Starting phenix.real_space_refine on Tue Nov 19 10:16:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jal_36129/11_2024/8jal_36129.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jal_36129/11_2024/8jal_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jal_36129/11_2024/8jal_36129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jal_36129/11_2024/8jal_36129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jal_36129/11_2024/8jal_36129.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jal_36129/11_2024/8jal_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-5513/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: 12.05, per 1000 atoms: 0.70 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: 4.79 Conformation dependent library (CDL) restraints added in 2.3 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: 1.92 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: 5.26 Time building geometry restraints manager: 5.26 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: 20.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 44.670 Find NCS groups from input model: 0.620 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.780 ------------------------------------------------------------------------------- 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 17597 Z= 0.220 Angle : 0.625 9.171 23744 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 *********************** 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 : 2.213 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: 0.3618 time to fit residues: 184.1696 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 : 2.025 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 17597 Z= 0.241 Angle : 0.551 8.152 23744 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 *********************** 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 : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 PHE cc_start: 0.8214 (t80) cc_final: 0.7997 (t80) REVERT: A 451 MET cc_start: 0.7810 (mmt) cc_final: 0.7525 (mmt) REVERT: E 85 VAL cc_start: 0.2154 (p) cc_final: 0.1943 (p) REVERT: E 218 TYR cc_start: 0.8327 (t80) cc_final: 0.7856 (t80) REVERT: B 159 TRP cc_start: 0.8446 (m-90) cc_final: 0.7812 (m-90) REVERT: B 289 ASP cc_start: 0.8261 (m-30) cc_final: 0.8030 (m-30) REVERT: B 451 MET cc_start: 0.7421 (mmp) cc_final: 0.6949 (mmp) REVERT: I 263 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7715 (tp) outliers start: 20 outliers final: 12 residues processed: 282 average time/residue: 0.3509 time to fit residues: 147.2573 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 : 2.142 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 C 42 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS I 267 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17597 Z= 0.362 Angle : 0.570 6.719 23744 Z= 0.301 Chirality : 0.040 0.281 2585 Planarity : 0.004 0.045 3038 Dihedral : 4.176 14.967 2331 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.61 % Allowed : 8.45 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.18), residues: 2091 helix: 0.47 (0.13), residues: 1489 sheet: -1.28 (0.91), residues: 25 loop : -1.27 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 159 HIS 0.007 0.001 HIS I 190 PHE 0.018 0.002 PHE A 424 TYR 0.021 0.002 TYR B 294 ARG 0.007 0.001 ARG C 43 *********************** 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 282 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7781 (mmt) cc_final: 0.7550 (mmt) REVERT: A 505 LEU cc_start: 0.8656 (mt) cc_final: 0.8373 (mp) REVERT: B 159 TRP cc_start: 0.8532 (m-90) cc_final: 0.7913 (m-90) REVERT: B 451 MET cc_start: 0.7571 (mmp) cc_final: 0.7078 (mmp) REVERT: I 75 ARG cc_start: 0.5303 (mtp180) cc_final: 0.4619 (mtp85) REVERT: I 206 ILE cc_start: 0.6516 (tp) cc_final: 0.6055 (mt) REVERT: I 263 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7790 (tp) outliers start: 30 outliers final: 17 residues processed: 270 average time/residue: 0.3257 time to fit residues: 130.8750 Evaluate side-chains 253 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 235 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 307 SER Chi-restraints excluded: chain A residue 377 SER 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 79 SER Chi-restraints excluded: chain I residue 243 LEU 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 186 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 I 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17597 Z= 0.276 Angle : 0.524 6.780 23744 Z= 0.277 Chirality : 0.038 0.265 2585 Planarity : 0.004 0.042 3038 Dihedral : 4.108 15.091 2331 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.55 % Allowed : 10.43 % Favored : 88.01 % 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: 0.11 (0.18), residues: 2091 helix: 0.66 (0.14), residues: 1495 sheet: -1.27 (0.90), residues: 25 loop : -1.26 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 135 