Starting phenix.real_space_refine on Wed Nov 19 01:27:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cfw_7468/11_2025/6cfw_7468.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cfw_7468/11_2025/6cfw_7468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cfw_7468/11_2025/6cfw_7468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cfw_7468/11_2025/6cfw_7468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cfw_7468/11_2025/6cfw_7468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cfw_7468/11_2025/6cfw_7468.map" } resolution = 3.7 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= 0.008 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: 6 Type Number sf(0) Gaussians Fe 13 7.16 5 Ni 1 6.56 5 S 105 5.16 5 C 12898 2.51 5 N 3187 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.04s 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: 19589 Number of models: 1 Model: "" Number of chains: 17 Chain: "H" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3850 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain: "G" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 866 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "D" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 579 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 811 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "M" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2468 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 15, 'TRANS': 301} Chain: "F" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1073 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "A" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 10, 'TRANS': 154} Chain: "E" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "C" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 870 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 622 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "J" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 128} Chain: "K" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1362 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 14, 'TRANS': 151} Chain: "L" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2965 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "N" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 12, 'TRANS': 108} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'NFU': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16169 SG CYS L 71 45.337 75.236 138.924 1.00 60.30 S ATOM 18577 SG CYS L 377 43.936 72.038 136.557 1.00 75.46 S ATOM 16151 SG CYS L 68 46.014 71.530 139.271 1.00 55.16 S ATOM 16169 SG CYS L 71 45.337 75.236 138.924 1.00 60.30 S ATOM 18557 SG CYS L 374 47.889 71.986 136.372 1.00 75.19 S ATOM 18577 SG CYS L 377 43.936 72.038 136.557 1.00 75.46 S Time building chain proxies: 4.62, per 1000 atoms: 0.24 Number of scatterers: 19589 At special positions: 0 Unit cell: (125.12, 109.888, 184.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 1 28.00 Fe 13 26.01 S 105 16.00 O 3385 8.00 N 3187 7.00 C 12898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 866.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 J 201 " pdb="FE3 SF4 J 201 " - pdb=" SG CYS J 35 " pdb="FE4 SF4 J 201 " - pdb=" SG CYS J 38 " pdb="FE2 SF4 J 201 " - pdb=" SG CYS J 132 " pdb="FE1 SF4 J 201 " - pdb=" SG CYS J 102 " pdb=" SF4 N 201 " pdb="FE1 SF4 N 201 " - pdb=" SG CYS N 77 " pdb="FE3 SF4 N 201 " - pdb=" SG CYS N 56 " pdb="FE4 SF4 N 201 " - pdb=" SG CYS N 80 " pdb=" SF4 N 202 " pdb="FE1 SF4 N 202 " - pdb=" SG CYS N 87 " pdb="FE4 SF4 N 202 " - pdb=" SG CYS N 52 " pdb="FE3 SF4 N 202 " - pdb=" SG CYS N 46 " Number of angles added : 30 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 10 sheets defined 59.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 8 through 16 Processing helix chain 'H' and resid 21 through 25 removed outlier: 3.827A pdb=" N LEU H 24 " --> pdb=" O VAL H 21 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS H 25 " --> pdb=" O SER H 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 21 through 25' Processing helix chain 'H' and resid 27 through 54 removed outlier: 3.615A pdb=" N ILE H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET H 35 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU H 41 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 100 removed outlier: 3.846A pdb=" N MET H 87 " --> pdb=" O PHE H 83 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 92 " --> pdb=" O VAL H 88 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL H 94 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER H 95 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE H 96 " --> pdb=" O THR H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 123 removed outlier: 4.138A pdb=" N THR H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU H 123 " --> pdb=" O ILE H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 132 removed outlier: 4.200A pdb=" N ALA H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 154 removed outlier: 3.569A pdb=" N VAL H 140 " --> pdb=" O PHE H 136 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA H 154 " --> pdb=" O TYR H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 192 removed outlier: 3.531A pdb=" N ALA H 165 " --> pdb=" O GLU H 161 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY H 166 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS H 168 " --> pdb=" O GLU H 164 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA H 172 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU H 175 " --> pdb=" O PHE H 171 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY H 189 " --> pdb=" O ALA H 185 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 206 removed outlier: 4.080A pdb=" N ALA H 204 " --> pdb=" O ALA H 200 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU H 205 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN H 206 " --> pdb=" O LYS H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 223 removed outlier: 4.198A pdb=" N LEU H 215 " --> pdb=" O ALA H 211 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 217 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE H 218 " --> pdb=" O ALA H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 231 Processing helix chain 'H' and resid 232 through 239 removed outlier: 4.101A pdb=" N ALA H 236 " --> pdb=" O HIS H 232 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 248 Processing helix chain 'H' and resid 260 through 269 Processing helix chain 'H' and resid 276 through 298 removed outlier: 4.230A pdb=" N ILE H 280 " --> pdb=" O ASN H 276 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP H 282 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE H 286 " --> pdb=" O TRP H 282 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE H 287 " --> pdb=" O ILE H 283 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU H 292 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE H 293 " --> pdb=" O CYS H 289 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET H 298 " --> pdb=" O VAL H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 313 removed outlier: 3.652A pdb=" N LEU H 309 " --> pdb=" O LEU H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 330 removed outlier: 3.775A pdb=" N ILE H 320 " --> pdb=" O GLN H 316 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL H 329 " --> pdb=" O GLY H 325 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA H 330 " --> pdb=" O ILE H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 368 removed outlier: 3.688A pdb=" N VAL H 348 " --> pdb=" O ILE H 344 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL H 360 " --> pdb=" O LEU H 356 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 361 " --> pdb=" O LEU H 357 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE H 368 " --> pdb=" O VAL H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 382 Processing helix chain 'H' and resid 383 through 399 removed outlier: 3.674A pdb=" N THR H 387 " --> pdb=" O MET H 383 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE H 397 " --> pdb=" O GLY H 393 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL H 398 " --> pdb=" O ALA H 394 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY H 399 " --> pdb=" O ALA H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 420 removed outlier: 4.227A pdb=" N LEU H 411 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE H 412 " --> pdb=" O SER H 408 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN H 420 " --> pdb=" O SER H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 444 removed outlier: 3.927A pdb=" N GLY H 424 " --> pdb=" O ASN H 420 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA H 425 " --> pdb=" O PRO H 421 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS H 434 " --> pdb=" O GLY H 430 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 