Starting phenix.real_space_refine on Tue May 5 20:52:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ub8_64002/05_2026/9ub8_64002.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ub8_64002/05_2026/9ub8_64002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ub8_64002/05_2026/9ub8_64002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ub8_64002/05_2026/9ub8_64002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ub8_64002/05_2026/9ub8_64002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ub8_64002/05_2026/9ub8_64002.map" } resolution = 4.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 20772 2.51 5 N 5063 2.21 5 O 5785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31758 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4428 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 21, 'TRANS': 535} Chain breaks: 1 Chain: "B" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3173 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 374} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4419 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3857 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 454} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 4420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4420 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 37, 'TRANS': 520} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3179 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain: "G" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3856 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 454} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4426 Classifications: {'peptide': 558} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 520} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 7.25, per 1000 atoms: 0.23 Number of scatterers: 31758 At special positions: 0 Unit cell: (157.94, 148.4, 221.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 5785 8.00 N 5063 7.00 C 20772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 246 " - pdb=" SG CYS C 254 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 246 " - pdb=" SG CYS H 254 " distance=2.03 Simple disulfide: pdb=" SG CYS H 290 " - pdb=" SG CYS H 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 336 " - pdb=" SG CYS H 361 " distance=2.03 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: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7580 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 26 sheets defined 49.7% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 23 through 41 Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.601A pdb=" N TRP A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 103 removed outlier: 3.504A pdb=" N TRP A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 removed outlier: 3.563A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.536A pdb=" N HIS A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.642A pdb=" N GLY A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.782A pdb=" N VAL A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.881A pdb=" N THR A 263 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.971A pdb=" N ALA A 294 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 295 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 331 removed outlier: 4.031A pdb=" N ILE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.778A pdb=" N ASN A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.034A pdb=" N TYR A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 378 removed outlier: 3.791A pdb=" N VAL A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.921A pdb=" N PHE A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 468 removed outlier: 3.945A pdb=" N TYR A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 528 through 543 Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 564 through 577 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 3 through 23 Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.710A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 removed outlier: 3.848A pdb=" N LEU B 77 " --> pdb=" O PHE B 73 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 106 removed outlier: 3.698A pdb=" N PHE B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 123 removed outlier: 3.805A pdb=" N LEU B 118 " --> pdb=" O TRP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 136 through 152 removed outlier: 4.576A pdb=" N ILE B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 186 through 212 removed outlier: 3.656A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 230 removed outlier: 4.340A pdb=" N TYR B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.360A pdb=" N GLU B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 242 through 247' Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.825A pdb=" N ALA B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.696A pdb=" N THR B 292 " --> pdb=" O TRP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.531A pdb=" N THR B 312 " --> pdb=" O PRO B 309 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 4.580A pdb=" N GLY B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 318 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 344 removed outlier: 4.463A pdb=" N SER B 324 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Proline residue: B 336 - end of helix Processing helix chain 'B' and resid 349 through 381 removed outlier: 4.416A pdb=" N PHE B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 364 " --> pdb=" O TYR B 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 23 Processing helix chain 'E' and resid 23 through 41 removed outlier: 3.627A pdb=" N ALA E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 68 through 83 removed outlier: 3.657A pdb=" N TRP E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 150 through 164 Processing helix chain 'E' and resid 183 through 195 removed outlier: 3.720A pdb=" N HIS E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 248 removed outlier: 3.626A pdb=" N VAL E 238 " --> pdb=" O ASN E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.891A pdb=" N THR E 263 " --> pdb=" O ASP E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 283 Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 315 through 331 removed outlier: 3.924A pdb=" N ILE E 321 " --> pdb=" O THR E 317 " (cutoff:3.500A) Proline residue: E 322 - end of helix removed outlier: 3.788A pdb=" N ASN E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 358 removed outlier: 4.189A pdb=" N TYR E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 378 removed outlier: 3.811A pdb=" N VAL E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 364 " --> pdb=" O SER E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 412 removed outlier: 3.545A pdb=" N PHE E 412 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 429 removed outlier: 3.974A pdb=" N MET E 422 " --> pdb=" O SER E 418 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 424 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 468 removed outlier: 3.942A pdb=" N TYR E 447 " --> pdb=" O GLU E 443 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET E 466 " --> pdb=" O THR E 462 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE E 467 " --> pdb=" O SER E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 480 Processing helix chain 'E' and resid 481 through 485 removed outlier: 3.724A pdb=" N VAL E 485 " --> pdb=" O MET E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 543 Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 564 through 577 Processing helix chain 'E' and resid 579 through 588 Processing helix chain 'E' and resid 588 through 598 Processing helix chain 'D' and resid 2 through 31 removed outlier: 3.708A pdb=" N PHE D 14 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Proline residue: D 24 - end of helix removed outlier: 3.522A pdb=" N THR D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 71 through 86 removed outlier: 4.046A pdb=" N GLN D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 109 removed outlier: 3.915A pdb=" N GLU D 104 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 161 removed outlier: 3.533A pdb=" N THR D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 208 through 223 Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.882A pdb=" N ASP D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 270 removed outlier: 4.278A pdb=" N MET D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 356 removed outlier: 3.798A pdb=" N MET D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR D 346 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 401 removed outlier: 4.134A pdb=" N THR D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 430 removed outlier: 3.953A pdb=" N SER D 