Starting phenix.real_space_refine on Sun Aug 24 10:38:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jal_36129/08_2025/8jal_36129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jal_36129/08_2025/8jal_36129.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/8jal_36129/08_2025/8jal_36129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jal_36129/08_2025/8jal_36129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jal_36129/08_2025/8jal_36129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jal_36129/08_2025/8jal_36129.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= 0.018 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 95 5.16 5 C 10997 2.51 5 N 2946 2.21 5 O 3187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 17226 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: "E" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2382 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} Chain breaks: 1 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} 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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} 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: "I" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2382 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 272} 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 59.108 77.117 96.769 1.00 20.56 S ATOM 9050 SG CYS B 54 62.938 76.722 96.047 1.00 27.85 S Time building chain proxies: 3.18, per 1000 atoms: 0.18 Number of scatterers: 17226 At special positions: 0 Unit cell: (112.34, 134.48, 201.72, 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 95 16.00 O 3187 8.00 N 2946 7.00 C 10997 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: 1.22 Conformation dependent library (CDL) restraints added in 722.8 milliseconds Enol-peptide restraints added in 953.7 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 B 54 " pdb="ZN ZN B 601 " - pdb=" SG CYS A 54 " Number of angles added : 2 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4042 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 5 sheets defined 76.3% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.753A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.649A pdb=" N HIS A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.144A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 153 removed outlier: 4.299A pdb=" N LYS A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 Processing helix chain 'A' and resid 178 through 199 removed outlier: 3.751A pdb=" N GLU A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HIS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 261 through 280 removed outlier: 3.563A pdb=" N ALA A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 302 removed outlier: 3.825A pdb=" N ASP A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 322 removed outlier: 3.510A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 Processing helix chain 'A' and resid 351 through 368 removed outlier: 4.215A pdb=" N HIS A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.590A pdb=" N SER A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 421 removed outlier: 3.655A pdb=" N ARG A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.561A 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 445 through 462 removed outlier: 3.868A pdb=" N GLN A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 484 Processing helix chain 'A' and resid 487 through 506 removed outlier: 4.168A pdb=" N LYS A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 513 through 526 removed outlier: 3.560A pdb=" N GLY A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 551 removed outlier: 3.677A pdb=" N ARG A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.711A pdb=" N VAL A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 removed outlier: 4.072A pdb=" N THR E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.623A pdb=" N PHE E 39 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 40 " --> pdb=" O ASN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 79 removed outlier: 3.526A pdb=" N LEU E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS E 71 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 105 removed outlier: 3.637A 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 150 removed outlier: 3.683A pdb=" N LEU E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 172 removed outlier: 3.519A pdb=" N ILE E 160 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET E 162 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 192 removed outlier: 3.722A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL E 189 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU E 192 " --> pdb=" O PHE E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 207 Processing helix chain 'E' and resid 207 through 219 Processing