Starting phenix.real_space_refine on Sun Aug 24 09:08:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jar_36132/08_2025/8jar_36132.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jar_36132/08_2025/8jar_36132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jar_36132/08_2025/8jar_36132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jar_36132/08_2025/8jar_36132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jar_36132/08_2025/8jar_36132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jar_36132/08_2025/8jar_36132.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2476 atoms to isotropic. 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 Zn 1 6.06 5 S 89 5.16 5 C 10758 2.51 5 N 2875 2.21 5 O 3118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16841 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4613 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 6, 'TRANS': 564} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 830 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain: "D" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "S" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4630 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 6, 'TRANS': 566} Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 65 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "G" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 758 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "E" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2214 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "I" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2145 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 401 SG CYS A 54 60.557 51.050 101.711 1.00 1.95 S ATOM 6678 SG CYS B 54 64.232 50.237 102.846 1.00 10.81 S Time building chain proxies: 3.59, per 1000 atoms: 0.21 Number of scatterers: 16841 At special positions: 0 Unit cell: (119.72, 132.02, 186.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 89 16.00 O 3118 8.00 N 2875 7.00 C 10758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 547.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 89 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 89 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 54 " Number of angles added : 2 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 6 sheets defined 74.6% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 4.091A pdb=" N ASN A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 33 removed outlier: 4.009A pdb=" N ARG A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 50 removed outlier: 3.969A pdb=" N PHE A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.619A pdb=" N SER A 58 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 71 removed outlier: 4.125A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.861A pdb=" N LEU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.624A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 removed outlier: 4.247A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.865A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.837A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 removed outlier: 3.778A pdb=" N TYR A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.658A pdb=" N GLU A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 261 through 280 removed outlier: 4.411A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 Processing helix chain 'A' and resid 303 through 322 removed outlier: 3.572A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 3.549A pdb=" N TYR A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.812A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.655A pdb=" N ALA A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.888A pdb=" N LEU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 487 through 507 removed outlier: 4.271A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 526 removed outlier: 4.366A pdb=" N TYR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.587A pdb=" N GLY C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.532A pdb=" N PHE D 52 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 removed outlier: 3.752A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.516A pdb=" N MET D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.853A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.546A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 removed outlier: 3.951A pdb=" N HIS B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 109 removed outlier: 3.923A pdb=" N SER B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.998A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.679A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 235 Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.713A pdb=" N GLN B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 303 through 322 removed outlier: 