411 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 458 removed outlier: 3.522A pdb=" N ASN D 440 " --> pdb=" O ASP D 436 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 496 removed outlier: 4.006A pdb=" N VAL D 476 " --> pdb=" O HIS D 472 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) Proline residue: D 479 - end of helix Proline residue: D 483 - end of helix Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.749A pdb=" N LEU C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.620A pdb=" N ALA C 117 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 155 removed outlier: 4.161A pdb=" N GLY C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 Processing helix chain 'C' and resid 201 through 205 removed outlier: 4.043A pdb=" N ASN C 205 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.992A pdb=" N LEU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 225' Processing helix chain 'C' and resid 267 through 275 Processing helix chain 'C' and resid 314 through 319 removed outlier: 3.683A pdb=" N PHE C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 removed outlier: 3.645A pdb=" N ILE C 457 " --> pdb=" O GLN C 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 457' Processing helix chain 'C' and resid 549 through 573 removed outlier: 3.952A pdb=" N ILE C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 23 removed outlier: 3.554A pdb=" N ASN F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 32 removed outlier: 3.714A pdb=" N GLN F 29 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN F 32 " --> pdb=" O GLN F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 54 removed outlier: 3.603A pdb=" N LEU F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 77 removed outlier: 3.719A pdb=" N LEU F 77 " --> pdb=" O PHE F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 106 removed outlier: 3.656A pdb=" N ILE F 84 " --> pdb=" O SER F 80 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 106 " --> pdb=" O VAL F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 123 Processing helix chain 'F' and resid 123 through 132 Processing helix chain 'F' and resid 136 through 152 removed outlier: 4.624A pdb=" N ILE F 150 " --> pdb=" O SER F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 171 through 175 removed outlier: 3.734A pdb=" N ILE F 174 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 182 removed outlier: 3.815A pdb=" N GLY F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 212 removed outlier: 3.723A pdb=" N LEU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 223 Processing helix chain 'F' and resid 223 through 230 removed outlier: 3.913A pdb=" N ILE F 227 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.673A pdb=" N PHE F 243 " --> pdb=" O LEU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 265 removed outlier: 3.745A pdb=" N ALA F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 273 Processing helix chain 'F' and resid 277 through 292 removed outlier: 3.595A pdb=" N ALA F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 306 removed outlier: 3.655A pdb=" N ALA F 301 " --> pdb=" O SER F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 315 removed outlier: 3.802A pdb=" N THR F 312 " --> pdb=" O PRO F 309 " (cutoff:3.500A) Proline residue: F 313 - end of helix Processing helix chain 'F' and resid 320 through 344 removed outlier: 4.119A pdb=" N SER F 324 " --> pdb=" O TYR F 320 " (cutoff:3.500A) Proline residue: F 336 - end of helix Processing helix chain 'F' and resid 349 through 381 removed outlier: 4.336A pdb=" N PHE F 353 " --> pdb=" O ASN F 349 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE F 364 " --> pdb=" O TYR F 360 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 365 " --> pdb=" O ALA F 361 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F 366 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 367 " --> pdb=" O ALA F 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 31 removed outlier: 3.669A pdb=" N PHE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Proline residue: G 24 - end of helix removed outlier: 3.659A pdb=" N THR G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 100 through 108 removed outlier: 3.980A pdb=" N GLU G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 163 through 169 Processing helix chain 'G' and resid 208 through 223 Proline residue: G 218 - end of helix Processing helix chain 'G' and resid 253 through 260 removed outlier: 3.656A pdb=" N ASP G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS G 260 " --> pdb=" O PHE G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 270 removed outlier: 3.803A pdb=" N MET G 270 " --> pdb=" O GLU G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 341 through 356 removed outlier: 4.136A pdb=" N TYR G 346 " --> pdb=" O GLU G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 401 removed outlier: 3.810A pdb=" N THR G 371 " --> pdb=" O SER G 367 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG G 377 " --> pdb=" O ASP G 373 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU G 378 " --> pdb=" O SER G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 430 removed outlier: 3.807A pdb=" N SER G 411 " --> pdb=" O PRO G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 458 removed outlier: 3.555A pdb=" N PHE G 457 " --> pdb=" O CYS G 453 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE G 458 " --> pdb=" O GLU G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 497 removed outlier: 4.119A pdb=" N VAL G 476 " --> pdb=" O HIS G 472 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR G 477 " --> pdb=" O MET G 473 " (cutoff:3.500A) Proline residue: G 479 - end of helix Proline residue: G 483 - end of helix removed outlier: 3.708A pdb=" N LYS G 497 " --> pdb=" O TYR G 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 93 removed outlier: 3.661A pdb=" N LEU H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 114 through 119 Processing helix chain 'H' and resid 136 through 155 removed outlier: 3.778A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 162 Processing helix chain 'H' and resid 163 through 167 removed outlier: 3.746A pdb=" N ARG H 166 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 213 Processing helix chain 'H' and resid 220 through 225 removed outlier: 4.007A pdb=" N LEU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU H 225 " --> pdb=" O LEU H 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 225' Processing helix chain 'H' and resid 268 through 274 Processing helix chain 'H' and resid 314 through 319 removed outlier: 3.746A pdb=" N PHE H 318 " --> pdb=" O LEU H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 457 removed outlier: 3.634A pdb=" N ILE H 457 " --> pdb=" O GLN H 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 453 through 457' Processing helix chain 'H' and resid 506 through 510 removed outlier: 3.631A pdb=" N HIS H 509 " --> pdb=" O ASP H 506 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY H 510 " --> pdb=" O ALA H 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 506 through 510' Processing helix chain 'H' and resid 549 through 573 removed outlier: 3.606A pdb=" N ILE H 553 " --> pdb=" O PRO H 549 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.696A pdb=" N LEU A 344 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 113 removed outlier: 6.678A pdb=" N ALA A 134 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A 205 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 301 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 303 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 304 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A 223 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LYS A 306 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 221 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS A 308 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN A 310 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE A 217 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 441 through 442 removed outlier: 6.674A pdb=" N ILE A 441 " --> pdb=" O LYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA5, first strand: chain 'E' and resid 49 through 50 removed outlier: 3.538A pdb=" N LEU E 344 " --> pdb=" O VAL E 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 107 through 113 removed outlier: 6.710A pdb=" N GLU E 133 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE E 174 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N MET E 135 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL E 176 " --> pdb=" O MET E 135 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU E 137 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER E 178 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL E 139 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA E 134 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA E 205 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 301 " --> pdb=" O GLU E 204 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN E 310 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE E 218 " --> pdb=" O ASN E 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 441 through 442 removed outlier: 6.352A pdb=" N ILE E 488 " --> pdb=" O SER E 602 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 98 removed outlier: 6.246A pdb=" N LEU D 55 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N GLN D 95 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 57 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU D 97 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL D 59 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N VAL D 116 " --> pdb=" O PRO D 58 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR D 60 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU D 118 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS D 62 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU D 120 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 228 through 237 removed outlier: 8.646A pdb=" N VAL D 322 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN D 280 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE D 324 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA D 282 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AB2, first strand: chain 'C' and resid 193 through 196 removed outlier: 3.519A pdb=" N TRP C 129 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP C 235 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 41 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN C 57 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 37 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ARG C 334 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU C 38 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N CYS C 336 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU C 40 " --> pdb=" O CYS C 336 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AB4, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.580A pdb=" N LEU C 348 " --> pdb=" O PHE C 355 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 396 through 401 removed outlier: 3.597A pdb=" N TYR C 491 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN C 492 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N SER C 441 " --> pdb=" O GLN C 492 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N ASP C 494 " --> pdb=" O LEU C 439 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N LEU C 439 " --> pdb=" O ASP C 494 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 458 through 464 removed outlier: 6.323A pdb=" N THR C 478 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS C 461 " --> pdb=" O GLU C 476 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU C 476 " --> pdb=" O LYS C 461 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 463 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N HIS C 474 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS C 424 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 530 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 511 through 513 removed outlier: 3.550A pdb=" N LEU C 537 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 391 through 393 Processing sheet with id=AB9, first strand: chain 'G' and resid 92 through 98 removed outlier: 6.148A pdb=" N LEU G 55 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN G 95 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE G 57 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU G 97 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL G 59 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N VAL G 116 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR G 60 " --> pdb=" O VAL G 116 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LEU G 118 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS G 62 " --> pdb=" O LEU G 118 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU G 120 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS G 119 " --> pdb=" O VAL G 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 228 through 235 removed outlier: 8.786A pdb=" N LEU G 279 " --> pdb=" O ASN G 189 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS G 191 " --> pdb=" O LEU G 279 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU G 281 " --> pdb=" O HIS G 191 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER G 193 " --> pdb=" O LEU G 281 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE G 283 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR G 195 " --> pdb=" O ILE G 283 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN G 326 " --> pdb=" O VAL G 284 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AC3, first strand: chain 'H' and resid 193 through 196 removed outlier: 4.120A pdb=" N TRP H 129 " --> pdb=" O HIS H 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 262 " --> pdb=" O PHE H 54 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN H 57 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP H 37 " --> pdb=" O GLN H 57 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N ARG H 334 " --> pdb=" O TYR H 36 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU H 38 " --> pdb=" O ARG H 334 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N CYS H 336 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU H 40 " --> pdb=" O CYS H 336 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 132 through 134 Processing sheet with id=AC5, first strand: chain 'H' and resid 310 through 313 Processing sheet with id=AC6, first strand: chain 'H' and resid 396 through 402 removed outlier: 4.023A pdb=" N GLY H 410 " --> pdb=" O THR H 402 " (cutoff:3.500A) removed outlier: 11.167A pdb=" N ASP H 486 " --> pdb=" O ILE H 444 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N ILE H 444 " --> pdb=" O ASP H 486 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N VAL H 488 " --> pdb=" O LEU H 442 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N LEU H 442 " --> pdb=" O VAL H 488 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N THR H 490 " --> pdb=" O SER H 440 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N SER H 440 " --> pdb=" O THR H 490 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN H 492 " --> pdb=" O TYR H 438 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 458 through 464 removed outlier: 6.377A pdb=" N THR H 478 " --> pdb=" O LEU H 459 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS H 461 " --> pdb=" O GLU H 476 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU H 476 " --> pdb=" O LYS H 461 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR H 463 " --> pdb=" O HIS H 474 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HIS H 474 " --> pdb=" O TYR H 463 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS H 424 " --> pdb=" O LEU H 521 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR H 530 " --> pdb=" O VAL H 520 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 511 through 513 1566 hydrogen bonds defined for protein. 4464 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: 5.86 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9871 1.34 - 1.46: 8179 1.46 - 1.58: 14336 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 32618 Sorted by residual: bond pdb=" CA SER C 110 " pdb=" CB SER C 110 " ideal model delta sigma weight residual 1.536 1.484 0.052 1.53e-02 4.27e+03 1.14e+01 bond pdb=" N ASN B 55 " pdb=" CA ASN B 55 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.00e-02 1.00e+04 8.54e+00 bond pdb=" N ASN A 544 " pdb=" CA ASN A 544 " ideal model delta sigma weight residual 1.457 1.418 0.039 1.41e-02 5.03e+03 7.51e+00 bond pdb=" N PHE A 148 " pdb=" CA PHE A 148 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.02e+00 bond pdb=" N LEU A 344 " pdb=" CA LEU A 344 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.78e+00 ... (remaining 32613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 43109 1.90 - 3.79: 1133 3.79 - 5.69: 176 5.69 - 7.58: 27 7.58 - 9.48: 5 Bond angle restraints: 44450 Sorted by residual: angle pdb=" CA PHE A 148 " pdb=" CB PHE A 148 " pdb=" CG PHE A 148 " ideal model delta sigma weight residual 113.80 120.85 -7.05 1.00e+00 1.00e+00 4.96e+01 angle pdb=" C PHE A 148 " pdb=" N ASN A 149 " pdb=" CA ASN A 149 " ideal model delta sigma weight residual 122.77 115.00 7.77 1.33e+00 5.65e-01 3.42e+01 angle pdb=" N TYR F 172 " pdb=" CA TYR F 172 " pdb=" CB TYR F 172 " ideal model delta sigma weight residual 110.42 104.33 6.09 1.18e+00 7.18e-01 2.67e+01 angle pdb=" N VAL G 182 " pdb=" CA VAL G 182 " pdb=" C VAL G 182 " ideal