Starting phenix.real_space_refine on Wed Nov 19 09:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jrj_22446/11_2025/7jrj_22446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jrj_22446/11_2025/7jrj_22446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jrj_22446/11_2025/7jrj_22446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jrj_22446/11_2025/7jrj_22446.map" model { file = "/net/cci-nas-00/data/ceres_data/7jrj_22446/11_2025/7jrj_22446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jrj_22446/11_2025/7jrj_22446.cif" } resolution = 3.03 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 67 5.16 5 C 14587 2.51 5 N 3924 2.21 5 O 4346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22924 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1378 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2658 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1232 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 10, 'TRANS': 147} Chain: "I" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2517 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 19 Classifications: {'peptide': 4} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1094 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3611 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 439} Chain breaks: 3 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1955 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1955 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 1 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2717 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 329} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3168 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 377} Chain breaks: 1 Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'TRANS': 63} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'UNK:plan-1': 64} Unresolved non-hydrogen planarities: 64 Chain: "O" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 5.23, per 1000 atoms: 0.23 Number of scatterers: 22924 At special positions: 0 Unit cell: (131.095, 153.64, 259.685, 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 67 16.00 O 4346 8.00 N 3924 7.00 C 14587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 155 " distance=2.29 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: 2.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5610 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 27 sheets defined 39.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 472 through 477 Processing helix chain 'F' and resid 480 through 512 removed outlier: 3.596A pdb=" N SER F 512 " --> pdb=" O ALA F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 542 through 552 Processing helix chain 'F' and resid 720 through 725 removed outlier: 3.790A pdb=" N ILE F 724 " --> pdb=" O ALA F 720 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN F 725 " --> pdb=" O ALA F 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 720 through 725' Processing helix chain 'K' and resid 12 through 18 Processing helix chain 'K' and resid 20 through 31 Processing helix chain 'K' and resid 44 through 52 Processing helix chain 'K' and resid 53 through 56 removed outlier: 3.931A pdb=" N LYS K 56 " --> pdb=" O GLY K 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 56' Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 82 through 92 removed outlier: 3.670A pdb=" N ALA K 86 " --> pdb=" O GLY K 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG K 88 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 103 Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 125 through 137 Processing helix chain 'K' and resid 143 through 148 Processing helix chain 'K' and resid 151 through 161 removed outlier: 3.547A pdb=" N GLU K 155 " --> pdb=" O THR K 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 31 Processing helix chain 'I' and resid 35 through 98 removed outlier: 3.512A pdb=" N TYR I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 82 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 118 Processing helix chain 'I' and resid 194 through 198 removed outlier: 4.172A pdb=" N LYS I 197 " --> pdb=" O ASP I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 214 Processing helix chain 'I' and resid 237 through 239 No H-bonds generated for 'chain 'I' and resid 237 through 239' Processing helix chain 'I' and resid 240 through 245 Processing helix chain 'I' and resid 254 through 258 Processing helix chain 'I' and resid 305 through 333 Processing helix chain 'I' and resid 462 through 475 removed outlier: 3.574A pdb=" N HIS I 475 " --> pdb=" O LEU I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 485 Processing helix chain 'I' and resid 490 through 504 removed outlier: 3.663A pdb=" N HIS I 495 " --> pdb=" O GLN I 491 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 496 " --> pdb=" O GLY I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 518 Processing helix chain 'I' and resid 523 through 531 Processing helix chain 'G' and resid 281 through 353 removed outlier: 3.696A pdb=" N GLN G 285 " --> pdb=" O TRP G 281 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 309 " --> pdb=" O GLU G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 360 Processing helix chain 'G' and resid 369 through 389 removed outlier: 3.822A pdb=" N GLU G 373 " --> pdb=" O ALA G 369 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 383 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU G 384 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 483 Processing helix chain 'G' and resid 486 through 499 Processing helix chain 'H' and resid 20 through 26 Processing helix chain 'H' and resid 52 through 57 Processing helix chain 'H' and resid 84 through 95 removed outlier: 3.691A pdb=" N ASN H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU H 90 " --> pdb=" O GLU H 86 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL H 91 " --> pdb=" O TYR H 87 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG H 92 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 