3.857A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 360 through 368 removed outlier: 3.866A pdb=" N ILE B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 3.746A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 421 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 444 through 462 removed outlier: 3.591A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 487 through 507 Processing helix chain 'B' and resid 512 through 528 removed outlier: 4.030A pdb=" N ASP B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 549 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.664A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 577 removed outlier: 3.559A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 36 removed outlier: 4.123A pdb=" N GLY G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.223A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 109 removed outlier: 3.717A pdb=" N PHE H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 3.572A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.620A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.758A pdb=" N SER E 79 " --> pdb=" O ARG E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.588A pdb=" N GLU E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.645A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.644A pdb=" N ILE E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.880A pdb=" N ILE E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'E' and resid 200 through 207 removed outlier: 3.541A pdb=" N GLU E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 229 removed outlier: 3.625A pdb=" N THR E 213 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 222 " --> pdb=" O TYR E 218 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA E 223 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 224 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 4.010A pdb=" N LEU E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY E 241 " --> pdb=" O GLU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 257 No H-bonds generated for 'chain 'E' and resid 255 through 257' Processing helix chain 'E' and resid 258 through 271 removed outlier: 4.036A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN E 267 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN E 268 " --> pdb=" O HIS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.560A pdb=" N HIS E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA E 280 " --> pdb=" O GLN E 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.665A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 31 through 47 removed outlier: 3.658A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 79 Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 105 through 112 Processing helix chain 'I' and resid 138 through 151 removed outlier: 3.540A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.929A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 191 removed outlier: 4.189A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE I 188 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL I 189 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 195 Processing helix chain 'I' and resid 200 through 205 removed outlier: 3.937A pdb=" N GLU I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 218 removed outlier: 3.724A pdb=" N THR I 213 " --> pdb=" O SER I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 226 removed outlier: 3.818A pdb=" N SER I 224 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN I 225 " --> pdb=" O GLN I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 254 removed outlier: 3.520A pdb=" N VAL I 239 " --> pdb=" O TYR I 235 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU I 240 " --> pdb=" O MET I 236 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY I 241 " --> pdb=" O GLU I 237 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS I 252 " --> pdb=" O ILE I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 257 No H-bonds generated for 'chain 'I' and resid 255 through 257' Processing helix chain 'I' and resid 258 through 269 removed outlier: 3.607A pdb=" N VAL I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG I 269 " --> pdb=" O GLU I 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 17 through 18 removed outlier: 6.977A pdb=" N PHE C 4 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 75 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N MET C 6 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 77 " --> pdb=" O MET C 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 14 removed outlier: 6.206A pdb=" N THR C 13 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LYS D 32 " --> pdb=" O THR C 13 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR D 18 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N VAL D 60 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS D 