model delta sigma weight residual 111.91 107.70 4.21 8.90e-01 1.26e+00 2.23e+01 angle pdb=" C PHE A 148 " pdb=" CA PHE A 148 " pdb=" CB PHE A 148 " ideal model delta sigma weight residual 109.65 117.43 -7.78 1.71e+00 3.42e-01 2.07e+01 ... (remaining 44445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 17392 16.80 - 33.61: 1481 33.61 - 50.41: 228 50.41 - 67.22: 60 67.22 - 84.02: 29 Dihedral angle restraints: 19190 sinusoidal: 7494 harmonic: 11696 Sorted by residual: dihedral pdb=" CB CYS C 156 " pdb=" SG CYS C 156 " pdb=" SG CYS C 202 " pdb=" CB CYS C 202 " ideal model delta sinusoidal sigma weight residual -86.00 -170.02 84.02 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS H 156 " pdb=" SG CYS H 156 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 172.27 -79.27 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS H 290 " pdb=" SG CYS H 290 " pdb=" SG CYS H 301 " pdb=" CB CYS H 301 " ideal model delta sinusoidal sigma weight residual 93.00 20.39 72.61 1 1.00e+01 1.00e-02 6.73e+01 ... (remaining 19187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3891 0.050 - 0.099: 966 0.099 - 0.149: 199 0.149 - 0.198: 13 0.198 - 0.248: 5 Chirality restraints: 5074 Sorted by residual: chirality pdb=" CG LEU D 94 " pdb=" CB LEU D 94 " pdb=" CD1 LEU D 94 " pdb=" CD2 LEU D 94 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE D 307 " pdb=" CA ILE D 307 " pdb=" CG1 ILE D 307 " pdb=" CG2 ILE D 307 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG C 399 " pdb=" N ARG C 399 " pdb=" C ARG C 399 " pdb=" CB ARG C 399 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5071 not shown) Planarity restraints: 5578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 341 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C PHE A 341 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE A 341 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE A 342 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 54 " 0.244 9.50e-02 1.11e+02 1.09e-01 7.35e+00 pdb=" NE ARG B 54 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 54 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 54 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 54 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 166 " 0.019 2.00e-02 2.50e+03 1.58e-02 6.24e+00 pdb=" CG TRP E 166 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 166 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E 166 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 166 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 166 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 166 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 166 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 166 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 166 " 0.001 2.00e-02 2.50e+03 ... (remaining 5575 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3094 2.74 - 3.28: 33140 3.28 - 3.82: 52403 3.82 - 4.36: 60178 4.36 - 4.90: 103089 Nonbonded interactions: 251904 Sorted by model distance: nonbonded pdb=" OH TYR D 186 " pdb=" O LEU D 226 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR B 60 " pdb=" O HIS B 67 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR F 317 " pdb=" O PRO F 385 " model vdw 2.205 3.040 nonbonded pdb=" O LEU D 157 " pdb=" OG1 THR D 161 " model vdw 2.213 3.040 nonbonded pdb=" O GLY F 225 " pdb=" OG1 THR F 229 " model vdw 2.214 3.040 ... (remaining 251899 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' and (resid 15 through 269 or (resid 270 and (name N or name CA or nam \ e C or name O or name CB )) or resid 271 through 329 or (resid 330 and (name N o \ r name CA or name C or name O or name CB )) or resid 331 through 606)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 394)) } ncs_group { reference = (chain 'C' and (resid 23 through 428 or (resid 429 and (name N or name CA or nam \ e C or name O or name CB )) or resid 430 through 580)) selection = (chain 'H' and (resid 23 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 through 132 or (resid 133 through 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 580)) } ncs_group { reference = (chain 'D' and (resid 1 through 197 or (resid 198 and (name N or name CA or name \ C or name O or name CB )) or resid 199 through 498)) selection = chain 'G' } 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 group one per residue 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.340 Find NCS groups from input model: 0.550 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32626 Z= 0.228 Angle : 0.755 9.479 44466 Z= 0.424 Chirality : 0.045 0.248 5074 Planarity : 0.005 0.109 5578 Dihedral : 13.094 83.203 11586 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 3944 helix: 1.31 (0.13), residues: 1702 sheet: 0.62 (0.20), residues: 646 loop : -1.27 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 277 TYR 0.033 0.002 TYR F 274 PHE 0.034 0.002 PHE A 142 TRP 0.043 0.002 TRP E 166 HIS 0.010 0.002 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00449 (32618) covalent geometry : angle 0.75479 (44450) SS BOND : bond 0.00181 ( 8) SS BOND : angle 1.87942 ( 16) hydrogen bonds : bond 0.16519 ( 1566) hydrogen bonds : angle 6.46623 ( 4464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 793 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7737 (tt0) cc_final: 0.7475 (tm-30) REVERT: A 149 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7802 (p0) REVERT: A 236 ASP cc_start: 0.8681 (m-30) cc_final: 0.7841 (p0) REVERT: A 422 MET cc_start: 0.8988 (mtp) cc_final: 0.8644 (mmm) REVERT: A 449 LEU cc_start: 0.9475 (mt) cc_final: 0.9251 (tp) REVERT: A 456 TYR cc_start: 0.8358 (t80) cc_final: 0.8083 (t80) REVERT: A 468 ASN cc_start: 0.8925 (t0) cc_final: 0.8238 (t0) REVERT: A 563 PHE cc_start: 0.7208 (p90) cc_final: 0.6668 (p90) REVERT: A 585 CYS cc_start: 0.8800 (m) cc_final: 0.7677 (p) REVERT: B 201 LEU cc_start: 0.8862 (tp) cc_final: 0.8642 (tp) REVERT: B 240 TRP cc_start: 0.8648 (m-10) cc_final: 0.8235 (m100) REVERT: B 243 PHE cc_start: 0.8700 (t80) cc_final: 0.8416 (t80) REVERT: B 263 ILE cc_start: 0.9050 (mt) cc_final: 0.8833 (mm) REVERT: B 329 LEU cc_start: 0.9146 (tp) cc_final: 0.8727 (pp) REVERT: B 370 ASP cc_start: 0.8663 (m-30) cc_final: 0.7964 (t70) REVERT: B 372 ASN cc_start: 0.8935 (m-40) cc_final: 0.8519 (t0) REVERT: E 31 CYS cc_start: 0.8557 (m) cc_final: 0.8194 (m) REVERT: E 85 MET cc_start: 0.7809 (ptt) cc_final: 0.6950 (ptt) REVERT: E 174 ILE cc_start: 0.9151 (mt) cc_final: 0.8950 (mt) REVERT: E 229 ASN cc_start: 0.8598 (m-40) cc_final: 0.7462 (m-40) REVERT: E 399 PHE cc_start: 0.8997 (t80) cc_final: 0.8776 (t80) REVERT: E 422 MET cc_start: 0.7335 (mtp) cc_final: 0.6656 (mtt) REVERT: E 482 MET cc_start: 0.7955 (mtp) cc_final: 0.7587 (ttm) REVERT: E 579 TRP cc_start: 0.7849 (p90) cc_final: 0.7638 (p90) REVERT: E 588 TRP cc_start: 0.7947 (t60) cc_final: 0.7332 (t60) REVERT: E 595 ILE cc_start: 0.9230 (mm) cc_final: 0.8871 (mm) REVERT: D 10 VAL cc_start: 0.7617 (t) cc_final: 0.7119 (t) REVERT: D 229 PHE cc_start: 0.7638 (m-80) cc_final: 0.7020 (m-10) REVERT: D 461 GLU cc_start: 0.7033 (tt0) cc_final: 0.6790 (mp0) REVERT: D 496 MET cc_start: 0.7610 (tpt) cc_final: 0.7245 (ttp) REVERT: C 192 MET cc_start: 0.7395 (mtp) cc_final: 0.7081 (mtt) REVERT: C 318 PHE cc_start: 0.7926 (m-80) cc_final: 0.7526 (m-80) REVERT: C 354 ILE cc_start: 0.6797 (pt) cc_final: 0.6307 (pt) REVERT: C 401 LEU cc_start: 0.8888 (mt) cc_final: 0.8506 (mt) REVERT: C 575 MET cc_start: 0.6751 (ttp) cc_final: 0.5740 (tpp) REVERT: F 34 VAL cc_start: 0.9360 (m) cc_final: 0.9079 (p) REVERT: F 83 LEU cc_start: 0.8733 (mp) cc_final: 0.8379 (tt) REVERT: F 98 GLN cc_start: 0.8477 (mt0) cc_final: 0.8113 (tt0) REVERT: F 101 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8418 (mp0) REVERT: F 114 TRP cc_start: 0.8515 (p-90) cc_final: 0.8031 (p-90) REVERT: F 141 PHE cc_start: 0.8452 (t80) cc_final: 0.8233 (t80) REVERT: F 162 MET cc_start: 0.9153 (mmm) cc_final: 0.8910 (mmt) REVERT: F 204 LEU cc_start: 0.9291 (mt) cc_final: 0.8954 (mt) REVERT: F 332 ILE cc_start: 0.9084 (pt) cc_final: 0.8814 (mm) REVERT: G 1 MET cc_start: 0.4511 (mmp) cc_final: 0.4142 (mtt) REVERT: G 14 PHE cc_start: 0.8614 (m-80) cc_final: 0.8126 (m-80) REVERT: G 18 TYR cc_start: 0.8516 (t80) cc_final: 0.8265 (t80) REVERT: G 366 LEU cc_start: 0.8559 (tp) cc_final: 0.8020 (pp) REVERT: G 405 SER cc_start: 0.7511 (p) cc_final: 0.7282 (m) REVERT: G 466 ASN cc_start: 0.6541 (m-40) cc_final: 0.5718 (p0) REVERT: H 96 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: H 98 HIS cc_start: 0.7757 (m90) cc_final: 0.6956 (m90) REVERT: H 224 LEU cc_start: 0.9128 (mt) cc_final: 0.8879 (tp) REVERT: H 241 ASP cc_start: 0.6986 (p0) cc_final: 0.6737 (m-30) REVERT: H 401 LEU cc_start: 0.9064 (mt) cc_final: 0.8805 (mt) REVERT: H 435 MET cc_start: 0.8618 (mtp) cc_final: 0.8178 (ttm) REVERT: H 575 MET cc_start: 0.6755 (ttp) cc_final: 0.6439 (ptp) outliers start: 2 outliers final: 0 residues processed: 795 average time/residue: 0.1842 time to fit residues: 239.2963 Evaluate side-chains 420 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 418 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 GLN D 228 ASN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 429 ASN C 139 GLN C 300 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN G 114 HIS ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN G 440 ASN ** G 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 396 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.074012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060150 restraints weight = 175430.