Starting phenix.real_space_refine on Sat Jul 4 14:23:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0b_64660/07_2026/9v0b_64660.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0b_64660/07_2026/9v0b_64660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v0b_64660/07_2026/9v0b_64660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0b_64660/07_2026/9v0b_64660.map" model { file = "/net/cci-nas-00/data/ceres_data/9v0b_64660/07_2026/9v0b_64660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0b_64660/07_2026/9v0b_64660.cif" } resolution = 3.54 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= 0.045 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 125 5.16 5 C 13174 2.51 5 N 3559 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20731 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5711 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 679} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8682 Classifications: {'peptide': 1108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1067} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2897 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 20, 'TRANS': 354} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1141 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 660 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 583 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '835': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16518 SG CYS C 323 37.469 58.617 113.869 1.00206.67 S ATOM 16534 SG CYS C 326 35.985 61.019 111.272 1.00179.11 S ATOM 17028 SG CYS C 391 34.332 60.850 114.915 1.00221.18 S ATOM 17047 SG CYS C 394 33.840 58.390 112.597 1.00198.29 S ATOM 18693 SG CYS I 176 30.002 32.159 100.140 1.00338.92 S ATOM 18717 SG CYS I 179 28.007 33.670 97.291 1.00346.47 S ATOM 18484 SG CYS I 148 28.594 45.778 115.269 1.00178.37 S ATOM 18507 SG CYS I 151 30.064 48.732 117.557 1.00197.32 S ATOM 19664 SG CYS R 42 27.378 32.049 76.280 1.00187.15 S ATOM 19683 SG CYS R 45 30.775 31.928 74.769 1.00176.35 S ATOM 19931 SG CYS R 83 30.070 29.663 77.828 1.00216.43 S ATOM 19860 SG CYS R 75 14.276 34.254 80.314 1.00230.15 S ATOM 20027 SG CYS R 94 18.224 34.801 80.921 1.00197.82 S ATOM 19750 SG CYS R 53 31.075 26.597 74.639 1.00225.67 S ATOM 19773 SG CYS R 56 33.927 24.103 75.530 1.00226.81 S ATOM 19810 SG CYS R 68 31.122 22.979 73.267 1.00224.91 S Time building chain proxies: 4.26, per 1000 atoms: 0.21 Number of scatterers: 20731 At special positions: 0 Unit cell: (165.204, 132.375, 169.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 125 16.00 O 3867 8.00 N 3559 7.00 C 13174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 857.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 394 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 326 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 391 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 323 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 192 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 196 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 179 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 176 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 164 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 148 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 151 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 14 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 38 sheets defined 31.2% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 57 through 75 Processing helix chain 'A' and resid 82 through 96 removed outlier: 3.572A pdb=" N LEU A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.532A pdb=" N HIS A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 4.248A pdb=" N GLU A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 153 removed outlier: 3.942A pdb=" N MET A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 169 through 182 removed outlier: 3.582A pdb=" N LEU A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 removed outlier: 3.524A pdb=" N GLY A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 225 through 252 removed outlier: 4.626A pdb=" N ASP A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 245 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.647A pdb=" N TYR A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 295 removed outlier: 3.819A pdb=" N LEU A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 removed outlier: 5.314A pdb=" N ASP A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.828A pdb=" N ARG A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 354 removed outlier: 3.586A pdb=" N ALA A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.790A pdb=" N ASP A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS A 359 " --> pdb=" O GLU A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 359' Processing helix chain 'A' and resid 360 through 379 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.590A pdb=" N VAL A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.859A pdb=" N PHE A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 483 removed outlier: 3.531A pdb=" N GLU A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 515 removed outlier: 3.675A pdb=" N GLU A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 562 Processing helix chain 'A' and resid 593 through 603 Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.792A pdb=" N MET A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 634 Processing helix chain 'A' and resid 693 through 708 removed outlier: 3.657A pdb=" N ASP A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.814A