Starting phenix.real_space_refine on Mon Jun 16 22:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jal_36129/06_2025/8jal_36129.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jal_36129/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jal_36129/06_2025/8jal_36129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jal_36129/06_2025/8jal_36129.map" model { file = "/net/cci-nas-00/data/ceres_data/8jal_36129/06_2025/8jal_36129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jal_36129/06_2025/8jal_36129.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.96, per 1000 atoms: 0.69 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: 4.38 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.42 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: 5.49 Time building geometry restraints manager: 5.21 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 44.720 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (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 TRP 0.037 0.002 TRP B 159 HIS 0.015 0.001 HIS B 410 PHE 0.015 0.001 PHE A 160 TYR 0.017 0.002 TYR A 488 ARG 0.008 0.001 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.17956 ( 1080) hydrogen bonds : angle 7.25574 ( 3189) metal coordination : bond 0.00767 ( 4) metal coordination : angle 2.76260 ( 2) covalent geometry : bond 0.00336 (17597) covalent geometry : angle 0.62501 (23744) *********************** 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 : 1.767 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: 0.3247 time to fit residues: 165.1813 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 : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 120 optimal weight: 0.2980 chunk 187 optimal weight: 0.7980 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 400 GLN A 482 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133872 restraints weight = 22615.111| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.22 r_work: 0.3192 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17601 Z= 0.162 Angle : 0.552 8.152 23746 Z= 0.294 Chirality : 0.038 0.312 2585 Planarity : 0.004 0.053 3038 Dihedral : 4.195 18.672 2331 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.07 % Allowed : 6.31 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2091 helix: 0.30 (0.13), residues: 1492 sheet: -1.54 (0.90), residues: 25 loop : -1.27 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 159 HIS 0.013 0.001 HIS I 190 PHE 0.013 0.001 PHE A 322 TYR 0.020 0.002 TYR I 90 ARG 0.006 0.001 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 1080) hydrogen bonds : angle 4.92139 ( 3189) metal coordination : bond 0.01178 ( 4) metal coordination : angle 3.58823 ( 2) covalent geometry : bond 0.00368 (17597) covalent geometry : angle 0.55071 (23744) *********************** 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 291 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 271 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7889 (mmt) cc_final: 0.7648 (mmt) REVERT: E 218 TYR cc_start: 0.8307 (t80) cc_final: 0.7731 (t80) REVERT: B 159 TRP cc_start: 0.8407 (m-90) cc_final: 0.8014 (m-90) REVERT: B 226 TYR cc_start: 0.8482 (t80) cc_final: 0.8276 (t80) REVERT: B 289 ASP cc_start: 0.7970 (m-30) cc_final: 0.7710 (m-30) REVERT: B 451 MET cc_start: 0.7510 (mmp) cc_final: 0.7095 (mmp) REVERT: I 73 HIS cc_start: 0.8110 (t-170) cc_final: 0.7652 (t-170) REVERT: I 169 ASN cc_start: 0.8144 (m-40) cc_final: 0.7858 (m-40) REVERT: I 263 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7535 (tp) outliers start: 20 outliers final: 12 residues processed: 282 average time/residue: 0.3105 time to fit residues: 129.7380 Evaluate side-chains 253 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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 377 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 277 PHE 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 159 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 205 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 chunk 171 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 395 ASN A 565 GLN E 36 ASN ** 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 88 HIS I 267 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.163473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130793 restraints weight = 22566.695| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.25 r_work: 0.3178 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17601 Z= 0.158 Angle : 0.518 6.696 23746 Z= 0.274 Chirality : 0.038 0.259 2585 Planarity : 0.004 0.047 3038 Dihedral : 4.070 14.846 2331 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.61 % Allowed : 8.08 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2091 helix: 0.62 (0.13), residues: 1490 sheet: -1.19 (0.92), residues: 25 loop : -1.23 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 159 HIS 0.006 0.001 HIS B 180 PHE 0.015 0.001 PHE A 424 TYR 0.015 0.001 TYR B 294 ARG 0.007 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1080) hydrogen bonds : angle 4.61477 ( 3189) metal coordination : bond 0.01104 ( 4) metal coordination : angle 4.09332 ( 2) covalent geometry : bond 0.00366 (17597) covalent geometry : angle 0.51702 (23744) *********************** 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: 30 poor density : 250 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7898 (mmt) cc_final: 0.7670 (mmt) REVERT: A 505 LEU cc_start: 0.8610 (mt) cc_final: 0.8320 (mp) REVERT: E 218 TYR cc_start: 0.8299 (t80) cc_final: 0.7711 (t80) REVERT: C 70 GLN cc_start: 0.8693 (mp10) cc_final: 0.8460 (mp10) REVERT: B 159 TRP cc_start: 0.8394 (m-90) cc_final: 0.8078 (m-90) REVERT: B 451 MET cc_start: 0.7595 (mmp) cc_final: 0.7166 (mmp) REVERT: I 73 HIS cc_start: 0.7984 (t-170) cc_final: 0.7679 (t-170) REVERT: I 206 ILE cc_start: 0.6810 (tp) cc_final: 0.6226 (mt) REVERT: I 263 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7575 (tp) outliers start: 30 outliers final: 19 residues processed: 267 average time/residue: 0.3006 time to fit residues: 121.2081 Evaluate side-chains 258 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 240 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain E residue 76 VAL 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 21 ILE Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 263 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 0.0030 chunk 181 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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** I 267 GLN I 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131733 restraints weight = 22431.586| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.13 r_work: 0.3197 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17601 Z= 0.138 Angle : 0.495 6.741 23746 Z= 0.262 Chirality : 0.037 0.272 2585 Planarity : 0.004 0.044 3038 Dihedral : 3.987 14.756 2331 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.55 % Allowed : 9.63 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2091 helix: 0.84 (0.14), residues: 1491 sheet: -1.03 (0.94), residues: 25 loop : -1.20 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS B 180 PHE 0.011 0.001 PHE B 101 TYR 0.014 0.001 TYR H 76 ARG 0.006 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 1080) hydrogen bonds : angle 4.45270 ( 3189) metal coordination : bond 0.00957 ( 4) metal coordination : angle 4.11559 ( 2) covalent geometry : bond 0.00319 (17597) covalent geometry : angle 0.49344 (23744) *********************** 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 277 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 TYR cc_start: 0.8339 (t80) cc_final: 0.7774 (t80) REVERT: C 70 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8473 (mp10) REVERT: C 94 SER cc_start: 0.7784 (OUTLIER) cc_final: 0.7560 (m) REVERT: B 451 MET cc_start: 0.7591 (mmp) cc_final: 0.7153 (mmp) REVERT: G 28 LYS cc_start: 0.7954 (mppt) cc_final: 0.7573 (mppt) REVERT: G 49 GLN cc_start: 0.7308 (pp30) cc_final: 0.7052 (pp30) REVERT: I 73 HIS cc_start: 0.8017 (t-170) cc_final: 0.7814 (t-170) REVERT: I 75 ARG cc_start: 0.8301 (mtp180) cc_final: 0.8074 (ttp80) REVERT: I 263 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7631 (tp) outliers start: 29 outliers final: 18 residues processed: 263 average time/residue: 0.3117 time to fit residues: 123.1483 Evaluate side-chains 254 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 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 41 GLU Chi-restraints excluded: chain C residue 70 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 187 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.162803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129642 restraints weight = 22684.881| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.38 r_work: 0.3156 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17601 Z= 0.156 Angle : 0.511 12.337 23746 Z= 0.267 Chirality : 0.038 0.388 2585 Planarity : 0.004 0.064 3038 Dihedral : 3.972 14.863 2331 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.77 % Allowed : 10.86 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2091 helix: 0.93 (0.14), residues: 1494 sheet: -0.90 (0.96), residues: 25 loop : -1.15 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 135 HIS 0.004 0.001 HIS B 180 PHE 0.011 0.001 PHE B 101 TYR 0.028 0.001 TYR I 90 ARG 0.008 0.000 ARG I 89 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1080) hydrogen bonds : angle 4.39524 ( 3189) metal coordination : bond 0.00993 ( 4) metal coordination : angle 4.19690 ( 2) covalent geometry : bond 0.00366 (17597) covalent geometry : angle 0.50916 (23744) *********************** 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 276 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 TYR cc_start: 0.8296 (t80) cc_final: 0.7711 (t80) REVERT: C 70 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8517 (mp10) REVERT: C 94 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7712 (m) REVERT: B 445 PHE cc_start: 0.6078 (m-10) cc_final: 0.5792 (m-80) REVERT: B 451 MET cc_start: 0.7612 (mmp) cc_final: 0.7156 (mmp) REVERT: G 28 LYS cc_start: 0.7908 (mppt) cc_final: 0.7482 (mppt) REVERT: G 49 GLN cc_start: 0.7189 (pp30) cc_final: 0.6855 (pp30) REVERT: I 73 HIS cc_start: 0.8158 (t-170) cc_final: 0.7889 (t-170) REVERT: I 75 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8203 (ttp80) REVERT: I 263 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7587 (tp) outliers start: 33 outliers final: 20 residues processed: 261 average time/residue: 0.3371 time to fit residues: 132.8248 Evaluate side-chains 254 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 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 41 GLU Chi-restraints excluded: chain C residue 70 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 116 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 142 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN A 565 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 178 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 = 0.4114 r_free = 0.4114 target = 0.176243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138722 restraints weight = 23504.176| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.85 r_work: 0.3291 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17601 Z= 0.144 Angle : 0.501 8.871 23746 Z= 0.262 Chirality : 0.037 0.270 2585 Planarity : 0.004 0.043 3038 Dihedral : 3.954 16.818 2331 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.87 % Allowed : 11.99 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2091 helix: 1.05 (0.14), residues: 1493 sheet: -0.83 (0.97), residues: 25 loop : -1.13 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 135 HIS 0.004 0.001 HIS B 180 PHE 0.012 0.001 PHE E 277 TYR 0.014 0.001 TYR H 76 ARG 0.007 0.000 ARG G 68 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 1080) hydrogen bonds : angle 4.32626 ( 3189) metal coordination : bond 0.00935 ( 4) metal coordination : angle 4.19871 ( 2) covalent geometry : bond 0.00337 (17597) covalent geometry : angle 0.49955 (23744) *********************** 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 274 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 3.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 TYR cc_start: 0.8116 (t80) cc_final: 0.7506 (t80) REVERT: E 297 MET cc_start: 0.6224 (mmp) cc_final: 0.5949 (mmp) REVERT: C 94 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7741 (m) REVERT: B 149 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8365 (mp) REVERT: B 446 LYS cc_start: 0.7959 (tptp) cc_final: 0.7453 (mttp) REVERT: B 451 MET cc_start: 0.7574 (mmp) cc_final: 0.7059 (mmp) REVERT: F -5 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7196 (pp) REVERT: G 28 LYS cc_start: 0.7747 (mppt) cc_final: 0.7324 (mppt) REVERT: G 49 GLN cc_start: 0.6942 (pp30) cc_final: 0.6525 (pp30) REVERT: I 263 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7272 (tp) outliers start: 35 outliers final: 22 residues processed: 260 average time/residue: 0.3619 time to fit residues: 144.4674 Evaluate side-chains 252 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 2.463 ------------------------------------------------------------------------------- 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 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 E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 40 ASP 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 546 LEU Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain F residue -5 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 116 ASN 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 99 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 190 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 145 optimal weight: 3.9990 chunk 172 optimal weight: 0.0870 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN ** 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 = 0.4116 r_free = 0.4116 target = 0.176426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139943 restraints weight = 23407.388| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.82 r_work: 0.3290 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17601 Z= 0.136 Angle : 0.514 11.175 23746 Z= 0.267 Chirality : 0.038 0.447 2585 Planarity : 0.004 0.045 3038 Dihedral : 3.923 17.901 2331 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.61 % Allowed : 12.41 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2091 helix: 1.12 (0.14), residues: 1494 sheet: -0.80 (0.97), residues: 25 loop : -1.13 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 228 HIS 0.005 0.001 HIS B 180 PHE 0.012 0.001 PHE E 277 TYR 0.014 0.001 TYR H 76 ARG 0.008 0.000 ARG G 68 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1080) hydrogen bonds : angle 4.29075 ( 3189) metal coordination : bond 0.00871 ( 4) metal coordination : angle 4.28055 ( 2) covalent geometry : bond 0.00314 (17597) covalent geometry : angle 0.51232 (23744) *********************** 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 267 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7770 (m) REVERT: B 149 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8370 (mp) REVERT: B 451 MET cc_start: 0.7634 (mmp) cc_final: 0.7209 (mmp) REVERT: F -5 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7207 (pp) REVERT: G 28 LYS cc_start: 0.7768 (mppt) cc_final: 0.7346 (mppt) REVERT: G 49 GLN cc_start: 0.6920 (pp30) cc_final: 0.6586 (pp30) REVERT: I 75 ARG cc_start: 0.8616 (mtp180) cc_final: 0.8349 (ttp80) REVERT: I 263 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7323 (tp) outliers start: 30 outliers final: 20 residues processed: 257 average time/residue: 0.3648 time to fit residues: 143.4219 Evaluate side-chains 252 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 2.231 ------------------------------------------------------------------------------- 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 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 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 116 ASN 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 27 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 0.0370 chunk 83 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 GLN E 283 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.173779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137754 restraints weight = 23274.394| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.67 r_work: 0.3291 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17601 Z= 0.158 Angle : 0.526 13.218 23746 Z= 0.272 Chirality : 0.038 0.297 2585 Planarity : 0.004 0.046 3038 Dihedral : 3.926 19.382 2331 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.82 % Allowed : 12.63 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2091 helix: 1.15 (0.14), residues: 1492 sheet: -0.75 (0.86), residues: 35 loop : -1.16 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 228 HIS 0.005 0.001 HIS B 180 PHE 0.013 0.001 PHE E 277 TYR 0.018 0.001 TYR I 90 ARG 0.008 0.000 ARG G 68 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1080) hydrogen bonds : angle 4.27737 ( 3189) metal coordination : bond 0.01006 ( 4) metal coordination : angle 4.29804 ( 2) covalent geometry : bond 0.00373 (17597) covalent geometry : angle 0.52482 (23744) *********************** 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 278 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 244 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 151 MET cc_start: 0.8584 (tpp) cc_final: 0.8359 (tpp) REVERT: E 247 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: C 94 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7796 (m) REVERT: B 14 TYR cc_start: 0.8993 (t80) cc_final: 0.8617 (t80) REVERT: B 149 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 446 LYS cc_start: 0.8287 (mttp) cc_final: 0.8022 (mttp) REVERT: B 451 MET cc_start: 0.7676 (mmp) cc_final: 0.7405 (mmp) REVERT: F -5 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7198 (pp) REVERT: G 28 LYS cc_start: 0.7863 (mppt) cc_final: 0.7419 (mppt) REVERT: G 49 GLN cc_start: 0.6991 (pp30) cc_final: 0.6621 (pp30) REVERT: I 75 ARG cc_start: 0.8657 (mtp180) cc_final: 0.8239 (ttp80) REVERT: I 263 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7422 (tp) outliers start: 34 outliers final: 21 residues processed: 268 average time/residue: 0.3575 time to fit residues: 146.8757 Evaluate side-chains 258 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 2.296 ------------------------------------------------------------------------------- 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 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 149 LEU Chi-restraints excluded: chain B residue 334 GLU 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 116 ASN 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 154 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 163 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 140 optimal weight: 0.0070 chunk 98 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.172605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139846 restraints weight = 22919.933| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.28 r_work: 0.3345 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17601 Z= 0.143 Angle : 0.534 19.634 23746 Z= 0.273 Chirality : 0.038 0.442 2585 Planarity : 0.004 0.045 3038 Dihedral : 3.922 20.281 2331 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.55 % Allowed : 13.27 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2091 helix: 1.23 (0.14), residues: 1483 sheet: -0.76 (0.86), residues: 35 loop : -1.06 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.005 0.001 HIS B 180 PHE 0.015 0.001 PHE E 277 TYR 0.014 0.001 TYR A 468 ARG 0.008 0.000 ARG G 68 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1080) hydrogen bonds : angle 4.23823 ( 3189) metal coordination : bond 0.00923 ( 4) metal coordination : angle 4.27748 ( 2) covalent geometry : bond 0.00334 (17597) covalent geometry : angle 0.53246 (23744) *********************** 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 273 