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061527 restraints weight = 111161.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.062481 restraints weight = 78743.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063079 restraints weight = 61096.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063555 restraints weight = 51365.163| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 32626 Z= 0.227 Angle : 0.689 9.100 44466 Z= 0.354 Chirality : 0.044 0.174 5074 Planarity : 0.005 0.150 5578 Dihedral : 4.731 23.550 4243 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 3944 helix: 1.42 (0.13), residues: 1732 sheet: 0.64 (0.21), residues: 616 loop : -1.30 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 377 TYR 0.016 0.002 TYR B 354 PHE 0.025 0.002 PHE B 43 TRP 0.020 0.002 TRP G 92 HIS 0.011 0.002 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00498 (32618) covalent geometry : angle 0.68844 (44450) SS BOND : bond 0.00236 ( 8) SS BOND : angle 1.50082 ( 16) hydrogen bonds : bond 0.04914 ( 1566) hydrogen bonds : angle 5.25751 ( 4464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 534 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8143 (tt0) cc_final: 0.7619 (tm-30) REVERT: A 236 ASP cc_start: 0.8754 (m-30) cc_final: 0.8060 (p0) REVERT: A 468 ASN cc_start: 0.8648 (t0) cc_final: 0.7992 (t0) REVERT: A 585 CYS cc_start: 0.8749 (m) cc_final: 0.7828 (p) REVERT: B 172 TYR cc_start: 0.8890 (m-80) cc_final: 0.8683 (m-10) REVERT: B 263 ILE cc_start: 0.8979 (mt) cc_final: 0.8603 (mt) REVERT: B 370 ASP cc_start: 0.8716 (m-30) cc_final: 0.8090 (t70) REVERT: B 372 ASN cc_start: 0.9055 (m-40) cc_final: 0.8766 (t0) REVERT: B 375 MET cc_start: 0.8049 (tpp) cc_final: 0.7623 (tpp) REVERT: E 31 CYS cc_start: 0.8366 (m) cc_final: 0.8006 (m) REVERT: E 113 ASN cc_start: 0.8578 (t0) cc_final: 0.8322 (t0) REVERT: E 229 ASN cc_start: 0.8850 (m-40) cc_final: 0.6950 (t0) REVERT: D 461 GLU cc_start: 0.7041 (tt0) cc_final: 0.6574 (pp20) REVERT: D 496 MET cc_start: 0.7665 (tpt) cc_final: 0.7416 (ttp) REVERT: C 224 LEU cc_start: 0.8605 (pp) cc_final: 0.7808 (tp) REVERT: C 324 ASN cc_start: 0.7453 (m-40) cc_final: 0.7093 (m-40) REVERT: C 411 MET cc_start: 0.8558 (mmm) cc_final: 0.8285 (mmm) REVERT: C 575 MET cc_start: 0.6398 (ttp) cc_final: 0.5714 (tpp) REVERT: F 34 VAL cc_start: 0.9522 (m) cc_final: 0.9218 (p) REVERT: F 47 GLN cc_start: 0.8739 (mt0) cc_final: 0.8462 (mm-40) REVERT: F 83 LEU cc_start: 0.8700 (mp) cc_final: 0.8244 (tp) REVERT: F 90 LEU cc_start: 0.9555 (mt) cc_final: 0.9332 (mm) REVERT: F 114 TRP cc_start: 0.8439 (p-90) cc_final: 0.7987 (p-90) REVERT: F 141 PHE cc_start: 0.8540 (t80) cc_final: 0.8196 (t80) REVERT: F 162 MET cc_start: 0.8976 (mmm) cc_final: 0.8518 (mtm) REVERT: F 255 PHE cc_start: 0.8314 (m-80) cc_final: 0.8072 (m-80) REVERT: F 305 PHE cc_start: 0.8828 (m-80) cc_final: 0.8506 (m-80) REVERT: F 323 ILE cc_start: 0.9106 (tp) cc_final: 0.8890 (tp) REVERT: F 332 ILE cc_start: 0.9041 (pt) cc_final: 0.8829 (mm) REVERT: F 379 GLU cc_start: 0.8383 (pp20) cc_final: 0.8182 (pp20) REVERT: G 1 MET cc_start: 0.4014 (mmp) cc_final: 0.3632 (mtt) REVERT: G 14 PHE cc_start: 0.8697 (m-80) cc_final: 0.8226 (m-10) REVERT: G 270 MET cc_start: 0.7612 (ptp) cc_final: 0.7273 (mtm) REVERT: G 366 LEU cc_start: 0.8440 (tp) cc_final: 0.7874 (pp) REVERT: H 111 TRP cc_start: 0.8167 (m-10) cc_final: 0.7686 (m-10) outliers start: 2 outliers final: 1 residues processed: 536 average time/residue: 0.1798 time to fit residues: 159.5430 Evaluate side-chains 348 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 347 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 11 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 317 optimal weight: 9.9990 chunk 342 optimal weight: 5.9990 chunk 154 optimal weight: 0.3980 chunk 288 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 157 optimal weight: 0.4980 chunk 198 optimal weight: 8.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS E 313 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 ASN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 ASN H 139 GLN H 236 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.074084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060196 restraints weight = 173863.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.061628 restraints weight = 107723.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.062617 restraints weight = 75024.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.063235 restraints weight = 57591.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.063730 restraints weight = 47925.362| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32626 Z= 0.168 Angle : 0.633 9.290 44466 Z= 0.322 Chirality : 0.043 0.217 5074 Planarity : 0.004 0.045 5578 Dihedral : 4.572 24.335 4243 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3944 helix: 1.57 (0.13), residues: 1702 sheet: 0.71 (0.21), residues: 580 loop : -1.34 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 16 TYR 0.026 0.002 TYR B 320 PHE 0.024 0.002 PHE F 78 TRP 0.028 0.002 TRP E 579 HIS 0.010 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00366 (32618) covalent geometry : angle 0.63175 (44450) SS BOND : bond 0.00643 ( 8) SS BOND : angle 1.81426 ( 16) hydrogen bonds : bond 0.04017 ( 1566) hydrogen bonds : angle 4.90393 ( 4464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 488 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8930 (mt) cc_final: 0.8725 (tp) REVERT: A 236 ASP cc_start: 0.8625 (m-30) cc_final: 0.8059 (p0) REVERT: A 264 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8272 (t0) REVERT: A 299 ARG cc_start: 0.8242 (ttm110) cc_final: 0.8025 (ttm110) REVERT: A 552 PHE cc_start: 0.9166 (t80) cc_final: 0.8963 (t80) REVERT: B 92 ASP cc_start: 0.8744 (m-30) cc_final: 0.8310 (m-30) REVERT: B 370 ASP cc_start: 0.8675 (m-30) cc_final: 0.7987 (t70) REVERT: B 372 ASN cc_start: 0.8961 (m-40) cc_final: 0.8745 (t0) REVERT: B 375 MET cc_start: 0.8129 (tpp) cc_final: 0.7686 (tpp) REVERT: E 31 CYS cc_start: 0.8262 (m) cc_final: 0.8055 (m) REVERT: E 113 ASN cc_start: 0.8653 (t0) cc_final: 0.8376 (t0) REVERT: D 461 GLU cc_start: 0.7052 (tt0) cc_final: 0.6605 (pp20) REVERT: C 224 LEU cc_start: 0.8677 (pp) cc_final: 0.7980 (tt) REVERT: C 324 ASN cc_start: 0.7601 (m-40) cc_final: 0.7232 (m-40) REVERT: C 575 MET cc_start: 0.6564 (ttp) cc_final: 0.5661 (tpp) REVERT: F 83 LEU cc_start: 0.8690 (mp) cc_final: 0.8374 (tp) REVERT: F 114 TRP cc_start: 0.8376 (p-90) cc_final: 0.7949 (p-90) REVERT: F 141 PHE cc_start: 0.8586 (t80) cc_final: 0.8165 (t80) REVERT: F 162 MET cc_start: 0.8921 (mmm) cc_final: 0.8489 (mtt) REVERT: F 305 PHE cc_start: 0.8848 (m-80) cc_final: 0.8543 (m-80) REVERT: F 332 ILE cc_start: 0.9064 (pt) cc_final: 0.8830 (mm) REVERT: F 379 GLU cc_start: 0.8318 (pp20) cc_final: 0.7906 (pp20) REVERT: G 1 MET cc_start: 0.4162 (mmp) cc_final: 0.3759 (mtt) REVERT: G 14 PHE cc_start: 0.8540 (m-80) cc_final: 0.7766 (m-10) REVERT: G 366 LEU cc_start: 0.8534 (tp) cc_final: 0.7892 (pp) REVERT: H 224 LEU cc_start: 0.9216 (tp) cc_final: 0.8827 (tt) REVERT: H 492 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8541 (mm110) outliers start: 3 outliers final: 1 residues processed: 491 average time/residue: 0.1739 time to fit residues: 142.1230 Evaluate side-chains 357 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 219 optimal weight: 20.0000 chunk 338 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 245 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 367 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 351 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 HIS ** G 447 ASN ** 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 = 0.3552 r_free = 0.3552 target = 0.074484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.060691 restraints weight = 172070.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062143 restraints weight = 106099.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.063140 restraints weight = 73747.