435 " --> pdb=" O THR H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 480 removed outlier: 3.650A pdb=" N ILE H 468 " --> pdb=" O MET H 464 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE H 469 " --> pdb=" O LEU H 465 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY H 478 " --> pdb=" O ILE H 474 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE H 480 " --> pdb=" O VAL H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 488 removed outlier: 3.670A pdb=" N ILE H 484 " --> pdb=" O PHE H 480 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP H 486 " --> pdb=" O TRP H 482 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE H 488 " --> pdb=" O ILE H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 495 removed outlier: 3.889A pdb=" N ALA H 493 " --> pdb=" O MET H 489 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA H 495 " --> pdb=" O PRO H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 506 removed outlier: 3.520A pdb=" N TYR H 502 " --> pdb=" O ASP H 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 20 removed outlier: 3.723A pdb=" N LEU G 7 " --> pdb=" O ALA G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 46 removed outlier: 3.581A pdb=" N SER G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 101 removed outlier: 4.044A pdb=" N LEU G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR G 101 " --> pdb=" O THR G 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 36 removed outlier: 4.108A pdb=" N ILE D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 60 removed outlier: 3.558A pdb=" N ALA D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 50 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 removed outlier: 3.674A pdb=" N ALA D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 removed outlier: 4.493A pdb=" N TYR D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 8 through 31 removed outlier: 3.658A pdb=" N ILE I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS I 30 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER I 31 " --> pdb=" O TRP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 87 removed outlier: 4.030A pdb=" N THR I 84 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 85 " --> pdb=" O PHE I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 114 removed outlier: 3.785A pdb=" N TYR I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU I 113 " --> pdb=" O VAL I 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 35 removed outlier: 3.623A pdb=" N ILE M 8 " --> pdb=" O VAL M 4 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY M 9 " --> pdb=" O TYR M 5 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU M 10 " --> pdb=" O GLY M 6 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU M 22 " --> pdb=" O SER M 18 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU M 23 " --> pdb=" O VAL M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 56 removed outlier: 4.333A pdb=" N LEU M 51 " --> pdb=" O PHE M 47 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS M 56 " --> pdb=" O LYS M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 81 removed outlier: 3.668A pdb=" N LEU M 74 " --> pdb=" O ALA M 70 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU M 76 " --> pdb=" O PRO M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 86 removed outlier: 3.691A pdb=" N THR M 86 " --> pdb=" O LEU M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 120 removed outlier: 3.885A pdb=" N ALA M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP M 111 " --> pdb=" O LEU M 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE M 112 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 140 removed outlier: 3.515A pdb=" N ALA M 131 " --> pdb=" O ARG M 127 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG M 132 " --> pdb=" O ILE M 128 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY M 133 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU M 136 " --> pdb=" O ARG M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 155 removed outlier: 3.963A pdb=" N LEU M 146 " --> pdb=" O PRO M 142 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY M 147 " --> pdb=" O ALA M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 171 removed outlier: 3.699A pdb=" N LEU M 169 " --> pdb=" O LEU M 166 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR M 170 " --> pdb=" O SER M 167 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU M 171 " --> pdb=" O SER M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 200 removed outlier: 3.811A pdb=" N ALA M 184 " --> pdb=" O VAL M 180 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL M 186 " --> pdb=" O TRP M 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE M 200 " --> pdb=" O LEU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 250 removed outlier: 3.629A pdb=" N GLY M 228 " --> pdb=" O GLY M 224 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER M 235 " --> pdb=" O LYS M 231 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA M 242 " --> pdb=" O GLU M 238 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE M 250 " --> pdb=" O VAL M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 288 removed outlier: 3.601A pdb=" N ILE M 264 " --> pdb=" O GLN M 260 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL M 279 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER M 280 " --> pdb=" O VAL M 276 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR M 282 " --> pdb=" O LEU M 278 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR M 288 " --> pdb=" O PHE M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 removed outlier: 4.163A pdb=" N ASN M 298 " --> pdb=" O SER M 294 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU M 299 " --> pdb=" O GLN M 295 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU M 300 " --> pdb=" O ALA M 296 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP M 301 " --> pdb=" O VAL M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 317 Processing helix chain 'F' and resid 7 through 30 Proline residue: F 18 - end of helix removed outlier: 3.778A pdb=" N PHE F 23 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.848A pdb=" N GLY F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 4.105A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 84 removed outlier: 4.855A pdb=" N GLU F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY F 75 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL F 80 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 142 removed outlier: 3.762A pdb=" N THR F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 142 " --> pdb=" O PHE F 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 18 removed outlier: 3.952A pdb=" N LEU A 13 " --> pdb=" O TRP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.249A pdb=" N ALA A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.860A pdb=" N PHE A 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 88 removed outlier: 4.055A pdb=" N TRP A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 3.926A pdb=" N LYS A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.630A pdb=" N ILE A 111 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.807A pdb=" N TRP A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 Processing helix chain 'E' and resid 34 through 38 Processing helix chain 'E' and resid 40 through 49 Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.898A pdb=" N VAL E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 68 through 89 removed outlier: 4.103A pdb=" N THR E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 24 removed outlier: 3.600A pdb=" N ILE C 8 " --> pdb=" O TYR C 4 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 64 removed outlier: 4.361A pdb=" N LYS C 40 " --> pdb=" O HIS C 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C 60 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 100 removed outlier: 3.841A pdb=" N MET C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C 79 " --> pdb=" O HIS C 75 " (cutoff:3.500A) Proline residue: C 88 - end of helix Processing helix chain 'B' and resid 4 through 23 removed outlier: 3.648A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 21 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 52 removed outlier: 3.764A pdb=" N VAL B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 79 removed outlier: 4.019A pdb=" N ALA B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 23 Processing helix chain 'J' and resid 37 through 44 removed outlier: 3.934A pdb=" N GLU J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 78 No H-bonds generated for 'chain 'J' and resid 76 through 78' Processing helix chain 'J' and resid 79 through 86 removed outlier: 3.853A pdb=" N VAL J 83 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 122 Processing helix chain 'J' and