helix chain 'E' and resid 220 through 230 removed outlier: 3.503A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU E 229 " --> pdb=" O ASN E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 254 removed outlier: 3.779A pdb=" N GLU E 237 " --> pdb=" O SER E 233 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS E 252 " --> pdb=" O ILE E 248 " (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 269 removed outlier: 3.695A pdb=" N VAL E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 263 " --> pdb=" O TYR E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.591A pdb=" N HIS E 283 " --> pdb=" O HIS E 279 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 287 " --> pdb=" O HIS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'C' and resid 23 through 36 removed outlier: 3.690A pdb=" N LEU C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.553A pdb=" N CYS C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 47 through 52 removed outlier: 4.069A pdb=" N GLY D 50 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 83 removed outlier: 3.975A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.616A pdb=" N LEU D 101 " --> pdb=" O PRO D 97 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 28 through 33 removed outlier: 3.945A pdb=" N ARG B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 removed outlier: 3.543A pdb=" N ASP B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.847A pdb=" N GLU B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 71 removed outlier: 3.583A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 90 Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.094A pdb=" N LYS B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 175 removed outlier: 3.954A pdb=" N TRP B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 160 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.802A pdb=" N GLU B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 221 through 235 removed outlier: 3.741A pdb=" N LYS B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 261 through 280 removed outlier: 3.743A 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: 3.565A pdb=" N ALA B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 removed outlier: 3.503A pdb=" N TYR B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 368 removed outlier: 4.189A pdb=" N HIS B 366 " --> pdb=" O GLY B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 393 removed outlier: 4.334A pdb=" N ALA B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 387 " --> pdb=" O ALA B 383 " (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 463 Processing helix chain 'B' and resid 467 through 484 Processing helix chain 'B' and resid 487 through 507 removed outlier: 3.904A pdb=" N ALA B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU B 492 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 511 through 526 removed outlier: 4.204A pdb=" N TYR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 551 removed outlier: 3.719A pdb=" N ARG B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.862A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 577 removed outlier: 4.038A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 36 removed outlier: 4.158A pdb=" N LYS G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.544A pdb=" N GLN G 42 " --> pdb=" O PRO G 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 39 through 47 removed outlier: 3.535A pdb=" N SER H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 66 through 83 removed outlier: 4.326A pdb=" N LYS H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 98 No H-bonds generated for 'chain 'H' and resid 96 through 98' Processing helix chain 'H' and resid 99 through 111 Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.570A pdb=" N THR I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR I 20 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL I 25 " --> pdb=" O ILE I 21 " (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: 3.750A pdb=" N PHE I 39 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 78 removed outlier: 3.880A pdb=" N GLU I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 138 through 152 removed outlier: 3.592A pdb=" N LEU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL I 152 " --> pdb=" O ARG I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 172 removed outlier: 3.673A pdb=" N LEU I 159 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE I 160 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP I 170 " --> pdb=" O GLU I 166 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 186 removed outlier: 4.093A pdb=" N ILE I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE I 185 " --> pdb=" O ILE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'I' and resid 190 through 195 removed outlier: 3.579A pdb=" N GLN I 193 