HIS 0.007 0.001 HIS B 180 PHE 0.012 0.001 PHE B 101 TYR 0.014 0.001 TYR H 76 ARG 0.006 0.000 ARG B 30 *********************** 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 279 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7755 (mmt) cc_final: 0.7526 (mmt) REVERT: E 218 TYR cc_start: 0.8284 (t80) cc_final: 0.7854 (t80) REVERT: C 70 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8335 (mp10) REVERT: C 94 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7635 (m) REVERT: B 446 LYS cc_start: 0.7831 (tptp) cc_final: 0.7486 (mttp) REVERT: B 451 MET cc_start: 0.7610 (mmp) cc_final: 0.7095 (mmp) REVERT: B 483 TYR cc_start: 0.8891 (m-80) cc_final: 0.8614 (m-80) REVERT: G 28 LYS cc_start: 0.8016 (mppt) cc_final: 0.7635 (mppt) REVERT: I 32 ARG cc_start: 0.3932 (ttp80) cc_final: 0.3606 (ttp80) REVERT: I 72 LEU cc_start: 0.4223 (OUTLIER) cc_final: 0.3978 (tp) REVERT: I 75 ARG cc_start: 0.5236 (mtp180) cc_final: 0.4928 (ttm110) REVERT: I 263 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7823 (tp) outliers start: 29 outliers final: 18 residues processed: 264 average time/residue: 0.3292 time to fit residues: 128.2729 Evaluate side-chains 256 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 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 40 ASP 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 72 LEU Chi-restraints excluded: chain I residue 116 ASN 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 166 optimal weight: 0.3980 chunk 113 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 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** I 267 GLN I 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17597 Z= 0.225 Angle : 0.506 5.879 23744 Z= 0.268 Chirality : 0.038 0.422 2585 Planarity : 0.004 0.040 3038 Dihedral : 4.034 16.059 2331 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.61 % Allowed : 12.15 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2091 helix: 0.85 (0.14), residues: 1497 sheet: -1.19 (0.93), residues: 25 loop : -1.21 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 159 HIS 0.004 0.001 HIS B 180 PHE 0.012 0.001 PHE B 101 TYR 0.014 0.001 TYR H 76 ARG 0.006 0.000 ARG G 68 *********************** 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 274 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7764 (mmt) cc_final: 0.7542 (mmt) REVERT: E 218 TYR cc_start: 0.8270 (t80) cc_final: 0.7838 (t80) REVERT: E 297 MET cc_start: 0.5835 (mmp) cc_final: 0.5530 (mmp) REVERT: C 94 SER cc_start: 0.7880 (OUTLIER) cc_final: 0.7623 (m) REVERT: B 451 MET cc_start: 0.7652 (mmp) cc_final: 0.7224 (mmp) REVERT: F -5 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6544 (pp) REVERT: G 28 LYS cc_start: 0.8100 (mppt) cc_final: 0.7691 (mppt) REVERT: G 49 GLN cc_start: 0.7314 (pp30) cc_final: 0.7042 (pp30) REVERT: H 20 LYS cc_start: 0.8454 (tptm) cc_final: 0.8252 (tptm) REVERT: I 72 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.3750 (tp) REVERT: I 75 ARG cc_start: 0.5433 (mtp180) cc_final: 0.5058 (ttp80) REVERT: I 263 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7837 (tp) outliers start: 30 outliers final: 18 residues processed: 263 average time/residue: 0.3262 time to fit residues: 127.9201 Evaluate side-chains 250 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 2.237 ------------------------------------------------------------------------------- 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 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 H residue 60 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 116 ASN 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 67 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** I 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17597 Z= 0.237 Angle : 0.512 8.009 23744 Z= 0.270 Chirality : 0.038 0.270 2585 Planarity : 0.004 0.039 3038 Dihedral : 4.018 17.665 2331 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.55 % Allowed : 13.11 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.18), residues: 2091 helix: 0.97 (0.14), residues: 1491 sheet: -1.07 (0.95), residues: 25 loop : -1.20 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 135 HIS 0.005 0.001 HIS B 180 PHE 0.012 0.001 PHE B 101 TYR 0.014 0.001 TYR H 76 ARG 0.009 0.000 ARG I 89 *********************** 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 270 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7758 (mmt) cc_final: 0.7535 (mmt) REVERT: E 218 TYR cc_start: 0.8247 (t80) cc_final: 0.7830 (t80) REVERT: E 297 MET cc_start: 0.6014 (mmp) cc_final: 0.5695 (mmp) REVERT: C 94 SER cc_start: 0.7904 (OUTLIER) cc_final: 0.7635 (m) REVERT: B 149 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 451 MET cc_start: 0.7710 (mmp) cc_final: 0.7366 (mmp) REVERT: F -5 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6595 (pp) REVERT: G 28 LYS cc_start: 0.8124 (mppt) cc_final: 0.7875 (mppt) REVERT: G 49 GLN cc_start: 0.7214 (pp30) cc_final: 0.6860 (pp30) REVERT: H 20 LYS cc_start: 0.8498 (tptm) cc_final: 0.8294 (tptm) REVERT: I 72 LEU cc_start: 0.4011 (OUTLIER) cc_final: 0.3699 (tp) REVERT: I 263 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7830 (tp) outliers start: 29 outliers final: 17 residues processed: 260 average time/residue: 0.3188 time to fit residues: 124.0413 Evaluate side-chains 250 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 2.288 ------------------------------------------------------------------------------- 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 E residue 142 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain F residue -5 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 72 LEU 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 193 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 168 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 283 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17597 Z= 0.245 Angle : 0.517 7.324 23744 Z= 0.271 Chirality : 0.039 0.467 2585 Planarity : 0.004 0.039 3038 Dihedral : 4.013 19.599 2331 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.66 % Allowed : 13.22 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.18), residues: 2091 helix: 1.02 (0.14), residues: 1498 sheet: -0.96 (0.96), residues: 25 loop : -1.23 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 147 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 *********************** 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 268 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7761 (mmt) cc_final: 0.7529 (mmt) REVERT: E 218 TYR cc_start: 0.8263 (t80) cc_final: 0.7846 (t80) REVERT: C 94 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7701 (m) REVERT: B 149 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 293 ASP cc_start: 0.7772 (m-30) cc_final: 0.7568 (m-30) REVERT: B 451 MET cc_start: 0.7706 (mmp) cc_final: 0.7392 (mmp) REVERT: F -5 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6576 (pp) REVERT: G 28 LYS cc_start: 0.8116 (mppt) cc_final: 0.7670 (mppt) REVERT: G 49 GLN cc_start: 0.7158 (pp30) cc_final: 0.6936 (pp30) REVERT: I 72 LEU cc_start: 0.4337 (OUTLIER) cc_final: 0.3970 (tp) REVERT: I 263 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7844 (tp) outliers start: 31 outliers final: 20 residues processed: 257 average time/residue: 0.2978 time to fit residues: 116.8634 Evaluate side-chains 250 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 320 SER 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 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 20 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 72 LEU 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 123 optimal weight: 0.2980 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 126 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 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 565 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17597 Z= 0.224 Angle : 0.519 7.921 23744 Z= 0.270 Chirality : 0.038 0.295 2585 Planarity : 0.004 0.040 3038 Dihedral : 3.985 20.805 2331 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.55 % Allowed : 13.64 % Favored : 84.80 % 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: 0.65 (0.18), residues: 2091 helix: 1.09 (0.14), residues: 1494 sheet: -0.90 (0.97), residues: 25 loop : -1.17 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 147 HIS 0.005 0.001 HIS B 180 PHE 0.012 0.001 PHE E 277 TYR 0.014 0.001 TYR H 83 ARG 0.008 0.000 ARG G 68 *********************** 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 261 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7762 (mmt) cc_final: 0.7525 (mmt) REVERT: C 94 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7692 (m) REVERT: B 149 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 159 TRP cc_start: 0.8483 (m-90) cc_final: 0.8020 (m-90) REVERT: B 293 ASP cc_start: 0.7708 (m-30) cc_final: 0.7500 (m-30) REVERT: B 451 MET cc_start: 0.7699 (mmp) cc_final: 0.7367 (mmp) REVERT: F -5 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6587 (pp) REVERT: G 28 LYS cc_start: 0.8175 (mppt) cc_final: 0.7789 (mppt) REVERT: H 20 LYS cc_start: 0.8558 (tptm) cc_final: 0.8173 (tptm) REVERT: I 72 LEU cc_start: 0.4250 (OUTLIER) cc_final: 0.3891 (tp) REVERT: I 263 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7777 (tp) outliers start: 29 outliers final: 18 residues processed: 252 average time/residue: 0.2716 time to fit residues: 104.1566 Evaluate side-chains 251 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 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 H residue 67 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 72 LEU 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 181 optimal weight: 0.0980 chunk 191 optimal weight: 0.7980 chunk 174 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 57 optimal weight: 0.0470 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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** I 