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063764 restraints weight = 56622.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064250 restraints weight = 47098.124| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32626 Z= 0.132 Angle : 0.596 9.580 44466 Z= 0.302 Chirality : 0.042 0.192 5074 Planarity : 0.004 0.046 5578 Dihedral : 4.377 21.999 4243 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3944 helix: 1.65 (0.13), residues: 1712 sheet: 0.79 (0.22), residues: 568 loop : -1.32 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 172 TYR 0.018 0.001 TYR F 339 PHE 0.037 0.001 PHE B 43 TRP 0.039 0.002 TRP G 206 HIS 0.008 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00293 (32618) covalent geometry : angle 0.59499 (44450) SS BOND : bond 0.00679 ( 8) SS BOND : angle 1.97920 ( 16) hydrogen bonds : bond 0.03585 ( 1566) hydrogen bonds : angle 4.68686 ( 4464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8134 (tt0) cc_final: 0.7462 (tm-30) REVERT: A 457 PHE cc_start: 0.8859 (t80) cc_final: 0.8086 (t80) REVERT: B 305 PHE cc_start: 0.9090 (m-10) cc_final: 0.8584 (t80) REVERT: B 372 ASN cc_start: 0.9023 (m-40) cc_final: 0.8732 (t0) REVERT: B 375 MET cc_start: 0.8430 (tpp) cc_final: 0.7299 (tpt) REVERT: E 31 CYS cc_start: 0.8383 (m) cc_final: 0.8130 (m) REVERT: E 113 ASN cc_start: 0.8799 (t0) cc_final: 0.8527 (t0) REVERT: D 461 GLU cc_start: 0.7166 (tt0) cc_final: 0.6720 (pp20) REVERT: C 224 LEU cc_start: 0.8586 (pp) cc_final: 0.7858 (tp) REVERT: C 324 ASN cc_start: 0.7686 (m-40) cc_final: 0.7324 (m-40) REVERT: C 434 PHE cc_start: 0.8579 (p90) cc_final: 0.8305 (p90) REVERT: F 114 TRP cc_start: 0.8346 (p-90) cc_final: 0.7895 (p-90) REVERT: F 141 PHE cc_start: 0.8568 (t80) cc_final: 0.8345 (t80) REVERT: F 162 MET cc_start: 0.8873 (mmm) cc_final: 0.8496 (mtt) REVERT: F 305 PHE cc_start: 0.8861 (m-80) cc_final: 0.8568 (m-80) REVERT: F 332 ILE cc_start: 0.9115 (pt) cc_final: 0.8800 (mm) REVERT: G 1 MET cc_start: 0.4141 (mmp) cc_final: 0.3715 (mtt) REVERT: G 14 PHE cc_start: 0.8533 (m-80) cc_final: 0.7845 (m-80) REVERT: G 366 LEU cc_start: 0.8490 (tp) cc_final: 0.7876 (pp) REVERT: G 466 ASN cc_start: 0.6413 (m-40) cc_final: 0.5870 (p0) REVERT: H 111 TRP cc_start: 0.7985 (m-10) cc_final: 0.7625 (m-10) REVERT: H 224 LEU cc_start: 0.9203 (tp) cc_final: 0.8860 (tt) REVERT: H 492 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8522 (mm110) outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.1699 time to fit residues: 140.3203 Evaluate side-chains 351 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 87 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 280 optimal weight: 10.0000 chunk 229 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 224 optimal weight: 0.0030 chunk 319 optimal weight: 10.0000 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN A 391 ASN D 114 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN G 447 ASN ** H 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.060971 restraints weight = 172840.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062467 restraints weight = 105812.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.063433 restraints weight = 73409.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.064050 restraints weight = 56360.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.064335 restraints weight = 47054.040| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32626 Z= 0.119 Angle : 0.590 9.792 44466 Z= 0.297 Chirality : 0.042 0.275 5074 Planarity : 0.004 0.061 5578 Dihedral : 4.268 25.726 4243 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3944 helix: 1.65 (0.13), residues: 1720 sheet: 0.82 (0.22), residues: 568 loop : -1.27 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 172 TYR 0.023 0.001 TYR B 60 PHE 0.049 0.001 PHE B 43 TRP 0.040 0.002 TRP B 240 HIS 0.007 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00264 (32618) covalent geometry : angle 0.59002 (44450) SS BOND : bond 0.00626 ( 8) SS BOND : angle 1.37600 ( 16) hydrogen bonds : bond 0.03451 ( 1566) hydrogen bonds : angle 4.56455 ( 4464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7789 (tm-30) REVERT: A 299 ARG cc_start: 0.8231 (ttm110) cc_final: 0.7931 (ttm110) REVERT: A 422 MET cc_start: 0.8974 (mmm) cc_final: 0.8629 (mmp) REVERT: A 433 LEU cc_start: 0.9598 (mt) cc_final: 0.9392 (mm) REVERT: A 457 PHE cc_start: 0.8856 (t80) cc_final: 0.8198 (t80) REVERT: A 482 MET cc_start: 0.8350 (mtm) cc_final: 0.8100 (mtp) REVERT: B 99 LEU cc_start: 0.9751 (mt) cc_final: 0.9314 (tp) REVERT: B 372 ASN cc_start: 0.8959 (m-40) cc_final: 0.8738 (t0) REVERT: B 375 MET cc_start: 0.7639 (tpp) cc_final: 0.7389 (tpp) REVERT: E 31 CYS cc_start: 0.8451 (m) cc_final: 0.8155 (m) REVERT: E 113 ASN cc_start: 0.8678 (t0) cc_final: 0.7527 (p0) REVERT: E 295 PHE cc_start: 0.8271 (m-80) cc_final: 0.7958 (m-80) REVERT: D 461 GLU cc_start: 0.7274 (tt0) cc_final: 0.6804 (pp20) REVERT: C 224 LEU cc_start: 0.8555 (pp) cc_final: 0.7928 (tp) REVERT: C 324 ASN cc_start: 0.7738 (m-40) cc_final: 0.7412 (m-40) REVERT: C 434 PHE cc_start: 0.8543 (p90) cc_final: 0.8335 (p90) REVERT: F 101 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8424 (mt-10) REVERT: F 114 TRP cc_start: 0.8360 (p-90) cc_final: 0.7912 (p-90) REVERT: F 141 PHE cc_start: 0.8560 (t80) cc_final: 0.8132 (t80) REVERT: F 162 MET cc_start: 0.8871 (mmm) cc_final: 0.8513 (mtt) REVERT: F 300 ASP cc_start: 0.9084 (m-30) cc_final: 0.8666 (t70) REVERT: F 305 PHE cc_start: 0.8829 (m-80) cc_final: 0.8614 (m-80) REVERT: F 332 ILE cc_start: 0.9079 (pt) cc_final: 0.8798 (mm) REVERT: F 358 LEU cc_start: 0.9503 (mt) cc_final: 0.9283 (mt) REVERT: G 1 MET cc_start: 0.4111 (mmp) cc_final: 0.3675 (mtt) REVERT: G 14 PHE cc_start: 0.8473 (m-80) cc_final: 0.7686 (m-80) REVERT: G 366 LEU cc_start: 0.8549 (tp) cc_final: 0.7962 (pp) REVERT: G 466 ASN cc_start: 0.6633 (m-40) cc_final: 0.5976 (p0) REVERT: H 111 TRP cc_start: 0.7927 (m-10) cc_final: 0.7587 (m-10) REVERT: H 224 LEU cc_start: 0.9173 (tp) cc_final: 0.8852 (tt) REVERT: H 492 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8513 (mm110) REVERT: H 562 LEU cc_start: 0.9307 (tt) cc_final: 0.8995 (tt) outliers start: 1 outliers final: 1 residues processed: 480 average time/residue: 0.1695 time to fit residues: 138.3840 Evaluate side-chains 366 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 213 optimal weight: 20.0000 chunk 350 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 249 optimal weight: 20.0000 chunk 239 optimal weight: 0.0070 chunk 373 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN E 391 ASN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.075568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.061781 restraints weight = 171078.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.063291 restraints weight = 105242.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064213 restraints weight = 73036.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064909 restraints weight = 56394.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065282 restraints weight = 46738.455| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 32626 Z= 0.109 Angle : 0.579 10.652 44466 Z= 0.289 Chirality : 0.042 0.180 5074 Planarity : 0.004 0.047 5578 Dihedral : 4.148 28.202 4243 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3944 helix: 1.68 (0.13), residues: 1716 sheet: 0.78 (0.21), residues: 612 loop : -1.15 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 261 TYR 0.019 0.001 TYR F 320 PHE 0.036 0.001 PHE B 305 TRP 0.051 0.001 TRP B 240 HIS 0.007 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00240 (32618) covalent geometry : angle 0.57849 (44450) SS BOND : bond 0.00836 ( 8) SS BOND : angle 1.54542 ( 16) hydrogen bonds : bond 0.03181 ( 1566) hydrogen bonds : angle 4.46818 ( 4464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 ARG cc_start: 0.8260 (ttm110) cc_final: 0.8012 (ttm110) REVERT: A 414 LEU cc_start: 0.8725 (mp) cc_final: 0.8030 (tp) REVERT: A 433 LEU cc_start: 0.9619 (mt) cc_final: 0.9406 (mm) REVERT: A 457 PHE cc_start: 0.8804 (t80) cc_final: 0.8136 (t80) REVERT: A 482 MET cc_start: 0.8326 (mtm) cc_final: 0.8108 (mtp) REVERT: B 99 LEU cc_start: 0.9742 (mt) cc_final: 0.9311 (tp) REVERT: B 305 PHE cc_start: 0.9168 (m-80) cc_final: 0.8960 (m-80) REVERT: B 370 ASP cc_start: 0.8873 (t0) cc_final: 0.8597 (t70) REVERT: B 372 ASN cc_start: 0.9008 (m-40) cc_final: 0.8787 (t0) REVERT: E 31 CYS cc_start: 0.8299 (m) cc_final: 0.8021 (m) REVERT: E 113 ASN cc_start: 0.8693 (t0) cc_final: 0.7526 (p0) REVERT: E 295 PHE cc_start: 0.8265 (m-80) cc_final: 0.7939 (m-80) REVERT: E 386 LEU cc_start: 0.8565 (mp) cc_final: 0.8219 (tp) REVERT: D 461 GLU cc_start: 0.7267 (tt0) cc_final: 0.6790 (pp20) REVERT: C 224 LEU cc_start: 0.8460 (pp) cc_final: 