pdb=" N ASN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 742 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 987 through 990 removed outlier: 4.248A pdb=" N GLN B 990 " --> pdb=" O GLU B 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 990' Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1097 through 1100 removed outlier: 4.049A pdb=" N ILE B1100 " --> pdb=" O PHE B1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1097 through 1100' Processing helix chain 'B' and resid 1101 through 1109 Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.711A pdb=" N LEU B1129 " --> pdb=" O THR B1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.613A pdb=" N VAL C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS C 116 " --> pdb=" O ASN C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.053A pdb=" N LYS C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 233 through 238 removed outlier: 4.125A pdb=" N ASN C 236 " --> pdb=" O HIS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.724A pdb=" N TYR C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 3.697A pdb=" N GLN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 291 through 301 removed outlier: 3.676A pdb=" N ARG C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.697A pdb=" N GLU C 336 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.951A pdb=" N ARG D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 111 removed outlier: 3.782A pdb=" N CYS D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 131 through 145 Processing helix chain 'I' and resid 157 through 167 removed outlier: 3.660A pdb=" N LEU I 167 " --> pdb=" O ARG I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 197 removed outlier: 3.652A pdb=" N LEU I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR I 190 " --> pdb=" O ARG I 186 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY I 191 " --> pdb=" O ASP I 187 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER I 197 " --> pdb=" O LEU I 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 34 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'R' and resid 80 through 91 Processing helix chain 'U' and resid 22 through 35 removed outlier: 3.923A pdb=" N VAL U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 526 through 529 removed outlier: 3.610A pdb=" N TRP R 33 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS R 26 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL R 30 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 12.275A pdb=" N LEU R 32 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N THR A 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 639 through 642 Processing sheet with id=AA3, first strand: chain 'A' and resid 746 through 747 removed outlier: 3.780A pdb=" N GLU A 746 " --> pdb=" O HIS A 756 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1004 through 1009 removed outlier: 4.492A pdb=" N VAL B1006 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLY B1026 " --> pdb=" O SER B1042 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER B1042 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASN B 4 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 21 removed outlier: 4.187A pdb=" N GLY B 17 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 21 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG B 38 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B 39 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU B 54 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 41 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.863A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.940A pdb=" N ILE B 121 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 167 removed outlier: 7.338A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 184 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 164 through 167 removed outlier: 7.338A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP B 184 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 210 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB2, first strand: chain 'B' and resid 258 through 263 removed outlier: 3.619A pdb=" N ASP B 275 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU B 280 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU B 304 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N MET B 282 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL B 302 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 284 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 300 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 286 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 318 removed outlier: 6.727A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 359 through 365 removed outlier: 4.172A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 391 " --> pdb=" O HIS B 711 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 359 through 365 removed outlier: 4.172A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 396 through 403 removed outlier: 6.951A pdb=" N ILE B 701 " --> pdb=" O HIS B 399 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER B 401 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 699 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 410 through 413 removed outlier: 4.295A pdb=" N VAL B 435 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 457 through 463 removed outlier: 6.775A pdb=" N ILE B 471 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N CYS B 460 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 469 " --> pdb=" O CYS B 460 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN B 462 " --> pdb=" O GLN B 467 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN B 467 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 476 " --> pdb=" O TRP B 490 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER B 480 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU B 486 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 500 through 503 removed outlier: 6.864A pdb=" N LEU B 516 " --> pdb=" O HIS B 531 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS B 531 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TYR B 518 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.528A pdb=" N ASP B 542 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 578 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS B 570 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 576 " --> pdb=" O LYS B 570 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 588 through 595 removed outlier: 4.607A pdb=" N SER B 590 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 606 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 637 through 643 removed outlier: 9.312A pdb=" N THR B 647 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 661 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 649 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 657 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 720 through 727 removed outlier: 6.316A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP B 795 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 801 " --> pdb=" O ASP B 795 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 811 through 819 removed outlier: 5.554A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 847 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 850 " --> pdb=" O ALA B 862 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 862 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN B 852 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR B 860 " --> pdb=" O GLN B 852 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N SER B 854 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 874 through 875 Processing sheet with id=AC7, first strand: chain 'B' and resid 890 through 893 removed outlier: 6.909A pdb=" N LEU B 890 " --> pdb=" O GLU B 902 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 913 through 917 removed outlier: 3.633A pdb=" N VAL B 930 " --> pdb=" O ASP B 948 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 948 " --> pdb=" O VAL B 930 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA B 946 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS B 936 " --> pdb=" O PHE B 942 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE B 942 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 957 through 961 removed outlier: 6.529A pdb=" N ASN B 964 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY B 996 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1076 through 1078 Processing sheet with id=AD2, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.957A pdb=" N ILE C 81 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 180 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR C 138 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG C 164 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 136 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 120 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 96 through 100 removed outlier: 3.642A pdb=" N ALA C 159 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AD5, first strand: chain 'C' and resid 349 through 350 removed outlier: 3.960A pdb=" N TYR C 349 " --> pdb=" O HIS C 357 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS C 357 " --> pdb=" O TYR C 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 359 through 362 removed outlier: 4.354A pdb=" N PHE C 414 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 416 " --> pdb=" O TRP C 400 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.648A pdb=" N SER D 22 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 146 through 147 removed outlier: 3.574A pdb=" N PHE I 146 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 12 through 16 removed outlier: 3.592A pdb=" N LEU N 67 " --> pdb=" O LYS N 4 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AE2, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.834A pdb=" N SER U 65 " --> pdb=" O GLN U 2 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4575 1.33 - 1.45: 4511 1.45 - 1.58: 11863 1.58 - 1.70: 0 1.70 - 1.82: 187 Bond restraints: 21136 Sorted by residual: bond pdb=" N GLU I 171 " pdb=" CA GLU I 171 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.22e-02 6.72e+03 7.63e+00 bond pdb=" N HIS I 168 " pdb=" CA HIS I 168 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.00e-02 1.00e+04 5.55e+00 bond pdb=" N THR I 169 " pdb=" CA THR I 169 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.17e-02 7.31e+03 4.05e+00 bond pdb=" N GLY I 170 " pdb=" CA GLY I 170 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.45e-02 4.76e+03 3.68e+00 bond pdb=" CG HIS I 168 " pdb=" CD2 HIS I 168 " ideal model delta sigma weight residual 1.354 1.333 0.021 1.10e-02 8.26e+03 3.49e+00 ... (remaining 21131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 27621 1.63 - 3.26: 849 3.26 - 4.89: 95 4.89 - 6.52: 22 6.52 - 8.15: 4 Bond angle restraints: 28591 Sorted by residual: angle pdb=" N HIS I 168 " pdb=" CA HIS I 168 " pdb=" C HIS I 168 " ideal model delta sigma weight residual 112.54 104.39 8.15 1.51e+00 4.39e-01 2.92e+01 angle pdb=" CA GLU I 171 " pdb=" C GLU I 171 " pdb=" O GLU I 171 " ideal model delta sigma