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR I 194 " --> pdb=" O VAL I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 207 removed outlier: 3.900A pdb=" N ILE I 206 " --> pdb=" O PHE I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 228 removed outlier: 3.686A pdb=" N GLN I 221 " --> pdb=" O GLU I 217 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 222 " --> pdb=" O TYR I 218 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA I 223 " --> pdb=" O TYR I 219 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 231 through 251 removed outlier: 4.190A pdb=" N MET I 236 " --> pdb=" O CYS I 232 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU I 237 " --> pdb=" O SER I 233 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS I 238 " --> pdb=" O GLN I 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG I 249 " --> pdb=" O ASP I 245 " (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 268 removed outlier: 3.640A pdb=" N VAL I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE I 263 " --> pdb=" O TYR I 259 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN I 268 " --> pdb=" O HIS I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 289 removed outlier: 4.493A pdb=" N LEU I 278 " --> pdb=" O HIS I 274 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS I 279 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA I 280 " --> pdb=" O GLN I 276 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS I 283 " --> pdb=" O HIS I 279 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 300 removed outlier: 3.898A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN I 296 " --> pdb=" O ASN I 292 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL I 299 " --> pdb=" O ALA I 295 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 18 Processing sheet with id=AA2, first strand: chain 'D' and resid 28 through 32 removed outlier: 3.698A pdb=" N ASN D 58 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.645A pdb=" N ALA G 73 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 78 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG G 43 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 28 through 31 removed outlier: 3.791A pdb=" N LEU H 21 " --> pdb=" O PHE H 29 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 3189 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: 3.60 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5618 1.34 - 1.46: 3928 1.46 - 1.58: 7909 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 17597 Sorted by residual: bond pdb=" CA CYS I 46 " pdb=" C CYS I 46 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.37e-02 5.33e+03 2.48e+00 bond pdb=" CA VAL I 47 " pdb=" C VAL I 47 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.81e+00 bond pdb=" CA ASP G 48 " pdb=" CB ASP G 48 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.41e+00 bond pdb=" CB THR A 290 " pdb=" CG2 THR A 290 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.36e+00 bond pdb=" N ASP A 302 " pdb=" CA ASP A 302 " ideal model delta sigma weight residual 1.457 1.476 -0.018 1.58e-02 4.01e+03 1.34e+00 ... (remaining 17592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 23218 1.83 - 3.67: 437 3.67 - 5.50: 69 5.50 - 7.34: 15 7.34 - 9.17: 5 Bond angle restraints: 23744 Sorted by residual: angle pdb=" C PHE C 85 " pdb=" CA PHE C 85 " pdb=" CB PHE C 85 " ideal model delta sigma weight residual 115.79 110.12 5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" N VAL A 115 " pdb=" CA VAL A 115 " pdb=" C VAL A 115 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" C ASP G 47 " pdb=" N ASP G 48 " pdb=" CA ASP G 48 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C THR H 84 " pdb=" N ASN H 85 " pdb=" CA ASN H 85 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C VAL A 301 " pdb=" N ASP A 302 " pdb=" CA ASP A 302 " ideal model delta sigma weight residual 123.93 129.83 -5.90 1.54e+00 4.22e-01 1.47e+01 ... (remaining 23739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 9447 17.21 - 34.43: 944 34.43 - 51.64: 159 51.64 - 68.86: 36 68.86 - 86.07: 26 Dihedral angle restraints: 10612 sinusoidal: 4351 harmonic: 6261 Sorted by residual: dihedral pdb=" CA GLN A 487 " pdb=" C GLN A 487 " pdb=" N TYR A 488 " pdb=" CA TYR A 488 " ideal model delta harmonic sigma weight residual -180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP B 559 " pdb=" CB ASP B 559 " pdb=" CG ASP B 559 " pdb=" OD1 ASP B 559 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ARG E 148 " pdb=" C ARG E 148 " pdb=" N LYS E 149 " pdb=" CA LYS E 149 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 10609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2401 0.073 - 0.146: 173 0.146 - 0.219: 10 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 2585 Sorted by residual: chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA ASN H 85 " pdb=" N