20 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'G' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.718A pdb=" N ASN H 58 " --> pdb=" O TYR H 18 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 3081 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: 2.52 Time building geometry restraints manager: 1.83 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: 3821 1.33 - 1.45: 3699 1.45 - 1.57: 9553 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 17205 Sorted by residual: bond pdb=" C LEU I 155 " pdb=" N GLN I 156 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.36e-02 5.41e+03 4.53e+00 bond pdb=" CA LEU I 155 " pdb=" C LEU I 155 " ideal model delta sigma weight residual 1.525 1.499 0.026 1.27e-02 6.20e+03 4.12e+00 bond pdb=" C LEU I 155 " pdb=" O LEU I 155 " ideal model delta sigma weight residual 1.233 1.211 0.022 1.43e-02 4.89e+03 2.31e+00 bond pdb=" N VAL B 560 " pdb=" CA VAL B 560 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.21e+00 bond pdb=" CB ILE A 39 " pdb=" CG2 ILE A 39 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.36e-01 ... (remaining 17200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 22765 1.67 - 3.34: 393 3.34 - 5.01: 52 5.01 - 6.68: 8 6.68 - 8.35: 2 Bond angle restraints: 23220 Sorted by residual: angle pdb=" C THR D 84 " pdb=" N ASN D 85 " pdb=" CA ASN D 85 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N VAL A 21 " pdb=" CA VAL A 21 " pdb=" C VAL A 21 " ideal model delta sigma weight residual 113.39 108.52 4.87 1.47e+00 4.63e-01 1.10e+01 angle pdb=" N VAL B 560 " pdb=" CA VAL B 560 " pdb=" C VAL B 560 " ideal model delta sigma weight residual 106.21 109.08 -2.87 1.07e+00 8.73e-01 7.20e+00 angle pdb=" C ARG B 549 " pdb=" N GLN B 550 " pdb=" CA GLN B 550 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.41e+00 angle pdb=" O PRO I 154 " pdb=" C PRO I 154 " pdb=" N LEU I 155 " ideal model delta sigma weight residual 122.24 125.62 -3.38 1.34e+00 5.57e-01 6.37e+00 ... (remaining 23215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9279 17.96 - 35.93: 918 35.93 - 53.89: 128 53.89 - 71.86: 24 71.86 - 89.82: 18 Dihedral angle restraints: 10367 sinusoidal: 4240 harmonic: 6127 Sorted by residual: dihedral pdb=" CA ILE C 7 " pdb=" C ILE C 7 " pdb=" N ARG C 8 " pdb=" CA ARG C 8 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU E 27 " pdb=" C LEU E 27 " pdb=" N GLU E 28 " pdb=" CA GLU E 28 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 303 " pdb=" C ASN B 303 " pdb=" N ILE B 304 " pdb=" CA ILE B 304 " ideal model delta harmonic sigma weight residual -180.00 -161.96 -18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 10364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1998 0.047 - 0.094: 475 0.094 - 0.141: 53 0.141 - 0.188: 4 0.188 - 0.235: 1 Chirality restraints: 2531 Sorted by residual: chirality pdb=" CB VAL B 301 " pdb=" CA VAL B 301 " pdb=" CG1 VAL B 301 " pdb=" CG2 VAL B 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU I 155 " pdb=" CB LEU I 155 " pdb=" CD1 LEU I 155 " pdb=" CD2 LEU I 155 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.91e-01 ... (remaining 2528 not shown) Planarity restraints: 2969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER I 209 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO I 210 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO I 210 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 210 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 209 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO E 210 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 255 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO E 256 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 256 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 256 " -0.025 5.00e-02 4.00e+02 ... (remaining 2966 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 490 2.72 - 3.26: 17562 3.26 - 3.81: 28803 3.81 - 4.35: 35377 4.35 - 4.90: 60606 Nonbonded interactions: 142838 Sorted by model distance: nonbonded pdb=" OE1 GLU A 334 " pdb=" OG SER A 378 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR A 338 " pdb=" O GLY S 0 " model vdw 2.186 3.040 nonbonded pdb=" OG SER C 94 " pdb=" OD2 ASP D 25 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLU B 334 " pdb=" OG SER B 378 " model vdw 2.231 3.040 nonbonded pdb=" OG SER B 479 " pdb=" O THR F -4 " model vdw 2.242 3.040 ... (remaining 142833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 8 through 578) } ncs_group { reference = (chain 'C' and resid 2 through 97) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and resid 1 through 272) selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.490 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 0.037 17209 Z= 0.162 Angle : 0.542 8.350 23222 Z= 0.296 Chirality : 0.039 0.235 2531 Planarity : 0.004 0.050 2969 Dihedral : 14.401 89.821 6413 