117 removed outlier: 3.563A pdb=" N ARG H 101 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 156 removed outlier: 3.831A pdb=" N PHE H 153 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER H 154 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 173 Processing helix chain 'H' and resid 189 through 194 Processing helix chain 'H' and resid 207 through 226 Processing helix chain 'H' and resid 242 through 249 removed outlier: 3.605A pdb=" N GLY H 249 " --> pdb=" O TRP H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 269 removed outlier: 3.619A pdb=" N ALA H 255 " --> pdb=" O PRO H 251 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL H 257 " --> pdb=" O ALA H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 310 Processing helix chain 'H' and resid 342 through 350 Processing helix chain 'H' and resid 368 through 378 removed outlier: 3.704A pdb=" N LEU H 372 " --> pdb=" O ALA H 368 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS H 377 " --> pdb=" O ASP H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 426 Processing helix chain 'H' and resid 427 through 445 removed outlier: 3.799A pdb=" N VAL H 437 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 459 removed outlier: 3.759A pdb=" N VAL H 452 " --> pdb=" O LYS H 448 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA H 453 " --> pdb=" O PRO H 449 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU H 454 " --> pdb=" O GLU H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 490 Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.707A pdb=" N LEU H 499 " --> pdb=" O ASP H 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 507 through 515 Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 23 through 41 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.582A pdb=" N THR A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 23 through 41 Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.583A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'C' and resid 7 through 15 removed outlier: 3.595A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.597A pdb=" N GLU C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 266 through 283 removed outlier: 3.624A pdb=" N ALA C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 41 through 49 removed outlier: 4.474A pdb=" N GLU D 47 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 125 through 142 Processing helix chain 'D' and resid 191 through 196 removed outlier: 3.551A pdb=" N ASN D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 195 " --> pdb=" O GLY D 192 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR D 196 " --> pdb=" O VAL D 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 196' Processing helix chain 'D' and resid 215 through 223 Processing helix chain 'D' and resid 246 through 263 removed outlier: 3.637A pdb=" N ALA D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.152A pdb=" N GLU D 292 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET D 293 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.739A pdb=" N GLU D 337 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.704A pdb=" N ASP D 349 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 372 removed outlier: 3.789A pdb=" N UNK O 357 " --> pdb=" O UNK O 353 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N UNK O 360 " --> pdb=" O UNK O 356 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK O 362 " --> pdb=" O UNK O 358 " (cutoff:3.500A) Processing helix chain 'O' and resid 802 through 806 removed outlier: 3.764A pdb=" N UNK O 806 " --> pdb=" O UNK O 803 " (cutoff:3.500A) Processing helix chain 'O' and resid 808 through 811 removed outlier: 3.819A pdb=" N UNK O 811 " --> pdb=" O UNK O 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 808 through 811' Processing helix chain 'O' and resid 812 through 823 removed outlier: 3.691A pdb=" N UNK O 822 " --> pdb=" O UNK O 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AA2, first strand: chain 'E' and resid 201 through 203 removed outlier: 7.376A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 154 " --> pdb=" O GLY E 166 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP E 75 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 59 " --> pdb=" O TYR E 76 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS E 60 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU E 49 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR E 62 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS E 47 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 48 " --> pdb=" O MET E 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET E 28 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU E 29 " --> pdb=" O UNK M -3 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK M -3 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 523 through 528 removed outlier: 3.790A pdb=" N LYS F 452 " --> pdb=" O ARG F 528 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N UNK N -7 " --> pdb=" O UNK N -54 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N UNK N -57 " --> pdb=" O UNK N -45 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N UNK N -45 " --> pdb=" O UNK N -57 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N UNK N -55 " --> pdb=" O UNK N -47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 564 through 570 removed outlier: 3.573A pdb=" N SER F 564 " --> pdb=" O TYR F 581 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR F 566 " --> pdb=" O GLY F 579 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY F 579 " --> pdb=" O THR F 566 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG F 568 " --> pdb=" O TYR F 577 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR F 577 " --> pdb=" O ARG F 568 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU F 603 " --> pdb=" O HIS F 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 585 through 586 removed outlier: 3.645A pdb=" N VAL F 585 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLN F 635 " --> pdb=" O GLU F 626 