resid 135 through 155 removed outlier: 3.678A pdb=" N ILE J 139 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS J 155 " --> pdb=" O ALA J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 15 removed outlier: 3.611A pdb=" N ARG K 14 " --> pdb=" O LYS K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 52 removed outlier: 4.144A pdb=" N ARG K 49 " --> pdb=" O MET K 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU K 50 " --> pdb=" O LYS K 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP K 52 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 121 removed outlier: 3.775A pdb=" N PHE K 113 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU K 116 " --> pdb=" O GLN K 112 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'L' and resid 56 through 64 removed outlier: 3.646A pdb=" N ILE L 60 " --> pdb=" O ASN L 56 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET L 61 " --> pdb=" O TYR L 57 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR L 62 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 68 removed outlier: 3.899A pdb=" N CYS L 68 " --> pdb=" O GLU L 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 65 through 68' Processing helix chain 'L' and resid 73 through 88 removed outlier: 3.826A pdb=" N TYR L 79 " --> pdb=" O HIS L 75 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL L 80 " --> pdb=" O ASN L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 119 removed outlier: 3.613A pdb=" N GLU L 96 " --> pdb=" O PRO L 92 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N HIS L 109 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU L 113 " --> pdb=" O HIS L 109 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 135 removed outlier: 3.822A pdb=" N LEU L 128 " --> pdb=" O TYR L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 146 Processing helix chain 'L' and resid 166 through 180 removed outlier: 3.924A pdb=" N ASP L 174 " --> pdb=" O ARG L 170 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET L 175 " --> pdb=" O LEU L 171 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE L 176 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS L 177 " --> pdb=" O LEU L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 192 removed outlier: 3.534A pdb=" N PHE L 190 " --> pdb=" O ILE L 186 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS L 192 " --> pdb=" O ASP L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 199 Processing helix chain 'L' and resid 207 through 214 Processing helix chain 'L' and resid 218 through 225 removed outlier: 4.284A pdb=" N SER L 224 " --> pdb=" O THR L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 243 removed outlier: 3.679A pdb=" N LEU L 242 " --> pdb=" O TYR L 239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY L 243 " --> pdb=" O PRO L 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 239 through 243' Processing helix chain 'L' and resid 248 through 253 removed outlier: 4.063A pdb=" N VAL L 252 " --> pdb=" O THR L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 282 removed outlier: 3.878A pdb=" N LEU L 272 " --> pdb=" O ARG L 268 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP L 277 " --> pdb=" O TRP L 273 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU L 280 " --> pdb=" O LEU L 276 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA L 282 " --> pdb=" O LEU L 278 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 356 removed outlier: 4.159A pdb=" N ASN L 348 " --> pdb=" O PRO L 344 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA L 353 " --> pdb=" O LEU L 349 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS L 354 " --> pdb=" O PHE L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 369 removed outlier: 4.582A pdb=" N VAL L 366 " --> pdb=" O ALA L 362 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 372 No H-bonds generated for 'chain 'L' and resid 370 through 372' Processing helix chain 'L' and resid 374 through 378 removed outlier: 3.590A pdb=" N CYS L 377 " --> pdb=" O CYS L 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 15 removed outlier: 4.119A pdb=" N PHE N 15 " --> pdb=" O ILE N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 26 removed outlier: 3.812A pdb=" N LYS N 25 " --> pdb=" O PRO N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 56 removed outlier: 3.835A pdb=" N VAL N 55 " --> pdb=" O MET N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 77 No H-bonds generated for 'chain 'N' and resid 75 through 77' Processing helix chain 'N' and resid 114 through 122 Processing sheet with id=AA1, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AA2, first strand: chain 'G' and resid 57 through 58 removed outlier: 5.489A pdb=" N ALA G 69 " --> pdb=" O THR G 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'I' and resid 35 through 37 removed outlier: 6.395A pdb=" N ARG I 36 " --> pdb=" O ILE M 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 99 removed outlier: 4.025A pdb=" N TYR A 135 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU A 126 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS A 137 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR A 124 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 27 through 28 removed outlier: 6.322A pdb=" N LEU J 69 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE J 99 " --> pdb=" O LEU J 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 127 " --> pdb=" O VAL J 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 21 through 24 removed outlier: 5.039A pdb=" N SER K 86 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL K 32 " --> pdb=" O SER K 86 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL K 85 " --> pdb=" O LEU K 77 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU K 77 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS K 74 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE K 59 " --> pdb=" O HIS K 74 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU K 76 " --> pdb=" O TYR K 57 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR K 57 " --> pdb=" O LEU K 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 8 through 10 removed outlier: 3.508A pdb=" N VAL L 8 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE L 10 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE L 27 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS L 24 " --> pdb=" O LYS L 40 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN L 36 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP L 30 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 313 through 317 removed outlier: 3.666A pdb=" N VAL L 324 " --> pdb=" O ARG L 342 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'N' and resid 61 through 63 removed outlier: 3.767A pdb=" N VAL N 62 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR N 71 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU N 72 " --> pdb=" O TYR N 112 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2559 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: 2.98 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.45: 8921 1.45 - 1.75: 10934 1.75 - 2.04: 166 2.04 - 2.34: 36 2.34 - 2.64: 1 Bond restraints: 20058 Sorted by residual: bond pdb=" C2 NFU L 401 " pdb="FE NFU L 401 " ideal model delta sigma weight residual 1.940 1.826 0.114 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C1 NFU L 401 " pdb="FE NFU L 401 " ideal model delta sigma weight residual 1.939 1.825 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C ALA M 71 " pdb=" N PRO M 72 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" N ALA J 151 " pdb=" CA ALA J 151 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" C THR A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 1.334 1.407 -0.073 2.34e-02 1.83e+03 9.78e+00 ... (remaining 20053 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 26819 3.89 - 7.79: 423 7.79 - 11.68: 58 11.68 - 15.58: 5 15.58 - 19.47: 1 Bond angle restraints: 27306 Sorted by residual: angle pdb=" N PRO I 56 " pdb=" CA PRO I 56 " pdb=" CB PRO I 56 " ideal model delta sigma weight residual 103.25 110.56 -7.31 1.05e+00 9.07e-01 4.85e+01 angle pdb=" N HIS F 100 " pdb=" CA HIS F 100 " pdb=" C HIS F 100 " ideal model delta sigma weight residual 109.71 101.22 8.49 1.41e+00 5.03e-01 3.63e+01 angle pdb=" N PRO I 51 " pdb=" CA PRO I 51 " pdb=" CB PRO I 51 " ideal model delta sigma weight residual 103.25 109.49 -6.24 1.05e+00 9.07e-01 3.53e+01 angle pdb=" CA LEU H 4 " pdb=" CB LEU H 4 " pdb=" CG LEU H 4 " ideal model delta sigma weight residual 116.30 135.77 -19.47 3.50e+00 8.16e-02 3.10e+01 angle pdb=" N ASN L 298 " pdb=" CA ASN L 298 " pdb=" C ASN L 298 " ideal model delta sigma weight residual 113.43 106.43 7.00 1.26e+00 6.30e-01 3.08e+01 ... (remaining 27301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 10956 17.65 - 35.29: 675 35.29 - 