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.18), residues: 2047 helix: -0.21 (0.13), residues: 1447 sheet: -1.93 (1.23), residues: 20 loop : -1.11 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 9 TYR 0.016 0.001 TYR B 294 PHE 0.022 0.001 PHE A 41 TRP 0.010 0.001 TRP I 147 HIS 0.010 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00376 (17205) covalent geometry : angle 0.54146 (23220) hydrogen bonds : bond 0.16397 ( 1038) hydrogen bonds : angle 6.69723 ( 3081) metal coordination : bond 0.00977 ( 4) metal coordination : angle 3.17884 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 TYR cc_start: 0.6912 (t80) cc_final: 0.6706 (t80) REVERT: C 37 ARG cc_start: 0.6674 (mmm-85) cc_final: 0.5917 (mpt180) REVERT: B 396 LYS cc_start: 0.7611 (tptt) cc_final: 0.7357 (tppt) REVERT: G 43 ARG cc_start: 0.7014 (ptp-110) cc_final: 0.6777 (mtm110) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1367 time to fit residues: 59.7419 Evaluate side-chains 197 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 578 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS E 279 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.174819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137405 restraints weight = 22867.603| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.10 r_work: 0.3581 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17209 Z= 0.174 Angle : 0.545 8.358 23222 Z= 0.287 Chirality : 0.038 0.144 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.637 72.879 2283 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.99 % Allowed : 8.28 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.18), residues: 2047 helix: 0.28 (0.13), residues: 1493 sheet: -1.64 (1.18), residues: 20 loop : -1.30 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 9 TYR 0.020 0.001 TYR B 495 PHE 0.018 0.001 PHE A 41 TRP 0.030 0.002 TRP A 543 HIS 0.011 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00406 (17205) covalent geometry : angle 0.54384 (23220) hydrogen bonds : bond 0.04179 ( 1038) hydrogen bonds : angle 4.60194 ( 3081) metal coordination : bond 0.01277 ( 4) metal coordination : angle 4.44840 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8778 (mttp) cc_final: 0.8555 (mttt) REVERT: A 261 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7886 (mm-30) REVERT: B 193 MET cc_start: 0.7429 (ttp) cc_final: 0.7211 (ttp) REVERT: B 205 LYS cc_start: 0.8299 (mttt) cc_final: 0.7972 (mttt) REVERT: B 396 LYS cc_start: 0.7277 (tptt) cc_final: 0.6945 (tppt) REVERT: G 19 LYS cc_start: 0.5802 (mmmt) cc_final: 0.5403 (mmmt) REVERT: G 43 ARG cc_start: 0.7400 (ptp-110) cc_final: 0.6803 (mtm110) REVERT: I 82 GLN cc_start: 0.5300 (pp30) cc_final: 0.4712 (pp30) outliers start: 18 outliers final: 9 residues processed: 233 average time/residue: 0.1458 time to fit residues: 49.8972 Evaluate side-chains 209 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 200 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 17 MET Chi-restraints excluded: chain H residue 108 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 17 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN E 190 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.174326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137263 restraints weight = 23209.451| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.19 r_work: 0.3476 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17209 Z= 0.154 Angle : 0.514 10.062 23222 Z= 0.268 Chirality : 0.038 0.160 2531 Planarity : 0.004 0.043 2969 Dihedral : 4.530 72.932 2283 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.04 % Allowed : 11.02 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.18), residues: 2047 helix: 0.54 (0.14), residues: 1486 sheet: -1.88 (1.12), residues: 20 loop : -1.32 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 9 TYR 0.015 0.001 TYR B 294 PHE 0.016 0.001 PHE A 41 TRP 0.043 0.002 TRP A 543 HIS 0.009 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00358 (17205) covalent geometry : angle 0.51236 (23220) hydrogen bonds : bond 0.03956 ( 1038) hydrogen bonds : angle 4.39521 ( 3081) metal coordination : bond 0.01270 ( 4) metal coordination : angle 4.26034 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 GLU cc_start: 0.7198 (tt0) cc_final: 0.6875 (tt0) REVERT: G 19 LYS cc_start: 0.5909 (mmmt) cc_final: 0.5681 (mmmt) REVERT: G 41 GLU cc_start: 0.8126 (tt0) cc_final: 0.7856 (tt0) REVERT: E 146 MET cc_start: 0.7423 (mmt) cc_final: 0.7205 (mmp) REVERT: E 236 MET cc_start: 0.2043 (tmm) cc_final: 0.1698 (tmm) REVERT: I 82 GLN cc_start: 0.5458 (pp30) cc_final: 0.4682 (pp30) REVERT: I 253 TYR cc_start: 0.6185 (m-10) cc_final: 0.5933 (m-10) outliers start: 19 outliers final: 14 residues processed: 223 average time/residue: 0.1470 time to fit residues: 49.2334 Evaluate side-chains 208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain F residue -4 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain I residue 146 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 173 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 153 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 175 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS I 82 GLN ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.174666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137413 restraints weight = 22959.175| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.21 r_work: 0.3574 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17209 Z= 0.143 Angle : 0.496 8.885 23222 Z= 0.260 Chirality : 0.037 0.134 2531 Planarity : 0.004 0.045 2969 Dihedral : 4.476 73.367 2283 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.64 % Allowed : 12.12 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 2047 helix: 0.65 (0.14), residues: 1489 sheet: -1.80 (1.07), residues: 20 loop : -1.29 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 9 TYR 0.022 0.001 TYR A 468 PHE 0.026 0.001 PHE I 202 TRP 0.051 0.002 TRP A 543 HIS 0.008 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00331 (17205) covalent geometry : angle 0.49422 (23220) hydrogen bonds : bond 0.03724 ( 1038) hydrogen bonds : angle 4.25270 ( 3081) metal coordination : bond 0.01130 ( 4) metal coordination : angle 4.17845 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6182 (mpp) REVERT: E 236 MET cc_start: 0.1628 (tmm) cc_final: 0.1410 (tmm) outliers start: 30 outliers final: 17 residues processed: 225 average time/residue: 0.1255 time to fit residues: 43.1327 Evaluate side-chains 208 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain I residue 82 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 148 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 199 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 490 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 225 ASN I 268 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137141 restraints weight = 22930.461| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.19 r_work: 0.3567 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17209 Z= 0.159 Angle : 0.509 8.078 23222 Z= 0.265 Chirality : 0.037 0.138 2531 Planarity : 0.004 0.046 2969 Dihedral : 4.490 75.473 2283 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.92 % Allowed : 12.94 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.19), residues: 2047 helix: 0.70 (0.14), residues: 1489 sheet: -1.72 (1.06), residues: 20 loop : -1.33 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 9 TYR 0.028 0.001 TYR A 468 PHE 0.020 0.001 PHE B 445 TRP 0.059 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00374 (17205) covalent geometry : angle 0.50730 (23220) hydrogen bonds : bond 0.03734 ( 1038) hydrogen bonds : angle 4.22457 ( 3081) metal coordination : bond 0.01280 ( 4) metal coordination : angle 4.25502 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6201 (mpp) REVERT: G 19 LYS cc_start: 0.5569 (mmmt) cc_final: 0.5119 (mmmt) REVERT: G 91 GLU cc_start: 0.7562 (pm20) cc_final: 0.7266 (pm20) REVERT: E 28 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: E 236 MET cc_start: 0.1643 (tmm) cc_final: 0.1430 (tmm) REVERT: I 156 GLN cc_start: 0.7260 (tp40) cc_final: 0.6943 (tp-100) outliers start: 35 outliers final: 24 residues processed: 219 average time/residue: 0.1172 time to fit residues: 39.9159 Evaluate side-chains 213 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 158 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 57 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.181697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138021 restraints weight = 23747.276| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.97 r_work: 0.3505 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17209 Z= 0.137 Angle : 0.499 10.494 23222 Z= 0.260 Chirality : 0.037 0.133 2531 Planarity : 0.004 0.048 2969 Dihedral : 4.439 75.042 2283 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.70 % Allowed : 13.82 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.19), residues: 2047 helix: 0.78 (0.14), residues: 1493 sheet: -2.32 (0.76), residues: 35 loop : -1.29 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 9 TYR 0.028 0.001 TYR A 468 PHE 0.022 0.001 PHE B 445 TRP 0.044 0.002 TRP A 543 HIS 0.007 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00318 (17205) covalent geometry : angle 0.49793 (23220) hydrogen bonds : bond 0.03607 ( 1038) hydrogen bonds : angle 4.16612 ( 3081) metal coordination : bond 0.01071 ( 4) metal coordination : angle 4.14052 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6252 (mpp) REVERT: A 396 LYS cc_start: 0.7573 (mptt) cc_final: 0.7285 (mmmm) REVERT: D 111 ASP cc_start: 0.8692 (t0) cc_final: 0.8422 (t0) REVERT: G 5 LEU cc_start: 0.8449 (mp) cc_final: 0.8244 (mp) REVERT: G 91 