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL F 628 " --> pdb=" O GLU F 633 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU F 633 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER F 649 " --> pdb=" O PRO F 658 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 659 " --> pdb=" O GLY F 671 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY F 671 " --> pdb=" O GLY F 659 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 677 " --> pdb=" O LYS F 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 680 through 686 removed outlier: 6.419A pdb=" N ARG F 690 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR F 705 " --> pdb=" O ARG F 690 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU F 692 " --> pdb=" O THR F 703 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR F 703 " --> pdb=" O GLU F 692 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU F 694 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 708 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 680 through 686 removed outlier: 6.419A pdb=" N ARG F 690 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR F 705 " --> pdb=" O ARG F 690 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU F 692 " --> pdb=" O THR F 703 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR F 703 " --> pdb=" O GLU F 692 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU F 694 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 708 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 5 through 11 removed outlier: 3.774A pdb=" N GLU K 5 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU K 76 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE K 73 " --> pdb=" O LYS K 40 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS K 40 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA K 75 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS K 38 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL K 77 " --> pdb=" O ILE K 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 216 through 217 removed outlier: 6.783A pdb=" N ALA I 125 " --> pdb=" O VAL I 203 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA I 205 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA I 123 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS I 287 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL I 278 " --> pdb=" O LYS I 287 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU I 289 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS I 276 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA I 291 " --> pdb=" O GLN I 274 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN I 274 " --> pdb=" O ALA I 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 32 through 35 removed outlier: 5.376A pdb=" N GLU H 33 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU H 40 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 35 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 381 through 384 removed outlier: 6.713A pdb=" N ILE H 334 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLN H 358 " --> pdb=" O ILE H 334 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU H 336 " --> pdb=" O GLN H 358 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL H 287 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL H 337 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 289 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU H 286 " --> pdb=" O LEU H 232 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS H 235 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL H 44 " --> pdb=" O VAL H 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 313 through 315 removed outlier: 6.575A pdb=" N GLN H 313 " --> pdb=" O SER H 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.028A pdb=" N GLU A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A 48 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR A 66 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A 46 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 16.266A pdb=" N TRP A 251 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 11.365A pdb=" N THR A 47 " --> pdb=" O TRP A 251 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N SER A 253 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP A 49 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR A 240 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 75 through 78 removed outlier: 4.505A pdb=" N ALA A 69 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AB7, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'B' and resid 92 through 93 removed outlier: 6.028A pdb=" N GLU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU B 48 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR B 66 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU B 46 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 16.265A pdb=" N TRP B 251 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 11.365A pdb=" N THR B 47 " --> pdb=" O TRP B 251 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N SER B 253 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP B 49 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TYR B 240 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 78 removed outlier: 4.506A pdb=" N ALA B 69 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 119 through 124 Processing sheet with id=AC2, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AC3, first strand: chain 'C' and resid 229 through 230 removed outlier: 6.561A pdb=" N TYR C 167 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS C 159 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL C 169 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N ARG C 155 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N CYS C 414 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 157 " --> pdb=" O CYS C 414 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA C 403 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AC5, first strand: chain 'C' and resid 290 through 293 Processing sheet with id=AC6, first strand: chain 'D' and resid 