52.94: 121 52.94 - 70.58: 17 70.58 - 88.23: 6 Dihedral angle restraints: 11775 sinusoidal: 4536 harmonic: 7239 Sorted by residual: dihedral pdb=" CA ASP J 92 " pdb=" C ASP J 92 " pdb=" N PRO J 93 " pdb=" CA PRO J 93 " ideal model delta harmonic sigma weight residual -180.00 -109.40 -70.60 0 5.00e+00 4.00e-02 1.99e+02 dihedral pdb=" CA ALA J 117 " pdb=" C ALA J 117 " pdb=" N PRO J 118 " pdb=" CA PRO J 118 " ideal model delta harmonic sigma weight residual -180.00 -110.58 -69.42 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA VAL K 154 " pdb=" C VAL K 154 " pdb=" N PRO K 155 " pdb=" CA PRO K 155 " ideal model delta harmonic sigma weight residual 180.00 123.71 56.29 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 11772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3085 0.143 - 0.286: 110 0.286 - 0.429: 15 0.429 - 0.572: 2 0.572 - 0.715: 6 Chirality restraints: 3218 Sorted by residual: chirality pdb="FE3 SF4 J 201 " pdb=" S1 SF4 J 201 " pdb=" S2 SF4 J 201 " pdb=" S4 SF4 J 201 " both_signs ideal model delta sigma weight residual False -10.55 -9.84 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb="FE1 SF4 N 201 " pdb=" S2 SF4 N 201 " pdb=" S3 SF4 N 201 " pdb=" S4 SF4 N 201 " both_signs ideal model delta sigma weight residual False -10.55 -9.88 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb="FE4 SF4 J 201 " pdb=" S1 SF4 J 201 " pdb=" S2 SF4 J 201 " pdb=" S3 SF4 J 201 " both_signs ideal model delta sigma weight residual False 10.55 9.93 0.63 2.00e-01 2.50e+01 9.77e+00 ... (remaining 3215 not shown) Planarity restraints: 3363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 150 " 0.029 2.00e-02 2.50e+03 5.62e-02 3.16e+01 pdb=" C LEU J 150 " -0.097 2.00e-02 2.50e+03 pdb=" O LEU J 150 " 0.036 2.00e-02 2.50e+03 pdb=" N ALA J 151 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS J 102 " -0.088 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO J 103 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO J 103 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO J 103 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 141 " -0.086 5.00e-02 4.00e+02 1.31e-01 2.74e+01 pdb=" N PRO M 142 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO M 142 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO M 142 " -0.070 5.00e-02 4.00e+02 ... (remaining 3360 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 95 2.55 - 3.14: 14692 3.14 - 3.73: 28749 3.73 - 4.31: 37731 4.31 - 4.90: 63806 Nonbonded interactions: 145073 Sorted by model distance: nonbonded pdb=" O GLU L 250 " pdb=" O GLY L 254 " model vdw 1.968 3.040 nonbonded pdb=" N GLU L 255 " pdb=" OE1 GLU L 255 " model vdw 2.103 3.120 nonbonded pdb=" CD2 LEU L 19 " pdb=" O GLU L 21 " model vdw 2.110 3.460 nonbonded pdb=" O SER H 272 " pdb=" OG SER H 272 " model vdw 2.243 3.040 nonbonded pdb=" OG SER C 22 " pdb=" OG1 THR B 17 " model vdw 2.261 3.040 ... (remaining 145068 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.600 Find NCS groups from input model: 0.110 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.021 0.913 20069 Z= 0.684 Angle : 1.626 59.211 27336 Z= 0.667 Chirality : 0.075 0.715 3218 Planarity : 0.011 0.132 3363 Dihedral : 12.048 88.231 7151 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.67 % Favored : 88.97 % Rotamer: Outliers : 1.60 % Allowed : 8.36 % Favored : 90.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 6.30 % Twisted General : 0.33 % 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: -4.93 (0.13), residues: 2502 helix: -2.70 (0.11), residues: 1363 sheet: -2.16 (0.46), residues: 128 loop : -4.19 (0.15), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 82 TYR 0.055 0.004 TYR H 345 PHE 0.061 0.004 PHE K 135 TRP 0.053 0.004 TRP H 497 HIS 0.018 0.004 HIS K 164 Details of bonding type rmsd covalent geometry : bond 0.01013 (20058) covalent geometry : angle 1.26986 (27306) hydrogen bonds : bond 0.18810 ( 875) hydrogen bonds : angle 6.46273 ( 2559) metal coordination : bond 0.81646 ( 10) metal coordination : angle 30.66576 ( 30) Misc. bond : bond 0.11718 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 534 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 112 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8719 (mt) REVERT: H 164 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8129 (tm-30) REVERT: H 263 ILE cc_start: 0.9222 (mm) cc_final: 0.8983 (mt) REVERT: H 415 SER cc_start: 0.8796 (m) cc_final: 0.8480 (p) REVERT: D 56 GLU cc_start: 0.8892 (tp30) cc_final: 0.8687 (tp30) REVERT: I 12 ILE cc_start: 0.9325 (mm) cc_final: 0.9091 (mt) REVERT: I 114 ARG cc_start: 0.7196 (mtm180) cc_final: 0.6853 (ttt-90) REVERT: M 67 MET cc_start: 0.8876 (mmm) cc_final: 0.8667 (mmm) REVERT: F 123 LEU cc_start: 0.8879 (mm) cc_final: 0.8624 (mt) REVERT: A 11 TYR cc_start: 0.9351 (t80) cc_final: 0.9006 (t80) REVERT: A 39 SER cc_start: 0.9600 (t) cc_final: 0.9250 (p) REVERT: A 54 SER cc_start: 0.9006 (p) cc_final: 0.8518 (t) REVERT: A 58 ASN cc_start: 0.8605 (t0) cc_final: 0.8112 (m-40) REVERT: A 74 TRP cc_start: 0.6837 (t60) cc_final: 0.6581 (t60) REVERT: E 38 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8656 (ttpt) REVERT: K 49 ARG cc_start: 0.6471 (tpt-90) cc_final: 0.5596 (tpt-90) REVERT: K 131 LYS cc_start: 0.7576 (mtmt) cc_final: 0.7029 (mmtm) REVERT: K 144 ILE cc_start: 0.8176 (tt) cc_final: 0.7730 (mm) REVERT: K 149 THR cc_start: 0.9045 (p) cc_final: 0.8739 (p) REVERT: L 230 SER cc_start: 0.9258 (m) cc_final: 0.8770 (m) REVERT: L 242 LEU cc_start: 0.9029 (pp) cc_final: 0.8752 (pp) REVERT: L 330 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7374 (pt0) REVERT: N 107 ASP cc_start: 0.7807 (m-30) cc_final: 0.7523 (m-30) REVERT: N 111 ILE cc_start: 0.9310 (tt) cc_final: 0.9001 (mt) REVERT: N 114 THR cc_start: 0.8981 (t) cc_final: 0.8726 (p) outliers start: 33 outliers final: 11 residues processed: 564 average time/residue: 0.1622 time to fit residues: 137.5743 Evaluate side-chains 341 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 328 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain E residue 38 LYS Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 250 GLU Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.0050 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 ASN I 89 HIS M 212 GLN F 12 ASN C 26 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 17 ASN K 25 ASN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 109 HIS L 151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093564 restraints weight = 35798.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095973 restraints weight = 20486.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097593 restraints weight = 14282.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098533 restraints weight = 11302.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099317 restraints weight = 9780.419| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20069 Z= 0.136 Angle : 0.782 27.651 27336 Z= 0.360 Chirality : 0.043 0.230 3218 Planarity : 0.007 0.106 3363 Dihedral : 6.886 59.435 2751 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.39 % Favored : 91.41 % Rotamer: Outliers : 4.28 % Allowed : 14.10 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.17 % 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: -3.20 (0.15), residues: 2502 helix: -1.02 (0.13), residues: 1382 sheet: -1.91 (0.46), residues: 127 loop : -3.81 (0.16), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 34 TYR 0.025 0.001 TYR E 25 PHE 0.031 0.002 PHE K 135 TRP 0.020 0.001 TRP K 27 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00291 (20058) covalent geometry : angle 0.70674 (27306) hydrogen bonds : bond 0.05400 ( 875) hydrogen bonds : angle 4.28206 ( 2559) metal coordination : bond 0.00749 ( 10) metal coordination : angle 10.14084 ( 30) Misc. bond : bond 0.00288 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 428 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: H 164 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8060 (tm-30) REVERT: H 196 MET cc_start: 0.8215 (mtm) cc_final: 0.7973 (mtt) REVERT: H 237 ASP cc_start: 0.7778 (p0) cc_final: 0.7416 (p0) REVERT: H 266 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8735 (mt) REVERT: H 293 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8719 (pt) REVERT: H 353 MET cc_start: 0.8204 (ptp) cc_final: 0.7748 (mtm) REVERT: H 415 SER cc_start: 0.8816 (m) cc_final: 0.8403 (p) REVERT: G 51 MET cc_start: 0.7779 (mtp) cc_final: 0.7456 (mtp) REVERT: G 62 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: G 92 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8777 (tt) REVERT: I 114 ARG cc_start: 0.6126 (mtm180) cc_final: 0.5108 (ttt-90) REVERT: M 67 MET cc_start: 0.8679 (mmm) cc_final: 0.8416 (mmm) REVERT: F 97 ILE cc_start: 0.8853 (mt) cc_final: 0.8645 (tt) REVERT: F 123 LEU cc_start: 0.8700 (mm) cc_final: 0.8485 (mt) REVERT: A 54 SER cc_start: 0.8863 (p) cc_final: 0.8656 (m) REVERT: A 58 ASN cc_start: 0.8423 (t0) cc_final: 0.7949 (m-40) REVERT: A 112 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9330 (tp) REVERT: J 82 ARG cc_start: 0.7163 (mpt180) cc_final: 0.6930 (mpt90) REVERT: K 46 LYS cc_start: 0.8214 (tppp) cc_final: 0.7918 (tppp) REVERT: K 144 ILE cc_start: 0.7566 (tt) cc_final: 0.7297 (mm) REVERT: K 145 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7894 (m-10) REVERT: L 41 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7695 (pp) REVERT: L 53 MET cc_start: 0.8235 (ttm) cc_final: 0.8002 (mtp) REVERT: L 168 GLN cc_start: 0.8926 (mp10) cc_final: 0.8279 (mp10) REVERT: L 175 MET cc_start: 0.8171 (ptm) cc_final: 0.7875 (ptt) REVERT: L 186 ILE cc_start: 0.8772 (tp) cc_final: 0.8449 (mt) REVERT: L 230 SER cc_start: 0.9183 (m) cc_final: 0.8162 (m) REVERT: N 107 ASP cc_start: 0.7492 (m-30) cc_final: 0.7260 (m-30) outliers start: 88 outliers final: 28 residues processed: 490 average time/residue: 0.1410 time to fit residues: 109.3923 Evaluate side-chains 380 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 345 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 131 ILE Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 444 THR Chi-restraints excluded: chain H residue 498 ASP Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 18 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 236 optimal weight: 0.0470 chunk 155 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 192 optimal weight: 0.0070 chunk 186 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 253 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 HIS ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093267 restraints weight = 35948.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095741 restraints weight = 20349.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097408 restraints weight = 14150.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098518 restraints weight = 11160.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099158 restraints weight = 9527.897| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20069 Z= 0.124 Angle : 0.741 25.872 27336 Z= 0.335 Chirality : 0.043 0.388 3218 Planarity : 0.006 0.100 3363 Dihedral : 5.761 56.790 2730 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.43 % Favored : 91.41 % Rotamer: Outliers : 3.69 % Allowed : 17.45 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % 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: -2.42 (0.16), residues: 2502 helix: -0.22 (0.14), residues: 1376 sheet: -1.79 (0.47), residues: 118 loop : -3.66 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 34 TYR 0.021 0.001 TYR D 58 PHE 0.028 0.001 PHE K 135 TRP 0.018 0.001 TRP K 27 HIS 0.007 0.001 HIS K 164 Details of bonding type rmsd covalent geometry : bond 0.00273 (20058) covalent geometry : angle 0.66503 (27306) hydrogen bonds : bond 0.04668 ( 875) hydrogen bonds : angle 3.92826 ( 2559) metal coordination : bond 0.00799 ( 10) metal coordination : angle 9.90761 ( 30) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 378 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: H 164 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8183 (tm-30) REVERT: H 237 ASP cc_start: 0.7571 (p0) cc_final: 0.7297 (p0) REVERT: H 266 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8729 (mt) REVERT: H 293 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8617 (pt) REVERT: H 353 MET cc_start: 0.8156 (ptp) cc_final: 0.7851 (mtm) REVERT: H 383 MET cc_start: 0.8450 (ttm) cc_final: 0.8091 (mtp) REVERT: H 415 SER cc_start: 0.8757 (m) cc_final: 0.8381 (p) REVERT: G 51 MET cc_start: 0.7694 (mtp) cc_final: 0.7457 (mtp) REVERT: G 92 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8758 (tt) REVERT: D 56 GLU cc_start: 0.8977 (tp30) cc_final: 0.8760 (tp30) REVERT: I 5 TRP cc_start: 0.8188 (OUTLIER) cc_final: 0.7344 (m-10) REVERT: I 114 ARG cc_start: 0.5981 (mtm180) cc_final: 0.5028 (ttt180) REVERT: M 67 MET cc_start: 0.8705 (mmm) cc_final: 0.8438 (mmt) REVERT: F 121 MET cc_start: 0.7875 (mmm) cc_final: 0.6983 (mtp) REVERT: F 123 LEU cc_start: 0.8676 (mm) cc_final: 0.8467 (mt) REVERT: A 54 SER cc_start: 0.8923 (p) cc_final: 0.8689 (m) REVERT: A 58 ASN cc_start: 0.8412 (t0) cc_final: 0.7921 (m-40) REVERT: A 112 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9281 (tp) REVERT: K 6 MET cc_start: 0.6939 (ppp) cc_final: 0.6710 (ppp) REVERT: K 46 LYS cc_start: 0.8251 (tppp) cc_final: 0.8023 (tppp) REVERT: K 144 ILE cc_start: 0.7671 (tt) cc_final: 0.7367 (mm) REVERT: K 145 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: L 41 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7646 (pp) REVERT: L 109 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.8468 (t70) REVERT: L 168 GLN cc_start: 0.8950 (mp10) cc_final: 0.8260 (mp10) REVERT: L 175 MET cc_start: 0.8213 (ptm) cc_final: 0.7998 (ptt) REVERT: L 186 ILE cc_start: 0.8749 (tp) cc_final: 0.8489 (mt) REVERT: L 230 SER cc_start: 0.9245 (m) cc_final: 0.8973 (m) REVERT: L 360 GLU cc_start: 0.7047 (tt0) cc_final: 0.6493 (mt-10) outliers start: 76 outliers final: 36 residues processed: 433 average time/residue: 0.1333 time to fit residues: 93.0101 Evaluate side-chains 391 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 498 ASP Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 246 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 65 optimal weight: 0.0980 chunk 207 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 349 ASN H 350 HIS G 5 GLN G 103 HIS I 89 HIS ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 25 ASN K 56 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.087497 restraints weight = 36323.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.089808 restraints weight = 21141.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.091355 restraints weight = 15027.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.092349 restraints weight = 12045.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.092877 restraints weight = 10445.138| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20069 Z= 0.197 Angle : 0.792 25.770 27336 Z= 0.365 Chirality : 0.046 0.381 3218 Planarity : 0.007 0.102 3363 Dihedral : 5.778 58.521 2730 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.35 % Favored : 90.41 % Rotamer: Outliers : 5.25 % Allowed : 18.13 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % 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: -2.08 (0.17), residues: 2502 helix: 0.09 (0.14), residues: 1368 sheet: -1.74 (0.50), residues: 112 loop : -3.53 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 34 TYR 0.027 0.002 TYR H 345 PHE 0.029 0.002 PHE K 135 TRP 0.023 0.002 TRP H 497 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00476 (20058) covalent geometry : angle 0.71973 (27306) hydrogen bonds : bond 0.06083 ( 875) hydrogen bonds : angle 4.12620 ( 2559) metal coordination : bond 0.01020 ( 10) metal coordination : angle 9.97067 ( 30) Misc. bond : bond 0.00144 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 340 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 164 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8153 (tm-30) REVERT: H 293 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8722 (pt) REVERT: H 353 MET cc_start: 0.8151 (ptp) cc_final: 0.7894 (mtm) REVERT: H 383 MET cc_start: 0.8537 (ttm) cc_final: 0.8201 (mtp) REVERT: H 415 SER cc_start: 0.8798 (m) cc_final: 0.8471 (p) REVERT: I 5 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.7481 (m-10) REVERT: I 114 ARG cc_start: 0.6611 (mtm180) cc_final: 0.5955 (ttt180) REVERT: M 67 MET cc_start: 0.8819 (mmm) cc_final: 0.8478 (mmm) REVERT: M 109 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8699 (tm) REVERT: M 196 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9191 (tp) REVERT: M 298 ASN cc_start: 0.8014 (p0) cc_final: 0.7653 (m-40) REVERT: F 123 LEU cc_start: 0.8740 (mm) cc_final: 0.8438 (mt) REVERT: A 54 SER cc_start: 0.9016 (p) cc_final: 0.8784 (m) REVERT: A 58 ASN cc_start: 0.8441 (t0) cc_final: 0.7925 (m-40) REVERT: K 46 LYS cc_start: 0.8237 (tppp) cc_final: 0.7931 (tppp) REVERT: K 144 ILE cc_start: 0.7739 (tt) cc_final: 0.7436 (mm) REVERT: K 145 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7386 (m-80) REVERT: L 41 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7870 (pp) REVERT: L 109 HIS cc_start: 0.9161 (OUTLIER) cc_final: 0.8514 (t70) REVERT: L 175 MET cc_start: 0.8258 (ptm) cc_final: 0.8035 (ptt) REVERT: L 186 ILE cc_start: 0.8776 (tp) cc_final: 0.8476 (mt) outliers start: 108 outliers final: 73 residues processed: 410 average time/residue: 0.1324 time to fit residues: 88.2523 Evaluate side-chains 403 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 323 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 298 MET Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 382 THR Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 498 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 246 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 164 HIS Chi-restraints excluded: chain L residue 10 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain L residue 366 VAL Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.088477 restraints weight = 36430.