weight residual 121.16 117.20 3.96 1.12e+00 7.97e-01 1.25e+01 angle pdb=" C ALA A 556 " pdb=" N PHE A 557 " pdb=" CA PHE A 557 " ideal model delta sigma weight residual 121.14 115.39 5.75 1.75e+00 3.27e-01 1.08e+01 angle pdb=" C HIS I 168 " pdb=" CA HIS I 168 " pdb=" CB HIS I 168 " ideal model delta sigma weight residual 110.41 117.04 -6.63 2.17e+00 2.12e-01 9.34e+00 angle pdb=" C ILE C 184 " pdb=" N LEU C 185 " pdb=" CA LEU C 185 " ideal model delta sigma weight residual 121.61 117.39 4.22 1.39e+00 5.18e-01 9.22e+00 ... (remaining 28586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11423 17.99 - 35.99: 1147 35.99 - 53.98: 187 53.98 - 71.97: 31 71.97 - 89.97: 27 Dihedral angle restraints: 12815 sinusoidal: 5206 harmonic: 7609 Sorted by residual: dihedral pdb=" CB CYS B 18 " pdb=" SG CYS B 18 " pdb=" SG CYS B 313 " pdb=" CB CYS B 313 " ideal model delta sinusoidal sigma weight residual 93.00 146.69 -53.69 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CA ARG B 928 " pdb=" C ARG B 928 " pdb=" N SER B 929 " pdb=" CA SER B 929 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY A 306 " pdb=" C GLY A 306 " pdb=" N LEU A 307 " pdb=" CA LEU A 307 " ideal model delta harmonic sigma weight residual -180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 12812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2181 0.039 - 0.079: 740 0.079 - 0.118: 263 0.118 - 0.157: 43 0.157 - 0.197: 3 Chirality restraints: 3230 Sorted by residual: chirality pdb=" CB ILE B 884 " pdb=" CA ILE B 884 " pdb=" CG1 ILE B 884 " pdb=" CG2 ILE B 884 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA GLU I 171 " pdb=" N GLU I 171 " pdb=" C GLU I 171 " pdb=" CB GLU I 171 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA ILE B 131 " pdb=" N ILE B 131 " pdb=" C ILE B 131 " pdb=" CB ILE B 131 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 3227 not shown) Planarity restraints: 3667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 167 " -0.026 2.00e-02 2.50e+03 5.24e-02 2.74e+01 pdb=" C LEU I 167 " 0.091 2.00e-02 2.50e+03 pdb=" O LEU I 167 " -0.034 2.00e-02 2.50e+03 pdb=" N HIS I 168 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 561 " 0.019 2.00e-02 2.50e+03 1.76e-02 7.78e+00 pdb=" CG TRP B 561 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 561 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 561 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 561 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 561 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 561 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 561 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 561 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 561 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1073 " -0.012 2.00e-02 2.50e+03 1.44e-02 5.20e+00 pdb=" CG TRP B1073 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B1073 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B1073 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1073 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1073 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B1073 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1073 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1073 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B1073 " -0.002 2.00e-02 2.50e+03 ... (remaining 3664 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 282 2.65 - 3.22: 19436 3.22 - 3.78: 29465 3.78 - 4.34: 39146 4.34 - 4.90: 65200 Nonbonded interactions: 153529 Sorted by model distance: nonbonded pdb=" OG SER B 499 " pdb=" O ALA B 511 " model vdw 2.092 3.040 nonbonded pdb=" OE1 GLU B 90 " pdb=" NH1 ARG B 103 " model vdw 2.183 3.120 nonbonded pdb=" OE1 GLU B 213 " pdb=" OG SER B 236 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASN R 41 " pdb=" OG1 THR U 9 " model vdw 2.188 3.040 nonbonded pdb=" ND2 ASN A 47 " pdb=" O VAL B 443 " model vdw 2.194 3.120 ... (remaining 153524 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=0.00 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.990 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.238 21159 Z= 0.191 Angle : 0.689 15.061 28607 Z= 0.367 Chirality : 0.045 0.197 3230 Planarity : 0.004 0.052 3667 Dihedral : 14.841 89.968 7880 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.04 % Allowed : 0.44 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2584 helix: 1.38 (0.20), residues: 718 sheet: -0.82 (0.21), residues: 657 loop : -2.01 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 144 TYR 0.019 0.002 TYR B 613 PHE 0.022 0.002 PHE A 397 TRP 0.047 0.002 TRP B 561 HIS 0.007 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (21136) covalent geometry : angle 0.67553 / 0.37 (28591) SS BOND : bond 0.00203 / 0.11 ( 1) SS BOND : angle 0.52156 / 0.31 ( 2) hydrogen bonds : bond 0.15000 / 10.26 ( 839) hydrogen bonds : angle 6.37555 / 4.63 ( 2397) metal coordination : bond 0.05191 / 1.87 ( 22) metal coordination : angle 6.09935 / 3.12 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 610 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7711 (mtm) cc_final: 0.7094 (mpp) REVERT: A 367 ASP cc_start: 0.9082 (m-30) cc_final: 0.8859 (m-30) REVERT: A 437 MET cc_start: 0.9480 (tpp) cc_final: 0.8983 (tmm) REVERT: A 477 SER cc_start: 0.9593 (t) cc_final: 0.9332 (p) REVERT: A 527 ILE cc_start: 0.9576 (mm) cc_final: 0.9186 (tp) REVERT: A 704 MET cc_start: 0.8470 (tpt) cc_final: 0.8199 (tpp) REVERT: A 706 MET cc_start: 0.8708 (tpp) cc_final: 0.8456 (tmm) REVERT: A 744 TYR cc_start: 0.7501 (m-80) cc_final: 0.7264 (m-80) REVERT: B 109 GLN cc_start: 0.9097 (tt0) cc_final: 