209 through 210 removed outlier: 6.829A pdb=" N TYR D 163 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY D 154 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL D 165 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE D 152 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU D 167 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL D 150 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR D 169 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 22.559A pdb=" N PHE D 400 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 16.439A pdb=" N THR D 149 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 14.877A pdb=" N SER D 402 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ARG D 151 " --> pdb=" O SER D 402 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N TYR D 404 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE D 153 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLY D 406 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS D 155 " --> pdb=" O GLY D 406 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA D 391 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 381 " --> pdb=" O CYS D 395 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 382 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 264 through 266 Processing sheet with id=AC8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC9, first strand: chain 'N' and resid -73 through -71 removed outlier: 3.555A pdb=" N UNK N -83 " --> pdb=" O UNK N -25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N UNK N -81 " --> pdb=" O UNK N -27 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N UNK N -27 " --> pdb=" O UNK N -81 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3027 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: 4.78 Time building geometry restraints manager: 2.72 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: 7609 1.34 - 1.46: 3861 1.46 - 1.57: 11881 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 23455 Sorted by residual: bond pdb=" N VAL H 495 " pdb=" CA VAL H 495 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.90e+00 bond pdb=" N GLY H 497 " pdb=" CA GLY H 497 " ideal model delta sigma weight residual 1.443 1.477 -0.035 1.37e-02 5.33e+03 6.37e+00 bond pdb=" N ASP H 496 " pdb=" CA ASP H 496 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.18e+00 bond pdb=" N CYS B 155 " pdb=" CA CYS B 155 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.93e+00 bond pdb=" N ARG B 154 " pdb=" CA ARG B 154 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.29e+00 ... (remaining 23450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 31111 1.60 - 3.20: 690 3.20 - 4.80: 95 4.80 - 6.40: 17 6.40 - 8.00: 3 Bond angle restraints: 31916 Sorted by residual: angle pdb=" C ALA B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.44 117.92 4.52 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C ALA A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta sigma weight residual 122.44 117.94 4.50 1.19e+00 7.06e-01 1.43e+01 angle pdb=" C GLU F 685 " pdb=" N GLN F 686 " pdb=" CA GLN F 686 " ideal model delta sigma weight residual 122.07 127.28 -5.21 1.44e+00 4.82e-01 1.31e+01 angle pdb=" CA GLN F 686 " pdb=" C GLN F 686 " pdb=" N PRO F 687 " ideal model delta sigma weight residual 117.68 120.19 -2.51 7.10e-01 1.98e+00 1.25e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" C THR B 164 " ideal model delta sigma weight residual 111.02 116.16 -5.14 1.52e+00 4.33e-01 1.14e+01 ... (remaining 31911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13213 17.93 - 35.86: 614 35.86 - 53.79: 114 53.79 - 71.73: 18 71.73 - 89.66: 11 Dihedral angle restraints: 13970 sinusoidal: 5230 harmonic: 8740 Sorted by residual: dihedral pdb=" CA LEU I 295 " pdb=" C LEU I 295 " pdb=" N PHE I 296 " pdb=" CA PHE I 296 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA TRP H 470 " pdb=" C TRP H 470 " pdb=" N SER H 471 " pdb=" CA SER H 471 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU D 325 " pdb=" C GLU D 325 " pdb=" N PRO D 326 " pdb=" CA PRO D 326 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 13967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2368 0.037 - 0.075: 870 0.075 - 0.112: 224 0.112 - 0.150: 57 0.150 - 0.187: 4 Chirality restraints: 3523 Sorted by residual: chirality pdb=" CB VAL H 495 " pdb=" CA VAL H 495 " pdb=" CG1 VAL H 495 " pdb=" CG2 VAL H 495 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA PHE I 296 " pdb=" N PHE I 296 " pdb=" C PHE I 296 " pdb=" CB PHE I 296 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA PRO F 687 " pdb=" N PRO F 687 " pdb=" C PRO F 687 " pdb=" CB PRO F 687 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 3520 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 325 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO D 326 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 326 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 326 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 686 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO F 687 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 687 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 687 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 765 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO F 766 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 766 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 766 " -0.023 5.00e-02 4.00e+02 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3191 2.75 - 3.29: 21368 3.29 - 3.82: 36424 3.82 - 4.36: 44063 4.36 - 4.90: 75949 Nonbonded interactions: 180995 Sorted by model distance: nonbonded pdb=" OH TYR H 480 " pdb=" OD1 ASP H 496 " model vdw 2.210 3.040 nonbonded pdb=" OG SER F 580 " pdb=" O HIS F 587 " model vdw 2.230 3.040 nonbonded pdb=" OG SER F 807 " pdb=" OG1 THR F 810 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP G 306 " pdb=" OH TYR D 24 " model vdw 2.234 3.040 nonbonded pdb=" OG SER K 123 " pdb=" OE1 GLU K 132 " model vdw 2.235 3.040 ... (remaining 