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7069 (mtt90) REVERT: S 234 GLU cc_start: 0.7963 (pt0) cc_final: 0.7733 (pt0) outliers start: 26 outliers final: 12 residues processed: 154 average time/residue: 1.3438 time to fit residues: 220.3819 Evaluate side-chains 151 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 257 LEU Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 176 GLN B 340 ASN ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9889 Z= 0.380 Angle : 0.652 13.080 13392 Z= 0.341 Chirality : 0.046 0.209 1512 Planarity : 0.005 0.072 1683 Dihedral : 5.509 43.043 1389 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.74 % Allowed : 11.81 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1209 helix: 2.30 (0.25), residues: 407 sheet: 0.81 (0.29), residues: 310 loop : -0.67 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 176 HIS 0.007 0.001 HIS A 213 PHE 0.020 0.002 PHE B 335 TYR 0.023 0.002 TYR S 190 ARG 0.008 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: A 195 HIS cc_start: 0.7738 (m-70) cc_final: 0.7500 (m90) REVERT: B 65 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7976 (p) REVERT: B 75 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7320 (mt0) REVERT: B 96 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7958 (mtt180) REVERT: B 197 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6983 (mtt90) REVERT: B 217 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7785 (pmm) REVERT: B 219 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6515 (mtt90) REVERT: B 293 ASN cc_start: 0.8251 (p0) cc_final: 0.7896 (p0) REVERT: R 313 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6225 (mtt-85) outliers start: 29 outliers final: 15 residues processed: 146 average time/residue: 1.4156 time to fit residues: 219.3186 Evaluate side-chains 156 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 86 THR Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 307 ARG Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain R residue 313 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9889 Z= 0.213 Angle : 0.559 10.423 13392 Z= 0.292 Chirality : 0.042 0.168 1512 Planarity : 0.004 0.045 1683 Dihedral : 5.276 43.982 1389 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.65 % Allowed : 11.91 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1209 helix: 2.43 (0.25), residues: 408 sheet: 0.87 (0.29), residues: 302 loop : -0.66 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 176 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: A 195 HIS cc_start: 0.7659 (m-70) cc_final: 0.7430 (m90) REVERT: B 75 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7189 (mm110) REVERT: B 96 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (mtt180) REVERT: B 197 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6991 (mtt90) REVERT: B 217 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7790 (pmm) REVERT: B 291 ASP cc_start: 0.6806 (m-30) cc_final: 0.6578 (m-30) REVERT: B 293 ASN cc_start: 0.8098 (p0) cc_final: 0.7772 (p0) outliers start: 28 outliers final: 14 residues processed: 149 average time/residue: 1.4290 time to fit residues: 226.2567 Evaluate side-chains 152 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 86 THR Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 0.4980 chunk 68 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9889 Z= 0.158 Angle : 0.521 9.945 13392 Z= 0.271 Chirality : 0.041 0.166 1512 Planarity : 0.004 0.044 1683 Dihedral : 5.039 43.474 1389 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.51 % Allowed : 13.42 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1209 helix: 2.55 (0.26), residues: 410 sheet: 0.88 (0.29), residues: 301 loop : -0.60 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 180 PHE 0.020 0.001 PHE R 101 TYR 0.009 0.001 TYR S 190 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: B 75 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7154 (mm110) REVERT: B 96 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7903 (mtt180) REVERT: B 195 ASP cc_start: 0.6943 (p0) cc_final: 0.6693 (p0) REVERT: B 293 ASN cc_start: 0.8023 (p0) cc_final: 0.7671 (p0) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 1.3984 time to fit residues: 215.7369 Evaluate side-chains 147 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 109 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9889 Z= 0.151 Angle : 0.520 11.121 13392 Z= 0.270 Chirality : 0.041 0.164 1512 Planarity : 0.003 0.044 1683 Dihedral : 4.971 42.951 1389 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.51 % Allowed : 13.61 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1209 helix: 2.63 (0.26), residues: 409 sheet: 0.93 (0.29), residues: 304 loop : -0.58 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 180 PHE 0.013 0.001 PHE R 85 TYR 0.010 0.001 TYR S 190 ARG 0.007 0.000 ARG B 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: B 75 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7153 (mm110) REVERT: B 96 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7895 (mtt180) REVERT: B 195 ASP cc_start: 0.6967 (p0) cc_final: 0.6727 (p0) REVERT: B 293 ASN cc_start: 0.7996 (p0) cc_final: 0.7652 (p0) outliers start: 16 outliers final: 11 residues processed: 144 average time/residue: 1.3978 time to fit residues: 214.1805 Evaluate side-chains 147 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain R residue 86 THR Chi-restraints excluded: chain R residue 287 GLU Chi-restraints excluded: chain R residue 311 TYR Chi-restraints excluded: chain S residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.178798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126733 restraints weight = 21688.431| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.66 r_work: 0.2937 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9889 Z= 0.150 Angle : 0.515 10.857 13392 Z= 0.267 Chirality : 0.041 0.162 1512 Planarity : 0.003 0.044 1683 Dihedral : 4.883 42.116 1389 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.42 % Allowed : 13.80 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1209 helix: 2.67 (0.26), residues: 409 sheet: 0.92 (0.29), residues: 305 loop : -0.57 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 180 PHE 0.020 0.001 PHE R 101 TYR 0.010 0.001 TYR S 190 ARG 0.007 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.21 seconds wall clock time: 75 minutes 35.18 seconds (4535.18 seconds total)