0.8749 (tm-30) REVERT: B 111 ARG cc_start: 0.9005 (ttt-90) cc_final: 0.8750 (tmm-80) REVERT: B 135 LEU cc_start: 0.9197 (mp) cc_final: 0.8917 (mp) REVERT: B 256 SER cc_start: 0.8741 (t) cc_final: 0.8512 (m) REVERT: B 351 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8393 (mp0) REVERT: B 546 LEU cc_start: 0.8258 (mm) cc_final: 0.7013 (mm) REVERT: B 600 HIS cc_start: 0.7981 (m-70) cc_final: 0.7536 (m170) REVERT: B 644 LEU cc_start: 0.8132 (mt) cc_final: 0.7891 (pp) REVERT: B 786 VAL cc_start: 0.8893 (t) cc_final: 0.8692 (p) REVERT: B 938 MET cc_start: 0.7781 (mmm) cc_final: 0.7558 (mmm) REVERT: B 1054 MET cc_start: 0.9048 (tpt) cc_final: 0.8551 (mtm) REVERT: C 89 MET cc_start: 0.7964 (tpp) cc_final: 0.7412 (tpt) REVERT: C 120 PHE cc_start: 0.8252 (p90) cc_final: 0.8033 (p90) REVERT: C 134 GLN cc_start: 0.8317 (mp10) cc_final: 0.8115 (pm20) REVERT: C 162 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.7938 (mtp180) REVERT: C 186 PRO cc_start: 0.8891 (Cg_endo) cc_final: 0.8568 (Cg_exo) REVERT: C 330 GLU cc_start: 0.7926 (tt0) cc_final: 0.7589 (mp0) REVERT: D 112 ASP cc_start: 0.9065 (t0) cc_final: 0.8832 (t0) REVERT: D 137 HIS cc_start: 0.8535 (t-170) cc_final: 0.8213 (t-170) REVERT: D 139 ARG cc_start: 0.8371 (mtm180) cc_final: 0.8157 (mmm-85) REVERT: N 1 MET cc_start: 0.8969 (ptp) cc_final: 0.8439 (ptm) REVERT: N 27 LYS cc_start: 0.9649 (mttp) cc_final: 0.9337 (ttmm) REVERT: N 51 ASN cc_start: 0.8744 (t0) cc_final: 0.8401 (t0) REVERT: R 54 ILE cc_start: 0.8202 (pt) cc_final: 0.7999 (pt) REVERT: R 55 GLU cc_start: 0.9040 (tp30) cc_final: 0.8815 (pm20) REVERT: R 90 THR cc_start: 0.8542 (m) cc_final: 0.8285 (p) REVERT: R 91 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7275 (ttt180) outliers start: 1 outliers final: 0 residues processed: 610 average time/residue: 0.1680 time to fit residues: 154.6794 Evaluate side-chains 401 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 HIS A 568 GLN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B1059 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN C 218 GLN C 353 HIS ** C 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN N 41 GLN U 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.115993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.086168 restraints weight = 64551.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089065 restraints weight = 31892.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090972 restraints weight = 20921.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092198 restraints weight = 16122.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.092927 restraints weight = 13731.968| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21159 Z= 0.135 Angle : 0.695 23.832 28607 Z= 0.342 Chirality : 0.045 0.200 3230 Planarity : 0.004 0.044 3667 Dihedral : 4.529 41.431 2819 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.45 % Allowed : 11.02 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2584 helix: 1.38 (0.20), residues: 728 sheet: -0.78 (0.20), residues: 671 loop : -1.78 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 900 TYR 0.022 0.001 TYR D 145 PHE 0.024 0.002 PHE A 557 TRP 0.022 0.002 TRP R 33 HIS 0.007 0.001 HIS D 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21136) covalent geometry : angle 0.67017 / 0.34 (28591) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.86653 / 0.48 ( 2) hydrogen bonds : bond 0.04358 / 2.92 ( 839) hydrogen bonds : angle 5.01054 / 3.62 ( 2397) metal coordination : bond 0.01246 / 1.08 ( 22) metal coordination : angle 8.30160 / 4.60 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 450 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9088 (tmm) cc_final: 0.8874 (tmm) REVERT: A 251 MET cc_start: 0.7913 (mtm) cc_final: 0.7118 (mpp) REVERT: A 367 ASP cc_start: 0.8946 (m-30) cc_final: 0.8671 (m-30) REVERT: A 397 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.6666 (t80) REVERT: A 437 MET cc_start: 0.9364 (tpp) cc_final: 0.8829 (tmm) REVERT: A 477 SER cc_start: 0.9510 (t) cc_final: 0.9187 (p) REVERT: A 527 ILE cc_start: 0.9403 (mm) cc_final: 0.8949 (tp) REVERT: A 539 MET cc_start: 0.7241 (pmm) cc_final: 0.6963 (pmm) REVERT: A 704 MET cc_start: 0.8298 (tpt) cc_final: 0.8068 (tpp) REVERT: A 706 MET cc_start: 0.8752 (tpp) cc_final: 0.8533 (tmm) REVERT: B 109 GLN cc_start: 0.8896 (tt0) cc_final: 0.8412 (tm-30) REVERT: B 256 SER cc_start: 0.8121 (t) cc_final: 0.7367 (m) REVERT: B 351 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8094 (mp0) REVERT: B 437 MET cc_start: 0.9310 (mtm) cc_final: 0.8998 (mtm) REVERT: B 785 GLU cc_start: 0.8196 (mp0) cc_final: 0.7978 (mm-30) REVERT: B 786 VAL cc_start: 0.8803 (t) cc_final: 0.8593 (p) REVERT: B 902 GLU cc_start: 0.8578 (tp30) cc_final: 0.8102 (tm-30) REVERT: B 941 ASN cc_start: 0.8805 (t0) cc_final: 0.7997 (p0) REVERT: B 1054 MET cc_start: 0.8785 (tpt) cc_final: 0.8477 (mtm) REVERT: C 120 PHE cc_start: 0.7553 (p90) cc_final: 0.7347 (p90) REVERT: C 140 GLU cc_start: 0.7649 (tp30) cc_final: 0.6524 (tm-30) REVERT: C 162 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.7584 (mtp180) REVERT: C 330 GLU cc_start: 0.7751 (tt0) cc_final: 0.7465 (mp0) REVERT: D 74 TYR cc_start: 0.7294 (t80) cc_final: 0.6096 (t80) REVERT: D 139 ARG cc_start: 0.8454 (mtm180) cc_final: 0.7979 (mmm-85) REVERT: D 145 TYR cc_start: 0.8219 (m-10) cc_final: 0.7973 (m-10) REVERT: N 24 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8948 (mm-30) REVERT: N 51 ASN cc_start: 0.8794 (t0) cc_final: 0.8437 (t0) REVERT: N 73 LEU cc_start: 0.8430 (tp) cc_final: 0.8149 (tp) REVERT: R 26 