180990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.920 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.006 0.260 23456 Z= 0.282 Angle : 0.601 8.467 31918 Z= 0.336 Chirality : 0.042 0.187 3523 Planarity : 0.004 0.058 4196 Dihedral : 11.334 89.658 8357 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -2.44 (0.14), residues: 2879 helix: -1.05 (0.14), residues: 1018 sheet: -1.33 (0.22), residues: 519 loop : -2.14 (0.15), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 107 TYR 0.016 0.002 TYR D 130 PHE 0.016 0.001 PHE E 122 TRP 0.016 0.001 TRP E 99 HIS 0.004 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00615 (23455) covalent geometry : angle 0.59909 (31916) SS BOND : bond 0.26030 ( 1) SS BOND : angle 5.99465 ( 2) hydrogen bonds : bond 0.13649 ( 1062) hydrogen bonds : angle 6.30229 ( 3027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 ASP cc_start: 0.7992 (t0) cc_final: 0.7728 (t0) REVERT: F 583 ASP cc_start: 0.7235 (t0) cc_final: 0.6994 (t0) REVERT: K 45 ARG cc_start: 0.7192 (tpt-90) cc_final: 0.6967 (ttm-80) REVERT: H 108 ILE cc_start: 0.8013 (tt) cc_final: 0.7738 (mt) REVERT: C 301 ARG cc_start: 0.7105 (ttm170) cc_final: 0.6441 (tpp80) REVERT: D 58 ASN cc_start: 0.7784 (t0) cc_final: 0.7431 (m-40) REVERT: D 90 ASP cc_start: 0.7350 (t0) cc_final: 0.6945 (t0) outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 0.2012 time to fit residues: 92.0721 Evaluate side-chains 155 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 495 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 544 HIS F 548 ASN F 686 GLN F 723 HIS F 725 GLN K 31 ASN K 55 HIS I 254 ASN H 267 ASN H 361 HIS A 3 GLN ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN B 3 GLN B 14 HIS B 27 GLN B 247 ASN C 269 ASN D 173 ASN D 305 HIS D 426 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.106979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080085 restraints weight = 52981.193| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.56 r_work: 0.3204 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23456 Z= 0.121 Angle : 0.539 7.050 31918 Z= 0.277 Chirality : 0.040 0.196 3523 Planarity : 0.004 0.051 4196 Dihedral : 4.149 26.856 3268 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.19 % Allowed : 9.34 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -0.93 (0.15), residues: 2879 helix: 0.45 (0.16), residues: 1033 sheet: -0.86 (0.23), residues: 511 loop : -1.33 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 44 TYR 0.015 0.001 TYR B 60 PHE 0.014 0.001 PHE A 186 TRP 0.013 0.001 TRP E 99 HIS 0.008 0.001 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00261 (23455) covalent geometry : angle 0.53944 (31916) SS BOND : bond 0.00844 ( 1) SS BOND : angle 0.94466 ( 2) hydrogen bonds : bond 0.04159 ( 1062) hydrogen bonds : angle 4.72572 ( 3027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 29 GLU cc_start: 0.5966 (mt-10) cc_final: 0.5733 (mp0) REVERT: F 583 ASP cc_start: 0.7997 (t0) cc_final: 0.7654 (t0) REVERT: K 160 ARG cc_start: 0.7905 (ptm-80) cc_final: 0.7619 (tmm160) REVERT: G 302 LYS cc_start: 0.9051 (tptt) cc_final: 0.8851 (tptp) REVERT: G 353 ARG cc_start: 0.8696 (mtp-110) cc_final: 0.8469 (mtm110) REVERT: G 472 ASP cc_start: 0.7755 (p0) cc_final: 0.7284 (p0) REVERT: G 480 MET cc_start: 0.7922 (mtp) cc_final: 0.7605 (ptp) REVERT: G 492 GLN cc_start: 0.8654 (tt0) cc_final: 0.8433 (tp40) REVERT: H 87 TYR cc_start: 0.7441 (m-80) cc_final: 0.6963 (m-10) REVERT: H 108 ILE cc_start: 0.7707 (tt) cc_final: 0.7435 (mt) REVERT: C 301 ARG cc_start: 0.6907 (ttm170) cc_final: 0.6439 (tpp80) REVERT: C 313 MET cc_start: 0.7973 (mtm) cc_final: 0.7675 (mtm) REVERT: D 58 ASN cc_start: 0.8086 (t0) cc_final: 0.7471 (m-40) outliers start: 27 outliers final: 10 residues processed: 198 average time/residue: 0.1893 time to fit residues: 56.7994 Evaluate side-chains 164 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 725 GLN Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 95 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 20 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 240 optimal weight: 0.0000 chunk 269 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 268 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 116 optimal weight: 0.4980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 722 GLN F 725 GLN H 109 GLN A 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.106736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077515 restraints weight = 53049.302| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.27 r_work: 0.3227 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23456 Z= 0.111 Angle : 0.505 10.084 31918 Z= 0.256 Chirality : 0.039 0.168 3523 Planarity : 0.004 0.048 4196 Dihedral : 3.915 24.756 3267 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.92 % Allowed : 10.17 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -0.30 (0.15), residues: 2879 helix: 1.02 (0.16), residues: 1033 sheet: -0.60 (0.23), residues: 516 loop : -0.96 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.013 0.001 TYR B 60 PHE 0.011 0.001 PHE A 186 TRP 0.013 0.001 TRP E 99 HIS 0.009 0.001 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00244 (23455) covalent geometry : angle 0.50515 (31916) SS BOND : bond 0.00481 ( 1) SS BOND : angle 1.84609 ( 2) hydrogen bonds : bond 0.03882 ( 1062) hydrogen bonds : angle 4.43768 ( 3027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: E 29 GLU cc_start: 0.6081 (mt-10) cc_final: 0.5860 (mp0) REVERT: F 550 PHE cc_start: 0.6527 (m-80) cc_final: 0.5865 (m-80) REVERT: F 583 ASP cc_start: 0.8020 (t0) cc_final: 0.7687 (t0) REVERT: K 160 ARG cc_start: 0.7872 (ptm-80) cc_final: 0.7565 (tmm160) REVERT: G 335 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8547 (ttt180) REVERT: G 356 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7655 (m) REVERT: G 472 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7489 (p0) REVERT: G 492 GLN cc_start: 0.8697 (tt0) cc_final: 0.8472 (tp40) REVERT: H 108 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7464 (mt) REVERT: H 109 GLN cc_start: 0.7964 (tm130) cc_final: 0.7609 (tm-30) REVERT: C 301 ARG cc_start: 0.6909 (ttm170) cc_final: 0.6620 (ttm170) REVERT: C 313 MET cc_start: 0.7918 (mtm) cc_final: 0.7608 (mtm) REVERT: D 58 ASN cc_start: 0.8103 (t0) cc_final: 0.7499 (m-40) REVERT: D 336 MET cc_start: 0.7939 (mtp) cc_final: 0.7679 (mmm) outliers start: 21 outliers final: 9 residues processed: 175 average time/residue: 0.1825 time to fit residues: 48.6262 Evaluate side-chains 157 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain B residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 144 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 215 optimal weight: 0.0570 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 272 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 270 optimal weight: 0.3980 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN H 22 ASN D 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.105042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.075566 restraints weight = 53156.544| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.26 r_work: 0.3180 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23456 Z= 0.168 Angle : 0.553 8.136 31918 Z= 0.282 Chirality : 0.041 0.190 3523 Planarity : 0.004 0.048 4196 Dihedral : 4.106 26.611 3267 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.67 % Allowed : 10.44 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -0.18 (0.16), residues: 2879 helix: 1.07 (0.16), residues: 1039 sheet: -0.52 (0.23), residues: 515 loop : -0.86 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 352 TYR 0.018 0.002 TYR B 60 PHE 0.017 0.002 PHE A 186 TRP 0.016 0.001 TRP E 99 HIS 0.010 0.001 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00392 (23455) covalent geometry : angle 0.55317 (31916) SS BOND : bond 0.00561 ( 1) SS BOND : angle 1.82453 ( 2) hydrogen bonds : bond 0.04245 ( 1062) hydrogen bonds : angle 4.49294 ( 3027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: E 29 GLU cc_start: 0.6041 (mt-10) cc_final: 0.5779 (mp0) REVERT: G 356 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7795 (m) REVERT: G 472 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7448 (p0) REVERT: H 108 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7563 (mt) REVERT: C 313 MET cc_start: 0.8064 (mtm) cc_final: 0.7723 (mtm) REVERT: D 58 ASN cc_start: 0.8101 (t0) cc_final: 0.7543 (m-40) outliers start: 38 outliers final: 20 residues processed: 180 average time/residue: 0.1808 time to fit residues: 50.0649 Evaluate side-chains 160 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 199 SER Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 44 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 274 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 193 optimal weight: 0.0030 chunk 257 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 279 optimal weight: 0.0010 chunk 113 optimal weight: 4.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 523 HIS F 548 ASN ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN I 32 GLN H 109 GLN H 165 GLN A 119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.103068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.076355 restraints weight = 52565.573| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.47 r_work: 0.3115 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 23456 Z= 0.240 Angle : 0.622 11.936 31918 Z= 0.316 Chirality : 0.044 0.203 3523 Planarity : 0.005 0.060 4196 Dihedral : 4.472 29.238 3267 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.25 % Allowed : 11.27 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -0.29 (0.16), residues: 2879 helix: 0.97 (0.16), residues: 1037 sheet: -0.60 (0.22), residues: 537 loop : -0.91 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 160 TYR 0.023 0.002 TYR B 60 PHE 0.022 0.002 PHE E 122 TRP 0.019 0.002 TRP E 99 HIS 0.011 0.002 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00569 (23455) covalent geometry : angle 0.62170 (31916) SS BOND : bond 0.00806 ( 1) SS BOND : angle 1.73134 ( 2) hydrogen bonds : bond 0.04701 ( 1062) hydrogen bonds : angle 4.69033 ( 3027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 0.942 Fit side-chains REVERT: I 108 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7750 (tm-30) REVERT: I 193 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8421 (t) REVERT: G 283 LYS cc_start: 0.8608 (mttt) cc_final: 0.8310 (mtmm) REVERT: G 356 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7849 (m) REVERT: G 472 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7443 (p0) REVERT: H 103 TRP cc_start: 0.8067 (t60) cc_final: 0.7714 (t60) REVERT: H 108 ILE cc_start: 0.7695 (tt) cc_final: 0.7461 (mt) REVERT: C 313 MET cc_start: 0.8114 (mtm) cc_final: 0.7750 (mtm) REVERT: D 58 ASN cc_start: 0.8019 (t0) cc_final: 0.7562 (m-40) outliers start: 51 outliers final: 29 residues processed: 176 average time/residue: 0.1722 time to fit residues: 47.5825 Evaluate side-chains 157 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 683 THR Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 370 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 383 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 34 optimal weight: 1.9990 chunk 260 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 149 optimal weight: 0.3980 chunk 239 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN I 32 GLN I 520 HIS H 477 GLN A 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.104645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078359 restraints weight = 52649.292| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.35 r_work: 0.3154 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23456 Z= 0.128 Angle : 0.522 8.317 31918 Z= 0.265 Chirality : 0.040 0.173 3523 Planarity : 0.004 0.053 4196 Dihedral : 4.133 26.546 3267 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.67 % Allowed : 12.51 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.06 (0.16), residues: 2879 helix: 1.32 (0.16), residues: 1041 sheet: -0.47 (0.23), residues: 520 loop : -0.74 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 298 TYR 0.014 0.001 TYR B 60 PHE 0.013 0.001 PHE E 122 TRP 0.014 0.001 TRP E 99 HIS 0.004 0.001 HIS H 445 Details of bonding type rmsd covalent geometry : bond 0.00293 (23455) covalent geometry : angle 0.52152 (31916) SS BOND : bond 0.00409 ( 1) SS BOND : angle 1.36137 ( 2) hydrogen bonds : bond 0.03894 ( 1062) hydrogen bonds : angle 4.42119 ( 3027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.892 Fit side-chains REVERT: I 108 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7742 (tm-30) REVERT: I 193 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8262 (t) REVERT: G 283 LYS cc_start: 0.8603 (mttt) cc_final: 0.8310 (mtmm) REVERT: G 353 ARG cc_start: 0.8550 (mtp-110) cc_final: 0.8350 (mtm110) REVERT: G 356 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7845 (m) REVERT: G 472 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7395 (p0) REVERT: G 492 GLN cc_start: 0.8694 (tt0) cc_final: 0.8452 (tp40) REVERT: H 108 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7504 (mt) REVERT: C 313 MET cc_start: 0.8068 (mtm) cc_final: 0.7753 (mtm) REVERT: D 58 ASN cc_start: 0.7952 (t0) cc_final: 0.7554 (m-40) outliers start: 38 outliers final: 24 residues processed: 165 average time/residue: 0.1777 time to fit residues: 45.3068 Evaluate side-chains 162 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 370 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 477 GLN Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 223 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN I 518 HIS I 520 HIS H 109 GLN A 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.103698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.077038 restraints weight = 52737.592| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.50 r_work: 0.3126 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23456 Z= 0.186 Angle : 0.561 8.298 31918 Z= 0.285 Chirality : 0.041 0.215 3523 Planarity : 0.004 0.045 4196 Dihedral : 4.221 26.827 3267 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.72 % Allowed : 12.90 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.00 (0.16), residues: 2879 helix: 1.26 (0.16), residues: 1043 sheet: -0.50 (0.23), residues: 522 loop : -0.76 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 160 TYR 0.018 0.002 TYR B 60 PHE 0.018 0.002 PHE E 122 TRP 0.015 0.001 TRP E 99 HIS 0.005 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00438 (23455) covalent geometry : angle 0.56107 (31916) SS BOND : bond 0.00598 ( 1) SS BOND : angle 1.47718 ( 2) hydrogen bonds : bond 0.04213 ( 1062) hydrogen bonds : angle 4.48100 ( 3027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.890 Fit side-chains REVERT: K 160 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7452 (tmm160) REVERT: I 108 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7742 (tm-30) REVERT: I 193 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8334 (t) REVERT: G 283 LYS cc_start: 0.8603 (mttt) cc_final: 0.8310 (mtmm) REVERT: G 356 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7891 (m) REVERT: G 472 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7409 (p0) REVERT: G 492 GLN cc_start: 0.8711 (tt0) cc_final: 0.8458 (tp40) REVERT: H 108 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7478 (mt) REVERT: C 313 MET cc_start: 0.8074 (mtm) cc_final: 0.7739 (mtm) REVERT: D 12 LEU cc_start: 0.8298 (tp) cc_final: 0.7340 (mt) REVERT: D 58 ASN cc_start: 0.7905 (t0) cc_final: 0.7487 (m-40) REVERT: D 336 MET cc_start: 0.7895 (tpt) cc_final: 0.7518 (mmm) outliers start: 39 outliers final: 29 residues processed: 165 average time/residue: 0.1780 time to fit residues: 45.4849 Evaluate side-chains 168 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 66 ASN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 370 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 279 optimal weight: 0.0770 chunk 232 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 169 optimal weight: 0.2980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.105282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078211 restraints weight = 52791.353| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.45 r_work: 0.3173 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23456 Z= 0.116 Angle : 0.511 7.916 31918 Z= 0.259 Chirality : 0.039 0.198 3523 Planarity : 0.004 0.051 4196 Dihedral : 4.028 25.560 3267 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.59 % Allowed : 12.86 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.28 (0.16), residues: 2879 helix: 1.50 (0.16), residues: 1042 sheet: -0.39 (0.23), residues: 530 loop : -0.59 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 160 TYR 0.014 0.001 TYR B 60 PHE 0.012 0.001 PHE E 122 TRP 0.014 0.001 TRP B 49 HIS 0.004 0.001 HIS H 445 Details of bonding type rmsd covalent geometry : bond 0.00263 (23455) covalent geometry : angle 0.51080 (31916) SS BOND : bond 0.00442 ( 1) SS BOND : angle 1.41974 ( 2) hydrogen bonds : bond 0.03777 ( 1062) hydrogen bonds : angle 4.31466 ( 3027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.940 Fit side-chains REVERT: K 160 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7478 (tmm160) REVERT: I 108 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7627 (tm-30) REVERT: I 193 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8228 (t) REVERT: I 520 HIS cc_start: 0.8214 (m170) cc_final: 0.7940 (m170) REVERT: G 283 LYS cc_start: 0.8580 (mttt) cc_final: 0.8290 (mtmm) REVERT: G 472 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: H 108 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7476 (mt) REVERT: C 313 MET cc_start: 0.8072 (mtm) cc_final: 0.7759 (mtm) REVERT: D 12 LEU cc_start: 0.8252 (tp) cc_final: 0.7321 (mt) REVERT: D 58 ASN cc_start: 0.7841 (t0) cc_final: 0.7433 (m-40) REVERT: D 336 MET cc_start: 0.7870 (tpt) cc_final: 0.7496 (mmm) outliers start: 36 outliers final: 27 residues processed: 166 average time/residue: 0.1899 time to fit residues: 