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 151 MET cc_start: 0.8529 (tpp) cc_final: 0.8287 (tpp) REVERT: E 247 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: C 94 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7711 (m) REVERT: B 149 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 445 PHE cc_start: 0.5893 (m-10) cc_final: 0.5637 (m-10) REVERT: B 451 MET cc_start: 0.7609 (mmp) cc_final: 0.7331 (mmp) REVERT: F -5 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7184 (pp) REVERT: G 28 LYS cc_start: 0.7856 (mppt) cc_final: 0.7415 (mppt) REVERT: G 49 GLN cc_start: 0.6924 (pp30) cc_final: 0.6601 (pp30) REVERT: I 75 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8244 (ttp80) REVERT: I 263 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7358 (tp) outliers start: 29 outliers final: 23 residues processed: 263 average time/residue: 0.2885 time to fit residues: 114.9304 Evaluate side-chains 261 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 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 120 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 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 116 ASN 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 166 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 204 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.175703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139085 restraints weight = 23348.294| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.78 r_work: 0.3296 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17601 Z= 0.147 Angle : 0.541 18.593 23746 Z= 0.277 Chirality : 0.038 0.325 2585 Planarity : 0.004 0.043 3038 Dihedral : 3.923 21.129 2331 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.61 % Allowed : 13.38 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2091 helix: 1.22 (0.14), residues: 1486 sheet: -0.75 (0.96), residues: 25 loop : -1.06 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS B 180 PHE 0.016 0.001 PHE E 277 TYR 0.014 0.001 TYR H 76 ARG 0.009 0.000 ARG G 68 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 1080) hydrogen bonds : angle 4.23266 ( 3189) metal coordination : bond 0.00935 ( 4) metal coordination : angle 4.30228 ( 2) covalent geometry : bond 0.00345 (17597) covalent geometry : angle 0.53981 (23744) ********************** 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 271 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 151 MET cc_start: 0.8584 (tpp) cc_final: 0.8353 (tpp) REVERT: E 247 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: C 94 SER cc_start: 0.8085 (OUTLIER) cc_final: 0.7803 (m) REVERT: B 14 TYR cc_start: 0.8987 (t80) cc_final: 0.8611 (t80) REVERT: B 149 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 168 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8173 (mtp85) REVERT: B 445 PHE cc_start: 0.5932 (m-10) cc_final: 0.5646 (m-80) REVERT: B 451 MET cc_start: 0.7656 (mmp) cc_final: 0.7360 (mmp) REVERT: F -5 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7309 (pp) REVERT: G 28 LYS cc_start: 0.7873 (mppt) cc_final: 0.7416 (mppt) REVERT: G 49 GLN cc_start: 0.6908 (pp30) cc_final: 0.6561 (pp30) REVERT: I 75 ARG cc_start: 0.8624 (mtp180) cc_final: 0.8322 (ttp80) REVERT: I 263 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7297 (tp) outliers start: 30 outliers final: 23 residues processed: 260 average time/residue: 0.3830 time to fit residues: 152.4797 Evaluate side-chains 263 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU 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 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 120 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 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 116 ASN 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 20 optimal weight: 0.0980 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 173 optimal weight: 0.0030 chunk 103 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.173352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140553 restraints weight = 22768.861| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.18 r_work: 0.3364 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17601 Z= 0.130 Angle : 0.532 17.276 23746 Z= 0.273 Chirality : 0.038 0.372 2585 Planarity : 0.004 0.043 3038 Dihedral : 3.909 21.609 2331 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.50 % Allowed : 13.64 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2091 helix: 1.28 (0.14), residues: 1483 sheet: -0.53 (0.99), residues: 27 loop : -1.00 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS B 180 PHE 0.024 0.001 PHE E 277 TYR 0.014 0.001 TYR I 90 ARG 0.007 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 1080) hydrogen bonds : angle 4.18508 ( 3189) metal coordination : bond 0.00822 ( 4) metal coordination : angle 4.26605 ( 2) covalent geometry : bond 0.00300 (17597) covalent geometry : angle 0.53029 (23744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9075.78 seconds wall clock time: 162 minutes 36.39 seconds (9756.39 seconds total)