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8476 (tmtt) REVERT: R 52 LEU cc_start: 0.8118 (tp) cc_final: 0.7829 (tt) REVERT: R 54 ILE cc_start: 0.8029 (pt) cc_final: 0.7619 (pt) REVERT: R 91 ARG cc_start: 0.7570 (mtp180) cc_final: 0.7356 (ttt180) REVERT: U 51 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7953 (mp0) outliers start: 33 outliers final: 16 residues processed: 467 average time/residue: 0.1471 time to fit residues: 106.5084 Evaluate side-chains 402 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 384 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain N residue 24 GLU Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 155 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 chunk 89 optimal weight: 0.4980 chunk 201 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 75 HIS D 77 ASN D 92 GLN N 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.110009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.079968 restraints weight = 66199.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082693 restraints weight = 33557.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.084475 restraints weight = 22397.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085609 restraints weight = 17476.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.086262 restraints weight = 15022.905| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 21159 Z= 0.289 Angle : 0.740 13.525 28607 Z= 0.380 Chirality : 0.046 0.162 3230 Planarity : 0.005 0.044 3667 Dihedral : 5.023 45.344 2819 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.68 % Allowed : 14.14 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2584 helix: 1.27 (0.20), residues: 725 sheet: -0.92 (0.20), residues: 655 loop : -1.85 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 111 TYR 0.027 0.002 TYR D 74 PHE 0.032 0.002 PHE B 668 TRP 0.028 0.003 TRP A 533 HIS 0.010 0.002 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.29 (21136) covalent geometry : angle 0.72568 / 0.38 (28591) SS BOND : bond 0.00118 / 0.06 ( 1) SS BOND : angle 0.51545 / 0.28 ( 2) hydrogen bonds : bond 0.04867 / 3.23 ( 839) hydrogen bonds : angle 5.21393 / 3.77 ( 2397) metal coordination : bond 0.01236 / 0.93 ( 22) metal coordination : angle 6.61738 / 3.35 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 373 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9038 (tmm) cc_final: 0.8703 (tmm) REVERT: A 251 MET cc_start: 0.8144 (mtm) cc_final: 0.7691 (tpp) REVERT: A 367 ASP cc_start: 0.9014 (m-30) cc_final: 0.8776 (m-30) REVERT: A 397 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6726 (t80) REVERT: A 437 MET cc_start: 0.9408 (tpp) cc_final: 0.8867 (tmm) REVERT: A 477 SER cc_start: 0.9587 (t) cc_final: 0.9277 (p) REVERT: A 527 ILE cc_start: 0.9621 (mm) cc_final: 0.9177 (tp) REVERT: A 704 MET cc_start: 0.8368 (tpt) cc_final: 0.8112 (tpp) REVERT: A 706 MET cc_start: 0.8776 (tpp) cc_final: 0.8527 (tmm) REVERT: A 744 TYR cc_start: 0.8211 (m-10) cc_final: 0.7458 (m-80) REVERT: B 303 GLU cc_start: 0.9103 (tp30) cc_final: 0.8856 (tp30) REVERT: B 351 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8094 (mp0) REVERT: B 437 MET cc_start: 0.9346 (mtm) cc_final: 0.9101 (mtm) REVERT: B 644 LEU cc_start: 0.8406 (mt) cc_final: 0.7975 (pp) REVERT: B 839 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: B 902 GLU cc_start: 0.8576 (tp30) cc_final: 0.8087 (tm-30) REVERT: B 941 ASN cc_start: 0.8670 (t0) cc_final: 0.8432 (p0) REVERT: B 990 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8329 (mm-40) REVERT: B 1080 ARG cc_start: 0.8745 (ptm160) cc_final: 0.8353 (mtm110) REVERT: C 89 MET cc_start: 0.8155 (tpp) cc_final: 0.7586 (mmm) REVERT: C 120 PHE cc_start: 0.8026 (p90) cc_final: 0.7822 (p90) REVERT: C 140 GLU cc_start: 0.7726 (tp30) cc_final: 0.6844 (tm-30) REVERT: C 162 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.7753 (mtp180) REVERT: C 203 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8448 (t0) REVERT: C 330 GLU cc_start: 0.8028 (tt0) cc_final: 0.7806 (mp0) REVERT: C 358 GLU cc_start: 0.8878 (mp0) cc_final: 0.8483 (mp0) REVERT: C 422 LEU cc_start: 0.8894 (tp) cc_final: 0.8657 (tt) REVERT: D 139 ARG cc_start: 0.8531 (mtm180) cc_final: 0.8192 (mmm-85) REVERT: N 22 LYS cc_start: 0.7675 (tppt) cc_final: 0.7332 (tppt) REVERT: N 27 LYS cc_start: 0.9563 (mttp) cc_final: 0.9246 (mtpt) REVERT: N 51 ASN cc_start: 0.8816 (t0) cc_final: 0.8470 (t0) REVERT: R 26 LYS cc_start: 0.8925 (ttpp) cc_final: 0.8714 (tmtt) REVERT: U 51 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8001 (mp0) outliers start: 61 outliers final: 48 residues processed: 409 average time/residue: 0.1408 time to fit residues: 88.6933 Evaluate side-chains 391 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 340 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 1002 GLU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain I residue 151 CYS Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 59 TYR Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 68 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 56 optimal weight: 40.0000 chunk 42 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 904 ASN ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.112720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082670 restraints weight = 65175.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085548 restraints weight = 32355.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087442 restraints weight = 21287.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088576 restraints weight = 16464.