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17597 Z= 0.189 Angle : 0.521 7.714 23744 Z= 0.271 Chirality : 0.038 0.408 2585 Planarity : 0.004 0.040 3038 Dihedral : 3.951 21.361 2331 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.39 % Allowed : 14.07 % Favored : 84.54 % 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: 0.80 (0.19), residues: 2091 helix: 1.19 (0.14), residues: 1489 sheet: -0.79 (0.86), residues: 35 loop : -1.07 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 147 HIS 0.005 0.001 HIS B 180 PHE 0.013 0.001 PHE E 277 TYR 0.015 0.001 TYR A 468 ARG 0.008 0.000 ARG G 68 *********************** 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 262 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7781 (mmt) cc_final: 0.7549 (mmt) REVERT: C 94 SER cc_start: 0.7942 (OUTLIER) cc_final: 0.7701 (m) REVERT: B 149 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 278 ASP cc_start: 0.8472 (t0) cc_final: 0.8225 (t0) REVERT: B 451 MET cc_start: 0.7654 (mmp) cc_final: 0.7328 (mmp) REVERT: F -5 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6586 (pp) REVERT: G 28 LYS cc_start: 0.8151 (mppt) cc_final: 0.7797 (mppt) REVERT: H 20 LYS cc_start: 0.8529 (tptm) cc_final: 0.8248 (tptp) REVERT: I 263 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7758 (tp) outliers start: 26 outliers final: 18 residues processed: 252 average time/residue: 0.2677 time to fit residues: 103.0998 Evaluate side-chains 247 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 540 LEU Chi-restraints excluded: chain A residue 566 SER 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 H residue 67 SER 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 196 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 164 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 0.0980 chunk 130 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17597 Z= 0.205 Angle : 0.535 18.355 23744 Z= 0.275 Chirality : 0.038 0.287 2585 Planarity : 0.004 0.041 3038 Dihedral : 3.944 21.844 2331 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.39 % Allowed : 14.50 % Favored : 84.11 % 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: 0.80 (0.19), residues: 2091 helix: 1.19 (0.14), residues: 1492 sheet: -0.74 (0.86), residues: 35 loop : -1.07 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 147 HIS 0.005 0.001 HIS B 180 PHE 0.014 0.001 PHE E 277 TYR 0.015 0.001 TYR I 90 ARG 0.009 0.000 ARG G 68 ********************** 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 253 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8317 (tp) REVERT: A 451 MET cc_start: 0.7779 (mmt) cc_final: 0.7546 (mmt) REVERT: C 94 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7690 (m) REVERT: B 149 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8358 (mp) REVERT: B 168 ARG cc_start: 0.8496 (mtt180) cc_final: 0.8078 (mtp85) REVERT: B 278 ASP cc_start: 0.8476 (t0) cc_final: 0.8231 (t0) REVERT: B 451 MET cc_start: 0.7651 (mmp) cc_final: 0.7295 (mmp) REVERT: F -5 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6591 (pp) REVERT: G 28 LYS cc_start: 0.8154 (mppt) cc_final: 0.7776 (mppt) REVERT: H 20 LYS cc_start: 0.8529 (tptm) cc_final: 0.8251 (tptp) REVERT: I 263 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7762 (tp) outliers start: 26 outliers final: 20 residues processed: 245 average time/residue: 0.3102 time to fit residues: 115.4599 Evaluate side-chains 246 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE 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 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 H residue 67 SER Chi-restraints excluded: chain I residue 55 GLU Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 206 ILE 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 174 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 164 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 144 optimal weight: 0.9980 overall best weight: 0.2958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.176445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143183 restraints weight = 22476.191| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.82 r_work: 0.3440 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17597 Z= 0.172 Angle : 0.527 16.564 23744 Z= 0.272 Chirality : 0.037 0.338 2585 Planarity : 0.004 0.042 3038 Dihedral : 3.902 22.134 2331 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.34 % Allowed : 14.77 % Favored : 83.90 % 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: 0.94 (0.19), residues: 2091 helix: 1.30 (0.14), residues: 1487 sheet: -0.50 (0.87), residues: 37 loop : -1.03 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 35 HIS 0.005 0.001 HIS B 180 PHE 0.015 0.001 PHE E 277 TYR 0.016 0.001 TYR A 468 ARG 0.007 0.000 ARG B 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4319.13 seconds wall clock time: 120 minutes 4.65 seconds (7204.65 seconds total)