GLU cc_start: 0.7536 (pm20) cc_final: 0.7227 (pm20) REVERT: E 28 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: E 162 MET cc_start: 0.7209 (mtt) cc_final: 0.6997 (mtp) REVERT: E 236 MET cc_start: 0.1569 (tmm) cc_final: 0.1357 (tmm) REVERT: I 156 GLN cc_start: 0.7357 (tp40) cc_final: 0.7153 (tp-100) outliers start: 31 outliers final: 23 residues processed: 219 average time/residue: 0.1146 time to fit residues: 39.4885 Evaluate side-chains 219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 28 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 167 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS B 279 HIS B 404 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.168006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132732 restraints weight = 22112.003| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.84 r_work: 0.3497 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17209 Z= 0.167 Angle : 0.524 10.272 23222 Z= 0.271 Chirality : 0.038 0.149 2531 Planarity : 0.004 0.050 2969 Dihedral : 4.481 77.617 2283 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.92 % Allowed : 14.47 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 2047 helix: 0.73 (0.14), residues: 1499 sheet: -2.30 (0.76), residues: 35 loop : -1.31 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 9 TYR 0.026 0.001 TYR A 468 PHE 0.029 0.001 PHE I 202 TRP 0.045 0.002 TRP A 543 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00394 (17205) covalent geometry : angle 0.52208 (23220) hydrogen bonds : bond 0.03677 ( 1038) hydrogen bonds : angle 4.17723 ( 3081) metal coordination : bond 0.01373 ( 4) metal coordination : angle 4.25132 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6327 (mpp) REVERT: A 396 LYS cc_start: 0.7632 (mptt) cc_final: 0.7358 (mmmm) REVERT: G 19 LYS cc_start: 0.5646 (mmmt) cc_final: 0.5176 (mmmt) REVERT: G 41 GLU cc_start: 0.7990 (pt0) cc_final: 0.7088 (pm20) REVERT: E 28 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: E 236 MET cc_start: 0.1929 (tmm) cc_final: 0.1682 (tmm) REVERT: I 219 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.7235 (m-10) outliers start: 35 outliers final: 26 residues processed: 227 average time/residue: 0.1212 time to fit residues: 41.8362 Evaluate side-chains 221 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 196 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 66 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 343 HIS B 24 ASN B 404 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.173186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.136238 restraints weight = 22975.900| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.23 r_work: 0.3463 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17209 Z= 0.159 Angle : 0.521 9.294 23222 Z= 0.271 Chirality : 0.037 0.136 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.495 78.648 2283 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.19 % Allowed : 15.08 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.19), residues: 2047 helix: 0.76 (0.14), residues: 1498 sheet: -1.63 (1.04), residues: 20 loop : -1.36 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 9 TYR 0.027 0.001 TYR A 468 PHE 0.027 0.001 PHE B 445 TRP 0.048 0.002 TRP A 543 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00374 (17205) covalent geometry : angle 0.51979 (23220) hydrogen bonds : bond 0.03640 ( 1038) hydrogen bonds : angle 4.17538 ( 3081) metal coordination : bond 0.01304 ( 4) metal coordination : angle 4.31858 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6231 (mpp) REVERT: A 396 LYS cc_start: 0.7677 (mptt) cc_final: 0.7413 (mmmm) REVERT: B 467 ASP cc_start: 0.7059 (t0) cc_final: 0.6837 (t70) REVERT: G 19 LYS cc_start: 0.5642 (mmmt) cc_final: 0.5144 (mmmt) REVERT: E 206 ILE cc_start: 0.7685 (tp) cc_final: 0.7376 (tp) REVERT: I 219 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: I 253 TYR cc_start: 0.6460 (m-10) cc_final: 0.6201 (m-10) outliers start: 40 outliers final: 28 residues processed: 226 average time/residue: 0.1198 time to fit residues: 41.8826 Evaluate side-chains 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 136 optimal weight: 0.2980 chunk 132 optimal weight: 0.0470 chunk 155 optimal weight: 0.6980 chunk 98 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 343 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 190 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 GLN ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135252 restraints weight = 22527.720| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.89 r_work: 0.3513 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17209 Z= 0.119 Angle : 0.508 9.559 23222 Z= 0.263 Chirality : 0.036 0.149 2531 Planarity : 0.004 0.049 2969 Dihedral : 4.410 74.350 2283 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.70 % Allowed : 15.62 