47.7913 Evaluate side-chains 165 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 66 ASN Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain G residue 370 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 183 optimal weight: 3.9990 chunk 83 optimal weight: 0.0050 chunk 146 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 240 optimal weight: 0.1980 chunk 283 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN H 104 ASN A 119 ASN C 374 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.105755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079773 restraints weight = 52368.712| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.41 r_work: 0.3189 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23456 Z= 0.095 Angle : 0.490 8.543 31918 Z= 0.247 Chirality : 0.039 0.238 3523 Planarity : 0.004 0.043 4196 Dihedral : 3.773 23.363 3267 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.23 % Allowed : 13.21 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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 (0.16), residues: 2879 helix: 1.74 (0.16), residues: 1041 sheet: -0.27 (0.23), residues: 528 loop : -0.47 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 47 TYR 0.018 0.001 TYR K 147 PHE 0.012 0.001 PHE B 242 TRP 0.016 0.001 TRP B 49 HIS 0.003 0.001 HIS H 445 Details of bonding type rmsd covalent geometry : bond 0.00210 (23455) covalent geometry : angle 0.49010 (31916) SS BOND : bond 0.00314 ( 1) SS BOND : angle 1.42002 ( 2) hydrogen bonds : bond 0.03407 ( 1062) hydrogen bonds : angle 4.13768 ( 3027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.841 Fit side-chains REVERT: F 542 ILE cc_start: 0.8635 (mt) cc_final: 0.8422 (pt) REVERT: K 160 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7479 (tmm160) REVERT: I 193 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8183 (t) REVERT: I 319 LEU cc_start: 0.8414 (tp) cc_final: 0.8149 (tp) REVERT: I 520 HIS cc_start: 0.8095 (m170) cc_final: 0.7762 (m170) REVERT: H 108 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7430 (mt) REVERT: C 313 MET cc_start: 0.8041 (mtm) cc_final: 0.7745 (mtm) REVERT: D 12 LEU cc_start: 0.8120 (tp) cc_final: 0.7197 (mt) REVERT: D 58 ASN cc_start: 0.7822 (t0) cc_final: 0.7487 (m-40) outliers start: 28 outliers final: 21 residues processed: 164 average time/residue: 0.1848 time to fit residues: 45.7636 Evaluate side-chains 161 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain G residue 370 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 149 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 114 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 273 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 264 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 HIS A 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.104539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077101 restraints weight = 53493.482| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.58 r_work: 0.3149 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23456 Z= 0.178 Angle : 0.558 8.814 31918 Z= 0.282 Chirality : 0.041 0.250 3523 Planarity : 0.004 0.044 4196 Dihedral : 4.029 25.592 3267 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.28 % Allowed : 13.52 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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 (0.16), residues: 2879 helix: 1.55 (0.16), residues: 1041 sheet: -0.34 (0.23), residues: 493 loop : -0.55 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 160 TYR 0.019 0.002 TYR K 147 PHE 0.016 0.001 PHE E 122 TRP 0.014 0.001 TRP H 103 HIS 0.008 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00418 (23455) covalent geometry : angle 0.55741 (31916) SS BOND : bond 0.00617 ( 1) SS BOND : angle 1.42933 ( 2) hydrogen bonds : bond 0.04032 ( 1062) hydrogen bonds : angle 4.33217 ( 3027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.868 Fit side-chains REVERT: E 52 MET cc_start: 0.5498 (mtm) cc_final: 0.5200 (ppp) REVERT: K 160 ARG cc_start: 0.7720 (ttp80) cc_final: 0.7469 (tmm160) REVERT: I 108 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7713 (tm-30) REVERT: I 193 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8337 (t) REVERT: C 313 MET cc_start: 0.8060 (mtm) cc_final: 0.7743 (mtm) REVERT: D 58 ASN cc_start: 0.7824 (t0) cc_final: 0.7475 (m110) outliers start: 29 outliers final: 25 residues processed: 158 average time/residue: 0.1780 time to fit residues: 43.2507 Evaluate side-chains 155 residues out of total 2281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain I residue 249 MET Chi-restraints excluded: chain G residue 370 ASP Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 383 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 51 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 548 ASN ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN I 520 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.104649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077292 restraints weight = 53111.614| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.61 r_work: 0.3149 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23456 Z= 0.164 Angle : 0.554 13.414 31918 Z= 0.280 Chirality : 0.041 0.229 3523 Planarity : 0.004 0.043 4196 Dihedral : 4.054 26.213 3267 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.41 % Allowed : 13.61 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.32 (0.16), residues: 2879 helix: 1.53 (0.16), residues: 1041 sheet: -0.35 (0.23), residues: 493 loop : -0.57 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 352 TYR 0.018 0.002 TYR K 147 PHE 0.015 0.001 PHE E 122 TRP 0.014 0.001 TRP E 99 HIS 0.007 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00384 (23455) covalent geometry : angle 0.55386 (31916) SS BOND : bond 0.00588 ( 1) SS BOND : angle 1.36819 ( 2) hydrogen bonds : bond 0.03958 ( 1062) hydrogen bonds : angle 4.34633 ( 3027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10705.64 seconds wall clock time: 182 minutes 13.24 seconds (10933.24 seconds total)