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090977 restraints weight = 20420.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092654 restraints weight = 14104.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093649 restraints weight = 11092.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094428 restraints weight = 9537.968| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20069 Z= 0.132 Angle : 0.725 23.673 27336 Z= 0.331 Chirality : 0.043 0.333 3218 Planarity : 0.006 0.101 3363 Dihedral : 5.492 59.397 2730 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.63 % Favored : 91.21 % Rotamer: Outliers : 4.38 % Allowed : 19.79 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % 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: -1.73 (0.17), residues: 2502 helix: 0.43 (0.14), residues: 1363 sheet: -1.75 (0.49), residues: 112 loop : -3.42 (0.17), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 34 TYR 0.029 0.001 TYR B 64 PHE 0.027 0.001 PHE K 135 TRP 0.018 0.001 TRP K 27 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00307 (20058) covalent geometry : angle 0.66252 (27306) hydrogen bonds : bond 0.04707 ( 875) hydrogen bonds : angle 3.81996 ( 2559) metal coordination : bond 0.00732 ( 10) metal coordination : angle 8.89290 ( 30) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 359 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 164 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8238 (tm-30) REVERT: H 237 ASP cc_start: 0.7739 (p0) cc_final: 0.7501 (p0) REVERT: H 266 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8640 (mt) REVERT: H 293 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8638 (pt) REVERT: H 353 MET cc_start: 0.8074 (ptp) cc_final: 0.7868 (mtm) REVERT: H 383 MET cc_start: 0.8563 (ttm) cc_final: 0.8130 (mtp) REVERT: H 415 SER cc_start: 0.8736 (m) cc_final: 0.8394 (p) REVERT: I 5 TRP cc_start: 0.8257 (OUTLIER) cc_final: 0.7491 (m-10) REVERT: I 114 ARG cc_start: 0.6190 (mtm180) cc_final: 0.5370 (ttt-90) REVERT: M 67 MET cc_start: 0.8769 (mmm) cc_final: 0.8430 (mmm) REVERT: M 196 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9159 (tp) REVERT: M 298 ASN cc_start: 0.7823 (p0) cc_final: 0.7578 (m-40) REVERT: F 32 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.7956 (m-70) REVERT: F 121 MET cc_start: 0.8055 (mmm) cc_final: 0.7736 (mmm) REVERT: F 123 LEU cc_start: 0.8644 (mm) cc_final: 0.8380 (mt) REVERT: A 11 TYR cc_start: 0.9177 (t80) cc_final: 0.8894 (t80) REVERT: A 54 SER cc_start: 0.9024 (p) cc_final: 0.8792 (m) REVERT: A 58 ASN cc_start: 0.8382 (t0) cc_final: 0.7784 (m-40) REVERT: C 60 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8326 (mtpp) REVERT: K 46 LYS cc_start: 0.8227 (tppp) cc_final: 0.7940 (tppp) REVERT: K 100 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8800 (mp) REVERT: K 144 ILE cc_start: 0.7677 (tt) cc_final: 0.7341 (mm) REVERT: K 145 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: L 41 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7760 (pp) REVERT: L 109 HIS cc_start: 0.9128 (OUTLIER) cc_final: 0.8372 (t70) REVERT: L 175 MET cc_start: 0.8189 (ptm) cc_final: 0.7986 (ptt) REVERT: L 186 ILE cc_start: 0.8729 (tp) cc_final: 0.8490 (mt) REVERT: L 192 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.7883 (p-80) REVERT: L 242 LEU cc_start: 0.8826 (pp) cc_final: 0.8471 (pp) outliers start: 90 outliers final: 55 residues processed: 422 average time/residue: 0.1265 time to fit residues: 87.3763 Evaluate side-chains 397 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 332 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 382 THR Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 498 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain F residue 32 HIS Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 164 HIS Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 177 optimal weight: 0.0980 chunk 109 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 187 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 25 ASN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.085564 restraints weight = 36403.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087872 restraints weight = 20622.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.089456 restraints weight = 14451.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.090511 restraints weight = 11479.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091165 restraints weight = 9872.611| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 20069 Z= 0.180 Angle : 0.759 23.405 27336 Z= 0.353 Chirality : 0.045 0.284 3218 Planarity : 0.006 0.107 3363 Dihedral : 5.551 58.894 2730 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.63 % Favored : 90.17 % Rotamer: Outliers : 4.86 % Allowed : 19.88 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % 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: -1.66 (0.17), residues: 2502 helix: 0.47 (0.14), residues: 1383 sheet: -1.65 (0.51), residues: 108 loop : -3.43 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 93 TYR 0.024 0.002 TYR D 58 PHE 0.029 0.002 PHE K 135 TRP 0.019 0.001 TRP H 497 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00436 (20058) covalent geometry : angle 0.70093 (27306) hydrogen bonds : bond 0.05623 ( 875) hydrogen bonds : angle 3.97252 ( 2559) metal coordination : bond 0.01007 ( 10) metal coordination : angle 8.80820 ( 30) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 341 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ILE cc_start: 0.9446 (tp) cc_final: 0.9090 (tp) REVERT: H 145 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.8028 (ttm) REVERT: H 164 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8198 (tm-30) REVERT: H 237 ASP cc_start: 0.7830 (p0) cc_final: 0.7574 (p0) REVERT: H 266 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8657 (mt) REVERT: H 415 SER cc_start: 0.8742 (m) cc_final: 0.8416 (p) REVERT: I 4 TYR cc_start: 0.8531 (t80) cc_final: 0.8053 (t80) REVERT: I 5 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.7526 (m-10) REVERT: I 114 ARG cc_start: 0.6464 (mtm180) cc_final: 0.5742 (ttt-90) REVERT: M 67 MET cc_start: 0.8822 (mmm) cc_final: 0.8488 (mmm) REVERT: M 109 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8667 (tm) REVERT: F 123 LEU cc_start: 0.8739 (mm) cc_final: 0.8444 (mt) REVERT: A 11 TYR cc_start: 0.9253 (t80) cc_final: 0.8974 (t80) REVERT: A 54 SER cc_start: 0.9042 (p) cc_final: 0.8820 (m) REVERT: A 58 ASN cc_start: 0.8404 (t0) cc_final: 0.7793 (m-40) REVERT: K 6 MET cc_start: 0.7111 (ppp) cc_final: 0.6816 (ppp) REVERT: K 46 LYS cc_start: 0.8174 (tppp) cc_final: 0.7898 (tppt) REVERT: K 144 ILE cc_start: 0.7738 (tt) cc_final: 0.7390 (mm) REVERT: K 145 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: L 41 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7837 (pp) REVERT: L 109 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8373 (t70) REVERT: L 168 GLN cc_start: 0.8945 (mp10) cc_final: 0.8307 (mp10) REVERT: L 175 MET cc_start: 0.8243 (ptm) cc_final: 0.8031 (ptt) REVERT: L 186 ILE cc_start: 0.8759 (tp) cc_final: 0.8502 (mt) REVERT: L 192 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.7873 (p-80) REVERT: N 21 ASN cc_start: 0.8650 (t0) cc_final: 0.8181 (t0) outliers start: 100 outliers final: 77 residues processed: 410 average time/residue: 0.1256 time to fit residues: 84.9477 Evaluate side-chains 416 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 331 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 382 THR Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 489 MET Chi-restraints excluded: chain H residue 496 LEU Chi-restraints excluded: chain H residue 498 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 246 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 63 GLN Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 118 MET Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 195 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.087700 restraints weight = 36356.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090181 restraints weight = 20441.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.091857 restraints weight = 14157.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092936 restraints weight = 11153.