ASN H 85 " pdb=" C ASN H 85 " pdb=" CB ASN H 85 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA ASP G 48 " pdb=" N ASP G 48 " pdb=" C ASP G 48 " pdb=" CB ASP G 48 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2582 not shown) Planarity restraints: 3038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 91 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.63e+00 pdb=" N PRO G 92 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 92 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 92 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 48 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO H 49 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 49 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 49 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 159 " -0.016 2.00e-02 2.50e+03 1.36e-02 4.60e+00 pdb=" CG TRP B 159 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 159 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 159 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 159 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 159 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 159 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 159 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 159 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 159 " -0.001 2.00e-02 2.50e+03 ... (remaining 3035 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3938 2.78 - 3.31: 17077 3.31 - 3.84: 29794 3.84 - 4.37: 35166 4.37 - 4.90: 60042 Nonbonded interactions: 146017 Sorted by model distance: nonbonded pdb=" OD1 ASP B 247 " pdb=" NZ LYS B 286 " model vdw 2.255 3.120 nonbonded pdb=" OG SER C 94 " pdb=" OD2 ASP D 25 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR E 219 " pdb=" OE1 GLU E 246 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR B 14 " pdb=" OD2 ASP B 42 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR G 23 " pdb=" OE1 GLU G 26 " model vdw 2.284 3.040 ... (remaining 146012 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' 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: 11.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 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:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.003 0.042 17601 Z= 0.152 Angle : 0.625 9.171 23746 Z= 0.332 Chirality : 0.042 0.365 2585 Planarity : 0.005 0.069 3038 Dihedral : 14.489 86.073 6570 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -1.29 (0.17), residues: 2091 helix: -0.49 (0.13), residues: 1458 sheet: -1.05 (1.43), residues: 10 loop : -1.43 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 318 TYR 0.017 0.002 TYR A 488 PHE 0.015 0.001 PHE A 160 TRP 0.037 0.002 TRP B 159 HIS 0.015 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00336 (17597) covalent geometry : angle 0.62501 (23744) hydrogen bonds : bond 0.17956 ( 1080) hydrogen bonds : angle 7.25574 ( 3189) metal coordination : bond 0.00767 ( 4) metal coordination : angle 2.76260 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8001 (t80) cc_final: 0.7760 (t80) REVERT: E 85 VAL cc_start: 0.2219 (p) cc_final: 0.1995 (p) REVERT: B 159 TRP cc_start: 0.8345 (m-90) cc_final: 0.7332 (m-90) REVERT: B 451 MET cc_start: 0.7258 (mmp) cc_final: 0.6815 (mmp) REVERT: G 28 LYS cc_start: 0.8039 (mppt) cc_final: 0.7813 (mppt) REVERT: I 116 ASN cc_start: 0.3779 (t0) cc_final: 0.3260 (t0) REVERT: I 156 GLN cc_start: 0.5393 (tp-100) cc_final: 0.5011 (tp40) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1628 time to fit residues: 83.2512 Evaluate side-chains 240 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 GLN A 565 GLN E 73 HIS E 225 ASN B 38 ASN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136462 restraints weight = 22546.960| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.12 r_work: 0.3235 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17601 Z= 0.137 Angle : 0.537 8.513 23746 Z= 0.287 Chirality : 0.038 0.306 2585 Planarity : 0.004 0.054 3038 Dihedral : 4.170 18.363 2331 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.02 % Allowed : 6.15 % Favored : 92.83 % 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: -0.25 (0.18), residues: 2091 helix: 0.35 (0.13), residues: 1491 sheet: -1.62 (0.89), residues: 25 loop : -1.24 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 56 TYR 0.019 0.001 TYR I 90 PHE 0.012 0.001 PHE A 160 TRP 0.018 0.001 TRP B 159 HIS 0.012 0.001 HIS I 190 Details of bonding type rmsd covalent geometry : bond 0.00295 (17597) covalent geometry : angle 0.53672 (23744) hydrogen bonds : bond 0.04732 ( 1080) hydrogen bonds : angle 4.92569 ( 3189) metal coordination : bond 0.00895 ( 4) metal coordination : angle 3.09235 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 271 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 TYR cc_start: 0.8323 (t80) cc_final: 0.7760 (t80) REVERT: B 159 TRP cc_start: 0.8309 (m-90) cc_final: 0.8014 (m-90) REVERT: B 226 TYR cc_start: 0.8425 (t80) cc_final: 0.8211 (t80) REVERT: B 289 ASP cc_start: 0.7931 (m-30) cc_final: 0.7660 (m-30) REVERT: B 451 MET cc_start: 0.7481 (mmp) cc_final: 0.7084 (mmp) REVERT: I 73 HIS cc_start: 0.8067 (t-170) cc_final: 0.7625 (t-170) REVERT: I 169 ASN cc_start: 0.8128 (m-40) cc_final: 0.7843 (m-40) REVERT: I 263 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7584 (tp) outliers start: 19 outliers final: 12 residues processed: 281 average time/residue: 0.1508 time to fit residues: 62.9808 Evaluate side-chains 255 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 0.0000 chunk 160 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 565 GLN ** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133365 restraints weight = 22859.209| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.27 r_work: 0.3201 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17601 Z= 0.138 Angle : 0.509 6.852 23746 Z= 0.269 Chirality : 0.037 0.253 2585 Planarity : 0.004 0.048 3038 Dihedral : 4.034 14.974 2331 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.34 % Allowed : 8.19 % Favored : 90.48 % 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: 0.12 (0.18), residues: 2091 helix: 0.66 (0.13), residues: 1488 sheet: -1.28 (0.91), residues: 25 loop : -1.21 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 43 TYR 0.019 0.001 TYR A 468 PHE 0.010 0.001 PHE B 101 TRP 0.011 0.001 TRP B 159 HIS 0.006 0.001 HIS I 190 Details of bonding type rmsd covalent geometry : bond 0.00314 (17597) covalent geometry : angle 0.50738 (23744) hydrogen bonds : bond 0.04185 ( 1080) hydrogen bonds : angle 4.59211 ( 3189) metal coordination : bond 0.00892 ( 4) metal coordination : angle 3.82733 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 LEU cc_start: 0.8611 (mt) cc_final: 0.8322 (mp) REVERT: E 218 TYR cc_start: 0.8271 (t80) cc_final: 0.7665 (t80) REVERT: B 159 TRP cc_start: 0.8412 (m-90) cc_final: 0.8112 (m-90) REVERT: B 226 TYR cc_start: 0.8454 (t80) cc_final: 0.8208 (t80) REVERT: B 451 MET cc_start: 0.7542 (mmp) cc_final: 0.7099 (mmp) REVERT: I 73 HIS cc_start: 0.8047 (t-170) cc_final: 0.7773 (t-170) REVERT: I 169 ASN cc_start: 0.8263 (m-40) cc_final: 0.7999 (m-40) outliers start: 25 outliers final: 14 residues processed: 269 average time/residue: 0.1470 time to fit residues: 59.5021 Evaluate side-chains 252 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain I residue 79 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 116 optimal weight: 0.4980 chunk 185 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 110 optimal weight: 0.3980 chunk 142 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 565 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 178 GLN I 267 GLN I 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133889 restraints weight = 22717.492| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.28 r_work: 0.3182 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17601 Z= 0.150 Angle : 0.502 6.635 23746 Z= 0.265 Chirality : 0.038 0.319 2585 Planarity : 0.004 0.043 3038 Dihedral : 3.985 14.561 2331 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.61 % Allowed : 10.01 % Favored : 88.39 % 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: 2091 helix: 0.83 (0.14), residues: 1491 sheet: -1.06 (0.94), residues: 25 loop : -1.23 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 30 TYR 0.017 0.001 TYR A 468 PHE 0.011 0.001 PHE B 101 TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00350 (17597) covalent geometry : angle 0.50117 (23744) hydrogen bonds : bond 0.03933 ( 1080) hydrogen bonds : angle 4.44087 ( 3189) metal coordination : bond 0.00983 ( 4) metal coordination : angle 4.00602 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 151 MET cc_start: 0.8513 (tpp) cc_final: 0.8283 (tpp) REVERT: E 218 TYR cc_start: 0.8332 (t80) cc_final: 0.7759 (t80) REVERT: E 297 MET cc_start: 0.5603 (mmp) cc_final: 0.5220 (mmp) REVERT: C 94 SER cc_start: 0.7808 (OUTLIER) cc_final: 0.7576 (m) REVERT: B 226 TYR cc_start: 0.8512 (t80) cc_final: 0.8291 (t80) REVERT: B 451 MET cc_start: 0.7572 (mmp) cc_final: 0.7115 (mmp) REVERT: G 49 GLN cc_start: 0.7288 (pp30) cc_final: 0.7024 (pp30) REVERT: I 75 ARG cc_start: 0.8329 (mtp180) cc_final: 0.8113 (ttp80) REVERT: I 169 ASN cc_start: 0.8328 (m-40) cc_final: 0.8066 (m-40) REVERT: I 263 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7629 (tp) outliers start: 30 outliers final: 17 residues processed: 266 average time/residue: 0.1491 time to fit residues: 59.5792 Evaluate side-chains 249 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 157 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 161 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN A 565 GLN E 36 ASN C 42 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS ** I 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.130910 restraints weight = 22557.148| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.36 r_work: 0.3156 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17601 Z= 0.158 Angle : 0.511 12.929 23746 Z= 0.268 Chirality : 0.038 0.290 2585 Planarity : 0.004 0.066 3038 Dihedral : 3.965 15.144 2331 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 11.45 % Favored : 87.27 % 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: 0.44 (0.18), residues: 2091 helix: 0.91 (0.14), residues: 1494 sheet: -1.00 (0.94), residues: 25 loop : -1.18 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 89 TYR 0.020 0.001 TYR I 90 PHE 0.011 0.001 PHE B 101 TRP 0.008 0.001 TRP E 35 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00371 (17597) covalent geometry : angle 0.50914 (23744) hydrogen bonds : bond 0.03887 ( 1080) hydrogen bonds : angle 4.38204 ( 3189) metal coordination : bond 0.01005 ( 4) metal coordination : angle 4.13199 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 151 MET cc_start: 0.8554 (tpp) cc_final: 0.8244 (tpp) REVERT: E 218 TYR cc_start: 0.8297 (t80) cc_final: 0.7704 (t80) REVERT: C 94 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7695 (m) REVERT: B 226 TYR cc_start: 0.8538 (t80) cc_final: 0.8326 (t80) REVERT: B 445 PHE cc_start: 0.5833 (m-10) cc_final: 0.5592 (m-80) REVERT: B 451 MET cc_start: 0.7648 (mmp) cc_final: 0.7159 (mmp) REVERT: G 28 LYS cc_start: 0.7911 (mppt) cc_final: 0.7488 (mppt) REVERT: G 49 GLN cc_start: 0.7207 (pp30) cc_final: 0.6881 (pp30) REVERT: I 75 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7635 (ttm110) REVERT: I 86 MET cc_start: 0.7830 (tpp) cc_final: 0.7574 (tpp) REVERT: I 206 ILE cc_start: 0.5847 (tt) cc_final: 0.5451 (mt) REVERT: I 263 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7606 (tp) outliers start: 24 outliers final: 19 residues processed: 256 average time/residue: 0.1494 time to fit residues: 57.7825 Evaluate side-chains 249 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 198 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 205 optimal weight: 7.9990 chunk 183 optimal weight: 0.5980 chunk 196 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN A 565 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 156 GLN I 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.162355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128786 restraints weight = 22526.383| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.42 r_work: 0.3133 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17601 Z= 0.169 Angle : 0.514 9.024 23746 Z= 0.269 Chirality : 0.038 0.437 2585 Planarity : 0.004 0.045 3038 Dihedral : 3.965 15.882 2331 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.71 % Allowed : 11.50 % Favored : 86.78 % 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: 0.52 (0.18), residues: 2091 helix: 0.98 (0.14), residues: 1495 sheet: -0.91 (0.96), residues: 25 loop : -1.17 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 68 TYR 0.014 0.001 TYR H 76 PHE 0.011 0.001 PHE B 101 TRP 0.008 0.001 TRP A 135 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00400 (17597) covalent geometry : angle 0.51228 (23744) hydrogen bonds : bond 0.03864 ( 1080) hydrogen bonds : angle 4.34147 ( 3189) metal coordination : bond 0.01070 ( 4) metal coordination : angle 4.23821 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 TYR cc_start: 0.8301 (t80) cc_final: 0.7723 (t80) REVERT: C 94 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7734 (m) REVERT: B 14 TYR cc_start: 0.8957 (t80) cc_final: 0.8630 (t80) REVERT: B 149 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 445 PHE cc_start: 0.5956 (m-10) cc_final: 0.5733 (m-80) REVERT: G 28 LYS cc_start: 0.7952 (mppt) cc_final: 0.7507 (mppt) REVERT: G 49 GLN cc_start: 0.7223 (pp30) cc_final: 0.6767 (pp30) REVERT: I 75 ARG cc_start: 0.8480 (mtp180) cc_final: 0.7630 (ttm110) REVERT: I 206 ILE cc_start: 0.5779 (tt) cc_final: 0.5361 (mt) REVERT: I 263 ILE cc_start: 0.7879 (OUTLIER) cc_final: 0.7580 (tp) outliers start: 32 outliers final: 22 residues processed: 259 average time/residue: 0.1451 time to fit residues: 57.2216 Evaluate side-chains 253 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 124 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.0040 chunk 89 optimal weight: 0.9980 chunk 196 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN E 283 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN I 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.162519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129229 restraints weight = 22521.323| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.35 r_work: 0.3150 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17601 Z= 0.148 Angle : 0.512 11.268 23746 Z= 0.267 Chirality : 0.037 0.286 2585 