0.7737 (tp) REVERT: C 324 ASN cc_start: 0.7762 (m-40) cc_final: 0.7434 (m-40) REVERT: C 434 PHE cc_start: 0.8560 (p90) cc_final: 0.8339 (p90) REVERT: F 114 TRP cc_start: 0.8268 (p-90) cc_final: 0.7576 (p-90) REVERT: F 141 PHE cc_start: 0.8541 (t80) cc_final: 0.8145 (t80) REVERT: F 149 CYS cc_start: 0.8467 (m) cc_final: 0.7855 (m) REVERT: F 162 MET cc_start: 0.8903 (mmm) cc_final: 0.8564 (mtm) REVERT: F 300 ASP cc_start: 0.9088 (m-30) cc_final: 0.8610 (t70) REVERT: F 332 ILE cc_start: 0.9085 (pt) cc_final: 0.8813 (mm) REVERT: G 1 MET cc_start: 0.4038 (mmp) cc_final: 0.3656 (mtt) REVERT: G 14 PHE cc_start: 0.8468 (m-80) cc_final: 0.7591 (m-80) REVERT: G 354 GLN cc_start: 0.8219 (tt0) cc_final: 0.7951 (tp40) REVERT: G 366 LEU cc_start: 0.8540 (tp) cc_final: 0.7974 (pp) REVERT: G 466 ASN cc_start: 0.6604 (m-40) cc_final: 0.6037 (p0) REVERT: H 111 TRP cc_start: 0.7946 (m-10) cc_final: 0.7558 (m-10) REVERT: H 492 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8472 (mm110) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.1622 time to fit residues: 135.1082 Evaluate side-chains 360 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 312 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 316 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN A 374 ASN B 215 GLN B 277 GLN E 468 ASN D 76 GLN ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN H 133 GLN H 139 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.075910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062366 restraints weight = 171978.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063734 restraints weight = 106909.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064689 restraints weight = 75730.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.065274 restraints weight = 58837.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065746 restraints weight = 49459.703| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32626 Z= 0.108 Angle : 0.587 11.107 44466 Z= 0.289 Chirality : 0.042 0.227 5074 Planarity : 0.004 0.047 5578 Dihedral : 4.070 28.144 4243 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.06 % Allowed : 0.87 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3944 helix: 1.75 (0.13), residues: 1694 sheet: 0.65 (0.21), residues: 624 loop : -1.05 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 172 TYR 0.014 0.001 TYR B 88 PHE 0.040 0.001 PHE A 163 TRP 0.029 0.001 TRP B 240 HIS 0.006 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00235 (32618) covalent geometry : angle 0.58618 (44450) SS BOND : bond 0.00659 ( 8) SS BOND : angle 2.04826 ( 16) hydrogen bonds : bond 0.03123 ( 1566) hydrogen bonds : angle 4.41774 ( 4464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 477 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7136 (mtp85) cc_final: 0.6749 (tpp80) REVERT: A 103 GLU cc_start: 0.7989 (tt0) cc_final: 0.7327 (tm-30) REVERT: A 414 LEU cc_start: 0.8750 (mp) cc_final: 0.8150 (tp) REVERT: A 482 MET cc_start: 0.8382 (mtm) cc_final: 0.8107 (mtp) REVERT: B 99 LEU cc_start: 0.9750 (mt) cc_final: 0.9321 (tp) REVERT: B 125 LEU cc_start: 0.9183 (mt) cc_final: 0.8918 (mm) REVERT: B 305 PHE cc_start: 0.9176 (m-80) cc_final: 0.8959 (m-80) REVERT: B 370 ASP cc_start: 0.8767 (t0) cc_final: 0.8499 (t70) REVERT: E 29 MET cc_start: 0.7914 (tmm) cc_final: 0.7645 (tmm) REVERT: E 113 ASN cc_start: 0.8706 (t0) cc_final: 0.7575 (p0) REVERT: E 163 PHE cc_start: 0.7784 (m-10) cc_final: 0.7377 (m-80) REVERT: E 295 PHE cc_start: 0.8304 (m-80) cc_final: 0.7974 (m-80) REVERT: E 386 LEU cc_start: 0.8568 (mp) cc_final: 0.8221 (tp) REVERT: E 468 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.5986 (m-40) REVERT: D 461 GLU cc_start: 0.7470 (tt0) cc_final: 0.7130 (tm-30) REVERT: C 224 LEU cc_start: 0.8434 (pp) cc_final: 0.7739 (tp) REVERT: C 318 PHE cc_start: 0.7602 (m-80) cc_final: 0.7370 (m-80) REVERT: C 434 PHE cc_start: 0.8583 (p90) cc_final: 0.8357 (p90) REVERT: C 479 MET cc_start: 0.7399 (mmt) cc_final: 0.7003 (mmm) REVERT: F 114 TRP cc_start: 0.8286 (p-90) cc_final: 0.7706 (p-90) REVERT: F 141 PHE cc_start: 0.8584 (t80) cc_final: 0.8231 (t80) REVERT: F 149 CYS cc_start: 0.8397 (m) cc_final: 0.7779 (m) REVERT: F 162 MET cc_start: 0.8902 (mmm) cc_final: 0.8562 (mtm) REVERT: F 300 ASP cc_start: 0.9066 (m-30) cc_final: 0.8553 (t0) REVERT: F 332 ILE cc_start: 0.9103 (pt) cc_final: 0.8811 (mm) REVERT: F 356 ILE cc_start: 0.9596 (tp) cc_final: 0.9386 (tp) REVERT: G 1 MET cc_start: 0.4106 (mmp) cc_final: 0.3700 (mtt) REVERT: G 14 PHE cc_start: 0.8432 (m-80) cc_final: 0.7488 (m-80) REVERT: G 354 GLN cc_start: 0.8222 (tt0) cc_final: 0.7946 (tp40) REVERT: G 366 LEU cc_start: 0.8473 (tp) cc_final: 0.7939 (pp) REVERT: G 466 ASN cc_start: 0.6496 (m-40) cc_final: 0.5966 (p0) REVERT: H 70 MET cc_start: 0.7175 (mmp) cc_final: 0.5126 (ttt) REVERT: H 111 TRP cc_start: 0.7961 (m-10) cc_final: 0.7563 (m-10) REVERT: H 492 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8489 (mm110) outliers start: 2 outliers final: 0 residues processed: 479 average time/residue: 0.1676 time to fit residues: 136.5650 Evaluate side-chains 358 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 277 GLN D 244 HIS ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN F 351 ASN G 260 HIS G 413 ASN H 133 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.072837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059484 restraints weight = 172865.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060834 restraints weight = 109260.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061729 restraints weight = 77179.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.062334 restraints weight = 60050.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062678 restraints weight = 50279.592| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32626 Z= 0.190 Angle : 0.651 10.756 44466 Z= 0.330 Chirality : 0.044 0.202 5074 Planarity : 0.005 0.052 5578 Dihedral : 4.462 27.321 4243 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3944 helix: 1.52 (0.13), residues: 1708 sheet: 0.43 (0.21), residues: 592 loop : -1.21 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 220 TYR 0.019 0.002 TYR F 339 PHE 0.029 0.002 PHE A 560 TRP 0.027 0.002 TRP B 241 HIS 0.006 0.001 HIS G 260 Details of bonding type rmsd covalent geometry : bond 0.00419 (32618) covalent geometry : angle 0.64980 (44450) SS BOND : bond 0.00773 ( 8) SS BOND : angle 1.98660 ( 16) hydrogen bonds : bond 0.03597 ( 1566) hydrogen bonds : angle 4.64767 ( 4464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7287 (mtp85) cc_final: 0.6931 (tpp80) REVERT: A 103 GLU cc_start: 0.8186 (tt0) cc_final: 0.7552 (tm-30) REVERT: A 563 PHE cc_start: 0.7636 (p90) cc_final: 0.7162 (p90) REVERT: A 588 TRP cc_start: 0.8297 (t-100) cc_final: 0.8003 (t-100) REVERT: B 183 MET cc_start: 0.7043 (mmt) cc_final: 0.6724 (tpp) REVERT: B 246 GLU cc_start: 0.6669 (mp0) cc_final: 0.5401 (mt-10) REVERT: B 254 PHE cc_start: 0.7945 (t80) cc_final: 0.7627 (t80) REVERT: B 305 PHE cc_start: 0.9142 (m-80) cc_final: 0.8879 (m-80) REVERT: B 370 ASP cc_start: 0.8799 (t0) cc_final: 0.8471 (t70) REVERT: E 113 ASN cc_start: 0.8757 (t0) cc_final: 0.7798 (p0) REVERT: D 454 GLU cc_start: 0.8774 (tp30) cc_final: 0.8183 (mt-10) REVERT: C 479 MET cc_start: 0.7370 (mmt) cc_final: 0.6979 (mmm) REVERT: F 101 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8396 (tt0) REVERT: F 255 PHE cc_start: 0.8286 (m-80) cc_final: 0.7938 (m-10) REVERT: F 300 ASP cc_start: 0.9146 (m-30) cc_final: 0.8617 (t0) REVERT: F 332 ILE cc_start: 0.9162 (pt) cc_final: 0.8843 (mm) REVERT: G 1 MET cc_start: 0.4234 (mmp) cc_final: 0.3738 (mtt) REVERT: G 14 PHE cc_start: 0.8561 (m-80) cc_final: 0.7529 (m-10) REVERT: G 366 LEU cc_start: 0.8514 (tp) cc_final: 0.8001 (pp) REVERT: G 466 ASN cc_start: 0.6754 (m-40) cc_final: 0.6100 (p0) REVERT: G 480 LEU cc_start: 0.9018 (mt) cc_final: 0.8776 (mt) REVERT: H 111 TRP cc_start: 0.8115 (m-10) cc_final: 0.7769 (m-10) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1612 time to fit residues: 120.9372 Evaluate side-chains 328 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 31 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 350 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 167 optimal weight: 0.0040 chunk 277 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 277 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 413 ASN G 447 ASN H 133 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.075245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061549 restraints weight = 169528.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.062996 restraints weight = 103697.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064006 restraints weight = 72398.