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093488 restraints weight = 9556.962| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 20069 Z= 0.140 Angle : 0.729 21.457 27336 Z= 0.336 Chirality : 0.043 0.268 3218 Planarity : 0.006 0.108 3363 Dihedral : 5.396 59.351 2730 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.07 % Favored : 90.77 % Rotamer: Outliers : 4.52 % Allowed : 20.32 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 4.72 % Twisted General : 0.08 % 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: -1.47 (0.17), residues: 2502 helix: 0.69 (0.14), residues: 1372 sheet: -1.61 (0.51), residues: 108 loop : -3.40 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 54 TYR 0.022 0.001 TYR D 58 PHE 0.027 0.001 PHE K 135 TRP 0.021 0.001 TRP K 27 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00330 (20058) covalent geometry : angle 0.67085 (27306) hydrogen bonds : bond 0.04776 ( 875) hydrogen bonds : angle 3.78116 ( 2559) metal coordination : bond 0.00746 ( 10) metal coordination : angle 8.67335 ( 30) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 344 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: H 100 ILE cc_start: 0.9380 (tp) cc_final: 0.8997 (tp) REVERT: H 164 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8221 (tm-30) REVERT: H 170 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7773 (ttm) REVERT: H 237 ASP cc_start: 0.7729 (p0) cc_final: 0.7509 (p0) REVERT: H 266 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8651 (mt) REVERT: H 305 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8646 (tp) REVERT: H 415 SER cc_start: 0.8722 (m) cc_final: 0.8403 (p) REVERT: G 24 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8184 (mtm-85) REVERT: I 4 TYR cc_start: 0.8516 (t80) cc_final: 0.8118 (t80) REVERT: I 5 TRP cc_start: 0.8285 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: I 33 MET cc_start: 0.7429 (mpp) cc_final: 0.6841 (mtp) REVERT: I 114 ARG cc_start: 0.6289 (mtm180) cc_final: 0.5236 (ttt-90) REVERT: M 67 MET cc_start: 0.8766 (mmm) cc_final: 0.8403 (mmm) REVERT: M 109 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8598 (tm) REVERT: F 123 LEU cc_start: 0.8664 (mm) cc_final: 0.8365 (mt) REVERT: A 11 TYR cc_start: 0.9259 (t80) cc_final: 0.8980 (t80) REVERT: A 54 SER cc_start: 0.8971 (p) cc_final: 0.8676 (m) REVERT: A 58 ASN cc_start: 0.8453 (t0) cc_final: 0.7799 (m-40) REVERT: J 92 ASP cc_start: 0.7284 (t0) cc_final: 0.6126 (t0) REVERT: K 6 MET cc_start: 0.6956 (ppp) cc_final: 0.6728 (ppp) REVERT: K 144 ILE cc_start: 0.7626 (tt) cc_final: 0.7322 (mm) REVERT: K 145 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: L 41 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7816 (pp) REVERT: L 109 HIS cc_start: 0.9061 (OUTLIER) cc_final: 0.8375 (t70) REVERT: L 168 GLN cc_start: 0.8952 (mp10) cc_final: 0.8361 (mp10) REVERT: L 186 ILE cc_start: 0.8730 (tp) cc_final: 0.8492 (mt) REVERT: L 192 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.7814 (p-80) REVERT: N 64 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8413 (pp) outliers start: 93 outliers final: 71 residues processed: 407 average time/residue: 0.1229 time to fit residues: 81.9477 Evaluate side-chains 414 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 333 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 266 ILE Chi-restraints excluded: chain H residue 291 THR Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 382 THR Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 489 MET Chi-restraints excluded: chain H residue 498 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 113 PHE Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 309 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 77 PHE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 107 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 63 GLN Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 226 optimal weight: 9.9990 chunk 95 optimal weight: 0.0870 chunk 216 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.090856 restraints weight = 35844.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.093426 restraints weight = 20012.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095137 restraints weight = 13742.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.096149 restraints weight = 10788.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.096970 restraints weight = 9265.926| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 20069 Z= 0.120 Angle : 0.707 20.118 27336 Z= 0.324 Chirality : 0.043 0.260 3218 Planarity : 0.006 0.105 3363 Dihedral : 5.152 55.952 2730 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.63 % Favored : 91.21 % Rotamer: Outliers : 3.89 % Allowed : 21.68 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.94 % Twisted General : 0.08 % 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: -1.25 (0.17), residues: 2502 helix: 0.92 (0.15), residues: 1370 sheet: -1.63 (0.50), residues: 108 loop : -3.36 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.021 0.001 TYR D 58 PHE 0.024 0.001 PHE K 135 TRP 0.019 0.001 TRP K 27 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00275 (20058) covalent geometry : angle 0.65114 (27306) hydrogen bonds : bond 0.03984 ( 875) hydrogen bonds : angle 3.58351 ( 2559) metal coordination : bond 0.00543 ( 10) metal coordination : angle 8.35473 ( 30) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 367 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: H 126 MET cc_start: 0.9004 (mtm) cc_final: 0.8756 (mtt) REVERT: H 164 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8282 (tm-30) REVERT: H 170 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7897 (ttm) REVERT: H 305 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8610 (tp) REVERT: H 415 SER cc_start: 0.8692 (m) cc_final: 0.8367 (p) REVERT: D 23 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8766 (mm) REVERT: I 1 MET cc_start: 0.7601 (tmm) cc_final: 0.7370 (tmm) REVERT: I 4 TYR cc_start: 0.8470 (t80) cc_final: 0.8072 (t80) REVERT: I 5 TRP cc_start: 0.8256 (OUTLIER) cc_final: 0.7427 (m-10) REVERT: I 114 ARG cc_start: 0.6011 (mtm180) cc_final: 0.4932 (ttt-90) REVERT: M 67 MET cc_start: 0.8727 (mmm) cc_final: 0.8372 (mmm) REVERT: M 109 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8583 (tm) REVERT: M 196 LEU cc_start: 0.9245 (tp) cc_final: 0.9030 (tp) REVERT: M 263 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7824 (pp) REVERT: F 121 MET cc_start: 0.8017 (mmm) cc_final: 0.7661 (mmm) REVERT: A 11 TYR cc_start: 0.9233 (t80) cc_final: 0.8953 (t80) REVERT: A 54 SER cc_start: 0.8966 (p) cc_final: 0.8677 (m) REVERT: A 58 ASN cc_start: 0.8395 (t0) cc_final: 0.7811 (m-40) REVERT: E 61 THR cc_start: 0.9162 (t) cc_final: 0.8836 (m) REVERT: J 92 ASP cc_start: 0.7268 (t0) cc_final: 0.6250 (t0) REVERT: K 6 MET cc_start: 0.6956 (ppp) cc_final: 0.6739 (ppp) REVERT: K 144 ILE cc_start: 0.7538 (tt) cc_final: 0.7022 (mm) REVERT: K 145 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: L 41 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7692 (pp) REVERT: L 105 LEU cc_start: 0.9371 (tt) cc_final: 0.9052 (tt) REVERT: L 109 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8329 (t70) REVERT: L 168 GLN cc_start: 0.8901 (mp10) cc_final: 0.8362 (mp10) REVERT: L 186 ILE cc_start: 0.8750 (tp) cc_final: 0.8535 (mt) REVERT: N 64 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8363 (pp) outliers start: 80 outliers final: 51 residues processed: 424 average time/residue: 0.1284 time to fit residues: 88.6781 Evaluate side-chains 402 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 341 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 489 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 113 PHE Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 15 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.091393 restraints weight = 35865.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093900 restraints weight = 19908.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095606 restraints weight = 13772.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096603 restraints weight = 10801.