Planarity : 0.004 0.040 3038 Dihedral : 3.934 17.639 2331 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.66 % Allowed : 12.25 % Favored : 86.09 % 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: 0.61 (0.18), residues: 2091 helix: 1.05 (0.14), residues: 1497 sheet: -0.85 (0.96), residues: 25 loop : -1.18 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 68 TYR 0.014 0.001 TYR H 76 PHE 0.012 0.001 PHE E 277 TRP 0.007 0.001 TRP A 135 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00348 (17597) covalent geometry : angle 0.51071 (23744) hydrogen bonds : bond 0.03781 ( 1080) hydrogen bonds : angle 4.29979 ( 3189) metal coordination : bond 0.00997 ( 4) metal coordination : angle 4.32980 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 151 MET cc_start: 0.8560 (tpp) cc_final: 0.8345 (tpp) REVERT: E 218 TYR cc_start: 0.8318 (t80) cc_final: 0.7789 (t80) REVERT: C 94 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7762 (m) REVERT: B 14 TYR cc_start: 0.8941 (t80) cc_final: 0.8628 (t80) REVERT: B 149 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8453 (mp) REVERT: B 159 TRP cc_start: 0.8464 (m-90) cc_final: 0.8204 (m-90) REVERT: B 446 LYS cc_start: 0.7886 (tptp) cc_final: 0.7409 (mttp) REVERT: F -5 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7195 (pp) REVERT: G 28 LYS cc_start: 0.8003 (mppt) cc_final: 0.7567 (mppt) REVERT: G 49 GLN cc_start: 0.7188 (pp30) cc_final: 0.6834 (pp30) REVERT: I 75 ARG cc_start: 0.8451 (mtp180) cc_final: 0.8245 (ttp80) REVERT: I 206 ILE cc_start: 0.5744 (tt) cc_final: 0.5318 (mt) REVERT: I 263 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7613 (tp) outliers start: 31 outliers final: 23 residues processed: 263 average time/residue: 0.1420 time to fit residues: 56.9724 Evaluate side-chains 256 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 131 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.170603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138420 restraints weight = 22910.980| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.35 r_work: 0.3330 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17601 Z= 0.206 Angle : 0.557 11.197 23746 Z= 0.288 Chirality : 0.040 0.493 2585 Planarity : 0.004 0.039 3038 Dihedral : 3.985 18.887 2331 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.98 % Allowed : 11.77 % Favored : 86.25 % 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: 0.54 (0.18), residues: 2091 helix: 1.01 (0.14), residues: 1497 sheet: -0.93 (0.95), residues: 25 loop : -1.23 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 68 TYR 0.018 0.001 TYR H 83 PHE 0.013 0.001 PHE E 277 TRP 0.009 0.001 TRP A 135 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00492 (17597) covalent geometry : angle 0.55522 (23744) hydrogen bonds : bond 0.03917 ( 1080) hydrogen bonds : angle 4.36310 ( 3189) metal coordination : bond 0.01295 ( 4) metal coordination : angle 4.54902 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 TYR cc_start: 0.8185 (t80) cc_final: 0.7621 (t80) REVERT: C 94 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7757 (m) REVERT: B 149 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8476 (mp) REVERT: B 408 ASP cc_start: 0.8726 (m-30) cc_final: 0.8454 (m-30) REVERT: B 451 MET cc_start: 0.7625 (mmp) cc_final: 0.7211 (mmp) REVERT: F -5 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7177 (pp) REVERT: G 28 LYS cc_start: 0.7928 (mppt) cc_final: 0.7430 (mppt) REVERT: G 49 GLN cc_start: 0.7046 (pp30) cc_final: 0.6665 (pp30) REVERT: I 162 MET cc_start: 0.7635 (ttm) cc_final: 0.7429 (ttp) REVERT: I 206 ILE cc_start: 0.5964 (tt) cc_final: 0.5527 (mt) REVERT: I 263 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7487 (tp) outliers start: 37 outliers final: 26 residues processed: 258 average time/residue: 0.1467 time to fit residues: 57.2816 Evaluate side-chains 260 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 107 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 184 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.175499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141991 restraints weight = 22561.853| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.02 r_work: 0.3402 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17601 Z= 0.129 Angle : 0.529 19.629 23746 Z= 0.271 Chirality : 0.037 0.306 2585 Planarity : 0.004 0.039 3038 Dihedral : 3.926 20.253 2331 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.77 % Allowed : 12.73 % Favored : 85.50 % 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: 0.78 (0.19), residues: 2091 helix: 1.19 (0.14), residues: 1493 sheet: -0.86 (0.95), residues: 25 loop : -1.12 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 68 TYR 0.015 0.001 TYR A 468 PHE 0.015 0.001 PHE E 277 TRP 0.007 0.001 TRP B 159 HIS 0.005 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00295 (17597) covalent geometry : angle 0.52712 (23744) hydrogen bonds : bond 0.03696 ( 1080) hydrogen bonds : angle 4.25649 ( 3189) metal coordination : bond 0.00869 ( 4) metal coordination : angle 4.40860 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 247 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: C 94 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7931 (m) REVERT: B 120 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8696 (mm) REVERT: B 149 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8413 (mp) REVERT: B 408 ASP cc_start: 0.8826 (m-30) cc_final: 0.8466 (m-30) REVERT: F -5 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7210 (pp) REVERT: G 28 LYS cc_start: 0.7949 (mppt) cc_final: 0.7460 (mppt) REVERT: G 49 GLN cc_start: 0.7047 (pp30) cc_final: 0.6743 (pp30) REVERT: I 263 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7485 (tp) outliers start: 33 outliers final: 21 residues processed: 262 average time/residue: 0.1385 time to fit residues: 55.6293 Evaluate side-chains 259 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 62 optimal weight: 0.0470 chunk 131 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 0.0870 chunk 182 optimal weight: 0.4980 chunk 193 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.142227 restraints weight = 22407.003| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.09 r_work: 0.3401 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17601 Z= 0.141 Angle : 0.546 18.827 23746 Z= 0.279 Chirality : 0.038 0.392 2585 Planarity : 0.004 0.040 3038 Dihedral : 3.929 20.657 2331 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.50 % Allowed : 13.06 % Favored : 85.45 % 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: 0.81 (0.19), residues: 2091 helix: 1.19 (0.14), residues: 1499 sheet: -0.69 (0.97), residues: 27 loop : -1.06 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 68 TYR 0.015 0.001 TYR A 468 PHE 0.015 0.001 PHE E 277 TRP 0.009 0.001 TRP I 35 HIS 0.004 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00326 (17597) covalent geometry : angle 0.54462 (23744) hydrogen bonds : bond 0.03718 ( 1080) hydrogen bonds : angle 4.24722 ( 3189) metal coordination : bond 0.00867 ( 4) metal coordination : angle 4.30458 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4182 Ramachandran restraints generated. 2091 Oldfield, 0 Emsley, 2091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 247 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: C 94 SER cc_start: 0.7948 (OUTLIER) cc_final: 0.7679 (m) REVERT: B 14 TYR cc_start: 0.8958 (t80) cc_final: 0.8578 (t80) REVERT: B 149 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8399 (mp) REVERT: B 408 ASP cc_start: 0.8629 (m-30) cc_final: 0.8334 (m-30) REVERT: B 445 PHE cc_start: 0.5930 (m-10) cc_final: 0.5669 (m-80) REVERT: B 451 MET cc_start: 0.7633 (mmp) cc_final: 0.7223 (mmp) REVERT: F -5 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7259 (pp) REVERT: G 28 LYS cc_start: 0.7917 (mppt) cc_final: 0.7458 (mppt) REVERT: G 49 GLN cc_start: 0.6938 (pp30) cc_final: 0.6681 (pp30) REVERT: I 75 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8384 (ttp80) REVERT: I 169 ASN cc_start: 0.8287 (m-40) cc_final: 0.8043 (m-40) REVERT: I 263 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7510 (tp) outliers start: 28 outliers final: 22 residues processed: 259 average time/residue: 0.1348 time to fit residues: 52.9056 Evaluate side-chains 259 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 163 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 152 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 94 optimal weight: 0.0000 chunk 144 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.177143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142013 restraints weight = 22974.752| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.40 r_work: 0.3353 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17601 Z= 0.143 Angle : 0.538 16.897 23746 Z= 0.276 Chirality : 0.038 0.312 2585 Planarity : 0.004 0.042 3038 Dihedral : 3.914 21.642 2331 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.50 % Allowed : 13.38 % Favored : 85.13 % 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: 0.85 (0.19), residues: 2091 helix: 1.23 (0.14), residues: 1486 sheet: -0.79 (0.97), residues: 25 loop : -1.04 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 30 TYR 0.014 0.001 TYR H 76 PHE 0.015 0.001 PHE E 277 TRP 0.008 0.001 TRP B 159 HIS 0.004 0.001 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00334 (17597) covalent geometry : angle 0.53701 (23744) hydrogen bonds : bond 0.03702 ( 1080) hydrogen bonds : angle 4.22505 ( 3189) metal coordination : bond 0.00895 ( 4) metal coordination : angle 4.26233 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.49 seconds wall clock time: 76 minutes 18.80 seconds (4578.80 seconds total)