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.064657 restraints weight = 55390.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.065147 restraints weight = 46028.560| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32626 Z= 0.111 Angle : 0.608 11.503 44466 Z= 0.301 Chirality : 0.043 0.254 5074 Planarity : 0.004 0.046 5578 Dihedral : 4.189 31.295 4243 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3944 helix: 1.63 (0.13), residues: 1688 sheet: 0.34 (0.21), residues: 618 loop : -1.07 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 408 TYR 0.016 0.001 TYR B 88 PHE 0.034 0.001 PHE F 305 TRP 0.047 0.001 TRP D 206 HIS 0.007 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00239 (32618) covalent geometry : angle 0.60730 (44450) SS BOND : bond 0.00565 ( 8) SS BOND : angle 1.73569 ( 16) hydrogen bonds : bond 0.03171 ( 1566) hydrogen bonds : angle 4.48141 ( 4464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7274 (mtp85) cc_final: 0.6987 (tpt-90) REVERT: A 103 GLU cc_start: 0.7980 (tt0) cc_final: 0.7324 (tm-30) REVERT: A 299 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7975 (ptp-110) REVERT: A 414 LEU cc_start: 0.8779 (mp) cc_final: 0.8244 (tp) REVERT: A 482 MET cc_start: 0.8300 (mtm) cc_final: 0.7860 (mtt) REVERT: A 563 PHE cc_start: 0.7221 (p90) cc_final: 0.6835 (p90) REVERT: B 99 LEU cc_start: 0.9749 (mt) cc_final: 0.9325 (tp) REVERT: B 125 LEU cc_start: 0.9118 (mt) cc_final: 0.8854 (mm) REVERT: B 183 MET cc_start: 0.6980 (mmt) cc_final: 0.6495 (mmt) REVERT: B 241 TRP cc_start: 0.8867 (p-90) cc_final: 0.8516 (p-90) REVERT: B 243 PHE cc_start: 0.8325 (t80) cc_final: 0.7756 (t80) REVERT: B 263 ILE cc_start: 0.8705 (mt) cc_final: 0.8479 (mt) REVERT: B 305 PHE cc_start: 0.9180 (m-80) cc_final: 0.8941 (m-80) REVERT: B 370 ASP cc_start: 0.8688 (t0) cc_final: 0.8478 (t70) REVERT: E 33 LEU cc_start: 0.8558 (mt) cc_final: 0.8321 (pp) REVERT: E 113 ASN cc_start: 0.8734 (t0) cc_final: 0.7780 (p0) REVERT: E 295 PHE cc_start: 0.8387 (m-80) cc_final: 0.8065 (m-80) REVERT: E 386 LEU cc_start: 0.8543 (mp) cc_final: 0.8212 (tp) REVERT: D 21 LEU cc_start: 0.8371 (tp) cc_final: 0.8171 (tp) REVERT: D 353 PHE cc_start: 0.7964 (t80) cc_final: 0.7690 (t80) REVERT: D 454 GLU cc_start: 0.8764 (tp30) cc_final: 0.8170 (mt-10) REVERT: C 72 TYR cc_start: 0.8775 (p90) cc_final: 0.8394 (p90) REVERT: C 224 LEU cc_start: 0.8454 (pp) cc_final: 0.7752 (tp) REVERT: C 411 MET cc_start: 0.8425 (mmm) cc_final: 0.8104 (mmm) REVERT: C 479 MET cc_start: 0.7450 (mmt) cc_final: 0.6961 (mmm) REVERT: F 101 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8352 (tt0) REVERT: F 141 PHE cc_start: 0.8712 (t80) cc_final: 0.8316 (t80) REVERT: F 183 MET cc_start: 0.9302 (mmm) cc_final: 0.9031 (mmp) REVERT: F 332 ILE cc_start: 0.9139 (pt) cc_final: 0.8836 (mm) REVERT: F 354 TYR cc_start: 0.8873 (t80) cc_final: 0.8593 (t80) REVERT: F 356 ILE cc_start: 0.9599 (tp) cc_final: 0.9395 (tp) REVERT: G 1 MET cc_start: 0.4133 (mmp) cc_final: 0.3706 (mtt) REVERT: G 14 PHE cc_start: 0.8441 (m-80) cc_final: 0.7567 (m-10) REVERT: G 366 LEU cc_start: 0.8447 (tp) cc_final: 0.7964 (pp) REVERT: G 466 ASN cc_start: 0.6603 (m-40) cc_final: 0.6048 (p0) REVERT: H 111 TRP cc_start: 0.7901 (m-10) cc_final: 0.7525 (m-10) REVERT: H 492 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8457 (mm110) REVERT: H 562 LEU cc_start: 0.9241 (tt) cc_final: 0.8809 (tt) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.1634 time to fit residues: 131.8158 Evaluate side-chains 348 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 191 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 369 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 212 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN B 277 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN H 133 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060123 restraints weight = 172136.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061440 restraints weight = 107186.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062367 restraints weight = 76567.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.062997 restraints weight = 59616.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063345 restraints weight = 49756.752| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32626 Z= 0.153 Angle : 0.636 11.489 44466 Z= 0.317 Chirality : 0.043 0.263 5074 Planarity : 0.004 0.047 5578 Dihedral : 4.342 29.234 4243 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3944 helix: 1.58 (0.13), residues: 1698 sheet: 0.32 (0.21), residues: 606 loop : -1.16 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 220 TYR 0.020 0.001 TYR F 339 PHE 0.028 0.002 PHE B 43 TRP 0.053 0.002 TRP A 588 HIS 0.012 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00344 (32618) covalent geometry : angle 0.63568 (44450) SS BOND : bond 0.00550 ( 8) SS BOND : angle 1.72016 ( 16) hydrogen bonds : bond 0.03379 ( 1566) hydrogen bonds : angle 4.56440 ( 4464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.7266 (mtp85) cc_final: 0.6888 (tpp80) REVERT: A 103 GLU cc_start: 0.8226 (tt0) cc_final: 0.7591 (tm-30) REVERT: A 135 MET cc_start: 0.5828 (mtt) cc_final: 0.5568 (mtt) REVERT: A 299 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7930 (ptp-110) REVERT: A 414 LEU cc_start: 0.8856 (mp) cc_final: 0.8353 (tp) REVERT: A 482 MET cc_start: 0.8231 (mtm) cc_final: 0.7910 (mtp) REVERT: A 563 PHE cc_start: 0.7335 (p90) cc_final: 0.6948 (p90) REVERT: B 99 LEU cc_start: 0.9762 (mt) cc_final: 0.9336 (tp) REVERT: B 125 LEU cc_start: 0.9176 (mt) cc_final: 0.8925 (mm) REVERT: B 183 MET cc_start: 0.7124 (mmt) cc_final: 0.6769 (tpp) REVERT: B 191 ILE cc_start: 0.8536 (mm) cc_final: 0.8321 (mm) REVERT: B 305 PHE cc_start: 0.9185 (m-80) cc_final: 0.8953 (m-80) REVERT: B 370 ASP cc_start: 0.8782 (t0) cc_final: 0.8457 (t70) REVERT: E 113 ASN cc_start: 0.8797 (t0) cc_final: 0.7914 (p0) REVERT: E 250 MET cc_start: 0.6757 (mmm) cc_final: 0.5920 (mmm) REVERT: E 295 PHE cc_start: 0.8410 (m-80) cc_final: 0.8078 (m-80) REVERT: D 353 PHE cc_start: 0.7926 (t80) cc_final: 0.7697 (t80) REVERT: C 72 TYR cc_start: 0.8863 (p90) cc_final: 0.8455 (p90) REVERT: C 434 PHE cc_start: 0.8610 (p90) cc_final: 0.8400 (p90) REVERT: C 479 MET cc_start: 0.7555 (mmt) cc_final: 0.7069 (mmm) REVERT: F 1 MET cc_start: 0.2938 (ppp) cc_final: 0.1939 (mmm) REVERT: F 101 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8341 (tt0) REVERT: F 300 ASP cc_start: 0.9098 (m-30) cc_final: 0.8573 (t0) REVERT: F 332 ILE cc_start: 0.9140 (pt) cc_final: 0.8831 (mm) REVERT: G 1 MET cc_start: 0.4315 (mmp) cc_final: 0.3878 (mtt) REVERT: G 14 PHE cc_start: 0.8564 (m-80) cc_final: 0.7445 (m-10) REVERT: G 366 LEU cc_start: 0.8418 (tp) cc_final: 0.7971 (pp) REVERT: G 445 LEU cc_start: 0.9141 (tt) cc_final: 0.8940 (mt) REVERT: H 70 MET cc_start: 0.7433 (mmp) cc_final: 0.5455 (ttt) REVERT: H 111 TRP cc_start: 0.8054 (m-10) cc_final: 0.7694 (m-10) REVERT: H 562 LEU cc_start: 0.9285 (tt) cc_final: 0.8824 (tt) REVERT: H 563 ILE cc_start: 0.9563 (mt) cc_final: 0.9311 (mt) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.1622 time to fit residues: 120.9669 Evaluate side-chains 342 residues out of total 3562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 209 optimal weight: 0.9980 chunk 253 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 358 optimal weight: 10.0000 chunk 350 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 HIS ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 447 ASN G 472 HIS H 133 GLN ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060758 restraints weight = 171421.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062198 restraints weight = 103855.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063196 restraints weight = 72390.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063814 restraints weight = 55448.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064065 restraints weight = 46247.381| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32626 Z= 0.117 Angle : 0.606 11.366 44466 Z= 0.299 Chirality : 0.043 0.332 5074 Planarity : 0.004 0.048 5578 Dihedral : 4.200 30.600 4243 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.14), residues: 3944 helix: 1.67 (0.13), residues: 1688 sheet: 0.32 (0.21), residues: 628 loop : -1.05 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 16 TYR 0.015 0.001 TYR B 88 PHE 0.026 0.001 PHE A 163 TRP 0.074 0.002 TRP A 588 HIS 0.009 0.001 HIS E 313 Details of bonding type rmsd covalent geometry : bond 0.00262 (32618) covalent geometry : angle 0.60499 (44450) SS BOND : bond 0.00529 ( 8) SS BOND : angle 1.61673 ( 16) hydrogen bonds : bond 0.03132 ( 1566) hydrogen bonds : angle 4.45001 ( 4464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4972.07 seconds wall clock time: 86 minutes 53.05 seconds (5213.05 seconds total)