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.097422 restraints weight = 9284.917| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20069 Z= 0.123 Angle : 0.719 19.432 27336 Z= 0.331 Chirality : 0.043 0.275 3218 Planarity : 0.006 0.103 3363 Dihedral : 5.111 59.478 2730 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.55 % Favored : 91.29 % Rotamer: Outliers : 3.06 % Allowed : 22.85 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.15 % Twisted General : 0.08 % 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: -1.12 (0.17), residues: 2502 helix: 1.03 (0.14), residues: 1373 sheet: -1.64 (0.51), residues: 108 loop : -3.33 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 82 TYR 0.024 0.001 TYR D 58 PHE 0.026 0.001 PHE A 3 TRP 0.024 0.001 TRP K 27 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00282 (20058) covalent geometry : angle 0.66504 (27306) hydrogen bonds : bond 0.03922 ( 875) hydrogen bonds : angle 3.53470 ( 2559) metal coordination : bond 0.00562 ( 10) metal coordination : angle 8.29979 ( 30) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 353 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: H 126 MET cc_start: 0.9008 (mtm) cc_final: 0.8768 (mtt) REVERT: H 164 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8283 (tm-30) REVERT: H 170 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7873 (ttm) REVERT: H 305 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8597 (tp) REVERT: H 415 SER cc_start: 0.8690 (m) cc_final: 0.8362 (p) REVERT: D 23 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8739 (mm) REVERT: I 4 TYR cc_start: 0.8422 (t80) cc_final: 0.8082 (t80) REVERT: I 5 TRP cc_start: 0.8246 (OUTLIER) cc_final: 0.7354 (m-10) REVERT: M 67 MET cc_start: 0.8673 (mmm) cc_final: 0.8328 (mmm) REVERT: M 109 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8594 (tm) REVERT: M 298 ASN cc_start: 0.7860 (p0) cc_final: 0.7397 (m-40) REVERT: F 121 MET cc_start: 0.7966 (mmm) cc_final: 0.7619 (mmm) REVERT: A 11 TYR cc_start: 0.9221 (t80) cc_final: 0.8942 (t80) REVERT: E 61 THR cc_start: 0.9152 (t) cc_final: 0.8899 (m) REVERT: C 60 LYS cc_start: 0.8485 (mtpp) cc_final: 0.7807 (mtpp) REVERT: C 69 TYR cc_start: 0.9020 (m-80) cc_final: 0.8473 (m-80) REVERT: K 144 ILE cc_start: 0.7523 (tt) cc_final: 0.6995 (mm) REVERT: L 41 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7720 (pp) REVERT: L 105 LEU cc_start: 0.9362 (tt) cc_final: 0.9035 (tt) REVERT: L 109 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.8391 (t70) REVERT: L 168 GLN cc_start: 0.8891 (mp10) cc_final: 0.8384 (mp10) REVERT: L 186 ILE cc_start: 0.8882 (tp) cc_final: 0.8668 (mt) REVERT: L 192 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.7737 (p-80) REVERT: N 21 ASN cc_start: 0.8587 (t0) cc_final: 0.8143 (t0) outliers start: 63 outliers final: 48 residues processed: 398 average time/residue: 0.1286 time to fit residues: 83.2386 Evaluate side-chains 393 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 337 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 489 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 177 optimal weight: 0.7980 chunk 96 optimal weight: 0.0370 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 25 ASN I 89 HIS F 30 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN K 25 ASN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091893 restraints weight = 35767.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094424 restraints weight = 19558.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096148 restraints weight = 13377.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097249 restraints weight = 10447.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098046 restraints weight = 8888.902| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20069 Z= 0.123 Angle : 0.726 19.162 27336 Z= 0.332 Chirality : 0.043 0.260 3218 Planarity : 0.006 0.120 3363 Dihedral : 5.062 56.209 2730 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.55 % Favored : 91.33 % Rotamer: Outliers : 3.01 % Allowed : 22.99 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.15 % Twisted General : 0.08 % 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: -1.00 (0.17), residues: 2502 helix: 1.14 (0.14), residues: 1377 sheet: -1.64 (0.51), residues: 108 loop : -3.29 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.024 0.001 TYR D 58 PHE 0.024 0.001 PHE A 3 TRP 0.019 0.001 TRP K 27 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00285 (20058) covalent geometry : angle 0.67207 (27306) hydrogen bonds : bond 0.03871 ( 875) hydrogen bonds : angle 3.51985 ( 2559) metal coordination : bond 0.00565 ( 10) metal coordination : angle 8.31195 ( 30) Misc. bond : bond 0.00216 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 342 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: H 126 MET cc_start: 0.9007 (mtm) cc_final: 0.8747 (mtt) REVERT: H 164 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8276 (tm-30) REVERT: H 170 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7901 (ttm) REVERT: H 305 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8592 (tp) REVERT: H 415 SER cc_start: 0.8667 (m) cc_final: 0.8342 (p) REVERT: D 23 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8720 (mm) REVERT: I 4 TYR cc_start: 0.8420 (t80) cc_final: 0.8060 (t80) REVERT: I 5 TRP cc_start: 0.8242 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: M 67 MET cc_start: 0.8677 (mmm) cc_final: 0.8340 (mmm) REVERT: M 109 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8583 (tm) REVERT: M 263 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7744 (mt) REVERT: M 298 ASN cc_start: 0.7759 (p0) cc_final: 0.7390 (m-40) REVERT: F 121 MET cc_start: 0.7995 (mmm) cc_final: 0.7679 (mmm) REVERT: A 11 TYR cc_start: 0.9237 (t80) cc_final: 0.8975 (t80) REVERT: A 58 ASN cc_start: 0.8211 (t0) cc_final: 0.7373 (m-40) REVERT: A 86 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8743 (mmt-90) REVERT: A 140 ASN cc_start: 0.8279 (m-40) cc_final: 0.7861 (m-40) REVERT: E 61 THR cc_start: 0.9134 (t) cc_final: 0.8897 (m) REVERT: C 60 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7757 (mtpp) REVERT: C 69 TYR cc_start: 0.9016 (m-80) cc_final: 0.8554 (m-80) REVERT: K 46 LYS cc_start: 0.8159 (tppt) cc_final: 0.7776 (tppt) REVERT: K 144 ILE cc_start: 0.7538 (tt) cc_final: 0.7036 (mm) REVERT: L 41 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7646 (pp) REVERT: L 105 LEU cc_start: 0.9356 (tt) cc_final: 0.9042 (tt) REVERT: L 109 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8356 (t70) REVERT: L 168 GLN cc_start: 0.8884 (mp10) cc_final: 0.8372 (mp10) REVERT: L 192 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.7691 (p-80) REVERT: N 21 ASN cc_start: 0.8614 (t0) cc_final: 0.8160 (t0) outliers start: 62 outliers final: 50 residues processed: 387 average time/residue: 0.1298 time to fit residues: 81.8052 Evaluate side-chains 394 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 335 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 124 LEU Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 360 VAL Chi-restraints excluded: chain H residue 465 LEU Chi-restraints excluded: chain H residue 489 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 62 TYR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain I residue 5 TRP Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 271 LEU Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 29 HIS Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 102 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 25 ASN Chi-restraints excluded: chain K residue 54 GLU Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 109 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 192 HIS Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 283 LEU Chi-restraints excluded: chain N residue 52 CYS Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 169 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 165 optimal weight: 0.0980 chunk 77 optimal weight: 0.2980 chunk 246 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 ASN L 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091693 restraints weight = 35796.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094256 restraints weight = 19777.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095967 restraints weight = 13610.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.097038 restraints weight = 10688.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097841 restraints weight = 9120.896| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 20069 Z= 0.150 Angle : 0.859 59.167 27336 Z= 0.438 Chirality : 0.046 0.927 3218 Planarity : 0.006 0.120 3363 Dihedral : 5.064 56.975 2730 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.47 % Favored : 91.37 % Rotamer: Outliers : 3.21 % Allowed : 22.85 % Favored : 73.94 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 3.15 % Twisted General : 0.08 % 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: -0.98 (0.17), residues: 2502 helix: 1.15 (0.14), residues: 1377 sheet: -1.56 (0.52), residues: 108 loop : -3.29 (0.17), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 135 TYR 0.014 0.001 TYR I 96 PHE 0.024 0.001 PHE K 135 TRP 0.017 0.001 TRP K 27 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00343 (20058) covalent geometry : angle 0.81372 (27306) hydrogen bonds : bond 0.03876 ( 875) hydrogen bonds : angle 3.51973 ( 2559) metal coordination : bond 0.00563 ( 10) metal coordination : angle 8.31218 ( 30) Misc. bond : bond 0.00048 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3302.87 seconds wall clock time: 57 minutes 48.49 seconds (3468.49 seconds total)