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 2047 helix: 0.92 (0.14), residues: 1490 sheet: -2.44 (0.79), residues: 25 loop : -1.37 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 9 TYR 0.015 0.001 TYR A 468 PHE 0.028 0.001 PHE B 445 TRP 0.050 0.002 TRP A 543 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00272 (17205) covalent geometry : angle 0.50688 (23220) hydrogen bonds : bond 0.03489 ( 1038) hydrogen bonds : angle 4.08726 ( 3081) metal coordination : bond 0.00794 ( 4) metal coordination : angle 4.07951 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8345 (tt) cc_final: 0.8081 (tt) REVERT: A 156 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6342 (mpp) REVERT: A 396 LYS cc_start: 0.7692 (mptt) cc_final: 0.7428 (mmmm) REVERT: A 468 TYR cc_start: 0.7472 (t80) cc_final: 0.7192 (t80) REVERT: B 156 MET cc_start: 0.6062 (mmt) cc_final: 0.5821 (mmt) REVERT: B 400 GLN cc_start: 0.6495 (mt0) cc_final: 0.6218 (mp10) REVERT: B 485 MET cc_start: 0.7067 (mmm) cc_final: 0.6834 (mmm) REVERT: G 5 LEU cc_start: 0.8422 (mp) cc_final: 0.8151 (mp) REVERT: G 19 LYS cc_start: 0.5648 (mmmt) cc_final: 0.5152 (mmmt) REVERT: I 219 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7306 (m-10) outliers start: 31 outliers final: 24 residues processed: 219 average time/residue: 0.1176 time to fit residues: 39.8576 Evaluate side-chains 213 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 161 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 343 HIS ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.174548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.137643 restraints weight = 22770.070| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.17 r_work: 0.3578 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17209 Z= 0.137 Angle : 0.512 8.754 23222 Z= 0.267 Chirality : 0.037 0.146 2531 Planarity : 0.004 0.052 2969 Dihedral : 4.414 75.011 2283 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.64 % Allowed : 15.73 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.19), residues: 2047 helix: 0.94 (0.14), residues: 1487 sheet: -2.37 (0.81), residues: 25 loop : -1.36 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 9 TYR 0.016 0.001 TYR A 468 PHE 0.031 0.001 PHE I 202 TRP 0.073 0.002 TRP A 543 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00320 (17205) covalent geometry : angle 0.51112 (23220) hydrogen bonds : bond 0.03547 ( 1038) hydrogen bonds : angle 4.09891 ( 3081) metal coordination : bond 0.00975 ( 4) metal coordination : angle 3.74905 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4094 Ramachandran restraints generated. 2047 Oldfield, 0 Emsley, 2047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.8299 (tt) cc_final: 0.8021 (tt) REVERT: A 156 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6318 (mpp) REVERT: A 396 LYS cc_start: 0.7677 (mptt) cc_final: 0.7409 (mmmm) REVERT: B 485 MET cc_start: 0.6954 (mmm) cc_final: 0.6711 (mmm) REVERT: G 5 LEU cc_start: 0.8424 (mp) cc_final: 0.8201 (mp) REVERT: E 146 MET cc_start: 0.7674 (mmt) cc_final: 0.7438 (mmp) REVERT: I 219 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.7266 (m-10) outliers start: 30 outliers final: 25 residues processed: 204 average time/residue: 0.1160 time to fit residues: 36.8927 Evaluate side-chains 210 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 165 CYS Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 229 CYS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain E residue 7 VAL Chi-restraints excluded: chain I residue 219 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 100 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 164 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 HIS B 400 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.170306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134427 restraints weight = 22402.736| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.97 r_work: 0.3508 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17209 Z= 0.153 Angle : 0.528 8.623 23222 Z= 0.275 Chirality : 0.037 0.140 2531 Planarity : 0.004 0.053 2969 Dihedral : 4.448 76.885 2283 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.75 % Allowed : 15.73 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.19), residues: 2047 helix: 0.92 (0.14), residues: 1480 sheet: -2.38 (0.81), residues: 25 loop : -1.38 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 9 TYR 0.021 0.001 TYR A 468 PHE 0.031 0.001 PHE I 202 TRP 0.072 0.002 TRP A 543 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00359 (17205) covalent geometry : angle 0.52664 (23220) hydrogen bonds : bond 0.03597 ( 1038) hydrogen bonds : angle 4.11917 ( 3081) metal coordination : bond 0.01149 ( 4) metal coordination : angle 3.82990 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4597.62 seconds wall clock time: 79 minutes 32.12 seconds (4772.12 seconds total)