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089364 restraints weight = 14092.889| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21159 Z= 0.131 Angle : 0.638 10.897 28607 Z= 0.323 Chirality : 0.044 0.235 3230 Planarity : 0.004 0.054 3667 Dihedral : 4.646 44.432 2819 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.93 % Allowed : 16.82 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.16), residues: 2584 helix: 1.46 (0.20), residues: 724 sheet: -0.86 (0.20), residues: 660 loop : -1.82 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 25 TYR 0.023 0.001 TYR B1048 PHE 0.021 0.001 PHE B 668 TRP 0.022 0.001 TRP A 533 HIS 0.009 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (21136) covalent geometry : angle 0.62686 / 0.32 (28591) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 0.51928 / 0.30 ( 2) hydrogen bonds : bond 0.04017 / 2.69 ( 839) hydrogen bonds : angle 4.75299 / 3.44 ( 2397) metal coordination : bond 0.01223 / 1.04 ( 22) metal coordination : angle 5.37800 / 2.79 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 383 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9033 (tmm) cc_final: 0.8610 (tmm) REVERT: A 251 MET cc_start: 0.8118 (mtm) cc_final: 0.7623 (tpp) REVERT: A 367 ASP cc_start: 0.9005 (m-30) cc_final: 0.8761 (m-30) REVERT: A 397 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6437 (t80) REVERT: A 437 MET cc_start: 0.9410 (tpp) cc_final: 0.8846 (tmm) REVERT: A 462 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9193 (pp) REVERT: A 477 SER cc_start: 0.9543 (t) cc_final: 0.9224 (p) REVERT: A 496 LYS cc_start: 0.9430 (pttm) cc_final: 0.9067 (pttm) REVERT: A 527 ILE cc_start: 0.9554 (mm) cc_final: 0.9156 (tp) REVERT: A 704 MET cc_start: 0.8366 (tpt) cc_final: 0.8125 (tpp) REVERT: A 706 MET cc_start: 0.8739 (tpp) cc_final: 0.8506 (tmm) REVERT: B 303 GLU cc_start: 0.9079 (tp30) cc_final: 0.8755 (tp30) REVERT: B 351 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8048 (mp0) REVERT: B 361 ASP cc_start: 0.8486 (t0) cc_final: 0.8264 (t0) REVERT: B 437 MET cc_start: 0.9379 (mtm) cc_final: 0.9104 (mtm) REVERT: B 644 LEU cc_start: 0.8343 (mt) cc_final: 0.7942 (pp) REVERT: B 839 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: B 902 GLU cc_start: 0.8609 (tp30) cc_final: 0.8085 (tm-30) REVERT: B 919 ASP cc_start: 0.8383 (p0) cc_final: 0.8072 (m-30) REVERT: B 920 PHE cc_start: 0.7781 (m-80) cc_final: 0.7536 (m-80) REVERT: B 938 MET cc_start: 0.7145 (mmm) cc_final: 0.6928 (ptp) REVERT: B 941 ASN cc_start: 0.8858 (t0) cc_final: 0.8534 (p0) REVERT: C 89 MET cc_start: 0.7889 (tpp) cc_final: 0.7641 (mmm) REVERT: C 140 GLU cc_start: 0.7634 (tp30) cc_final: 0.6864 (tm-30) REVERT: C 162 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.8014 (mtt180) REVERT: C 203 ASN cc_start: 0.8970 (t0) cc_final: 0.8707 (t0) REVERT: C 284 VAL cc_start: 0.9064 (t) cc_final: 0.8772 (p) REVERT: C 330 GLU cc_start: 0.8036 (tt0) cc_final: 0.7818 (mp0) REVERT: C 358 GLU cc_start: 0.8787 (mp0) cc_final: 0.8388 (mp0) REVERT: D 74 TYR cc_start: 0.6731 (t80) cc_final: 0.5975 (t80) REVERT: D 136 ARG cc_start: 0.8506 (ptm-80) cc_final: 0.8192 (tmm160) REVERT: N 14 GLU cc_start: 0.8928 (mp0) cc_final: 0.8710 (mp0) REVERT: N 22 LYS cc_start: 0.7841 (tppt) cc_final: 0.7407 (tppt) REVERT: N 24 GLU cc_start: 0.9231 (mp0) cc_final: 0.8899 (mm-30) REVERT: N 27 LYS cc_start: 0.9562 (mttp) cc_final: 0.9206 (ptpt) REVERT: N 50 MET cc_start: 0.8305 (mmt) cc_final: 0.8104 (mmp) REVERT: N 51 ASN cc_start: 0.8806 (t0) cc_final: 0.8444 (t0) REVERT: U 51 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8011 (mp0) outliers start: 44 outliers final: 31 residues processed: 402 average time/residue: 0.1516 time to fit residues: 94.4681 Evaluate side-chains 385 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 351 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain R residue 27 TRP Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 103 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS B 240 HIS ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.107294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077020 restraints weight = 66904.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079755 restraints weight = 34110.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.081549 restraints weight = 22756.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.082689 restraints weight = 17771.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083317 restraints weight = 15280.491| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 21159 Z= 0.324 Angle : 0.784 13.105 28607 Z= 0.400 Chirality : 0.047 0.236 3230 Planarity : 0.005 0.052 3667 Dihedral : 5.272 49.566 2819 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.86 % Allowed : 17.87 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.16), residues: 2584 helix: 1.10 (0.20), residues: 727 sheet: -1.01 (0.20), residues: 635 loop : -2.05 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 330 TYR 0.022 0.002 TYR B1048 PHE 0.026 0.002 PHE D 62 TRP 0.030 0.002 TRP A 533 HIS 0.009 0.002 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00739 / 0.32 (21136) covalent geometry : angle 0.77073 / 0.40 (28591) SS BOND : bond 0.00158 / 0.08 ( 1) SS BOND : angle 0.81436 / 0.43 ( 2) hydrogen bonds : bond 0.05069 / 3.37 ( 839) hydrogen bonds : angle 5.27262 / 3.83 ( 2397) metal coordination : bond 0.01215 / 0.90 ( 22) metal coordination : angle 6.64042 / 3.16 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 333 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9026 (tmm) cc_final: 0.8552 (tmm) REVERT: A 251 MET cc_start: 0.8256 (mtm) cc_final: 0.7762 (tpp) REVERT: A 367 ASP cc_start: 0.9061 (m-30) cc_final: 0.8846 (m-30) REVERT: A 397 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6917 (t80) REVERT: A 437 MET cc_start: 0.9417 (tpp) cc_final: 0.8847 (tmm) REVERT: A 456 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8601 (t0) REVERT: A 505 MET cc_start: 0.9019 (mmp) cc_final: 0.8680 (tpp) REVERT: A 527 ILE cc_start: 0.9600 (mm) cc_final: 0.9188 (tp) REVERT: A 704 MET cc_start: 0.8438 (tpt) cc_final: 0.8180 (tpp) REVERT: A 706 MET cc_start: 0.8767 (tpp) cc_final: 0.8527 (tmm) REVERT: A 744 TYR cc_start: 0.8246 (m-10) cc_final: 0.7308 (m-80) REVERT: B 437 MET cc_start: 0.9379 (mtm) cc_final: 0.9005 (mtm) REVERT: B 462 ASN cc_start: 0.8951 (t0) cc_final: 0.8523 (p0) REVERT: B 644 LEU cc_start: 0.8545 (mt) cc_final: 0.8214 (pp) REVERT: B 857 LYS cc_start: 0.8224 (tptp) cc_final: 0.7888 (tppt) REVERT: B 902 GLU cc_start: 0.8592 (tp30) cc_final: 0.8044 (tm-30) REVERT: B 1054 MET cc_start: 0.8977 (tpt) cc_final: 0.8446 (mmm) REVERT: C 89 MET cc_start: 0.8041 (tpp) cc_final: 0.7840 (mmm) REVERT: C 140 GLU cc_start: 0.7656 (tp30) cc_final: 0.7377 (tm-30) REVERT: C 162 ARG cc_start: 0.8461 (mtt-85) cc_final: 0.7692 (mtp180) REVERT: C 169 GLU cc_start: 0.6069 (pp20) cc_final: 0.5344 (pp20) REVERT: C 171 ARG cc_start: 0.7328 (mtm180) cc_final: 0.6805 (ptt-90) REVERT: C 203 ASN cc_start: 0.8947 (t0) cc_final: 0.8659 (t0) REVERT: C 303 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.7637 (p) REVERT: C 306 GLN cc_start: 0.9280 (mt0) cc_final: 0.8782 (mt0) REVERT: C 330 GLU cc_start: 0.8248 (tt0) cc_final: 0.8005 (mp0) REVERT: C 358 GLU cc_start: 0.8929 (mp0) cc_final: 0.8668 (mp0) REVERT: D 38 MET cc_start: 0.8885 (pmm) cc_final: 0.8622 (pmm) REVERT: D 136 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8211 (tmm160) REVERT: N 27 LYS cc_start: 0.9584 (mttp) cc_final: 0.9294 (ptpt) REVERT: N 50 MET cc_start: 0.8291 (mmt) cc_final: 0.7976 (mmp) REVERT: N 51 ASN cc_start: 0.8810 (t0) cc_final: 0.8462 (t0) REVERT: N 74 ARG cc_start: 0.8692 (tpp-160) cc_final: 0.8325 (tpp-160) REVERT: U 51 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8039 (mp0) REVERT: U 59 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6223 (m-10) outliers start: 88 outliers final: 59 residues processed: 382 average time/residue: 0.1529 time to fit residues: 89.9986 Evaluate side-chains 374 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 311 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 839 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 198 GLN Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain R residue 27 TRP Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 59 TYR Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 144 optimal weight: 8.9990 chunk 169 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 370 GLN B 670 ASN ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.109994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.079862 restraints weight = 64390.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082686 restraints weight = 32829.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.084556 restraints weight = 21902.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085711 restraints weight = 17051.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.086448 restraints weight = 14637.609| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21159 Z= 0.137 Angle : 0.646 12.205 28607 Z= 0.327 Chirality : 0.044 0.217 3230 Planarity : 0.004 0.047 3667 Dihedral : 4.769 48.145 2819 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.90 % Allowed : 19.54 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2584 helix: 1.40 (0.20), residues: 727 sheet: -0.91 (0.20), residues: 663 loop : -1.95 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 139 TYR 0.020 0.001 TYR B1048 PHE 0.019 0.001 PHE D 62 TRP 0.018 0.001 TRP A 533 HIS 0.009 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (21136) covalent geometry : angle 0.63761 / 0.33 (28591) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.43070 / 0.25 ( 2) hydrogen bonds : bond 0.04005 / 2.67 ( 839) hydrogen bonds : angle 4.73210 / 3.43 ( 2397) metal coordination : bond 0.01483 / 1.26 ( 22) metal coordination : angle 4.83588 / 2.39 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.8990 (tmm) cc_final: 0.8406 (tmm) REVERT: A 194 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8653 (p0) REVERT: A 251 MET cc_start: 0.8122 (mtm) cc_final: 0.7638 (tpp) REVERT: A 330 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8427 (ttp80) REVERT: A 360 ASP cc_start: 0.7975 (p0) cc_final: 0.7509 (p0) REVERT: A 367 ASP cc_start: 0.9026 (m-30) cc_final: 0.8811 (m-30) REVERT: A 397 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 437 MET cc_start: 0.9412 (tpp) cc_final: 0.8854 (tmm) REVERT: A 505 MET cc_start: 0.8986 (mmp) cc_final: 0.8700 (tpp) REVERT: A 527 ILE cc_start: 0.9545 (mm) cc_final: 0.9110 (tp) REVERT: A 706 MET cc_start: 0.8739 (tpp) cc_final: 0.8503 (tmm) REVERT: A 744 TYR cc_start: 0.8272 (m-10) cc_final: 0.7516 (m-80) REVERT: B 361 ASP cc_start: 0.8578 (t0) cc_final: 0.8273 (t0) REVERT: B 437 MET cc_start: 0.9382 (mtm) cc_final: 0.9040 (mtm) REVERT: B 644 LEU cc_start: 0.8513 (mt) cc_final: 0.8143 (pp) REVERT: B 857 LYS cc_start: 0.8201 (tptp) cc_final: 0.7900 (tppt) REVERT: B 902 GLU cc_start: 0.8605 (tp30) cc_final: 0.8031 (tm-30) REVERT: B 919 ASP cc_start: 0.8246 (p0) cc_final: 0.8014 (m-30) REVERT: B 941 ASN cc_start: 0.8857 (t0) cc_final: 0.8391 (p0) REVERT: C 140 GLU cc_start: 0.7651 (tp30) cc_final: 0.6678 (tm-30) REVERT: C 162 ARG cc_start: 0.8442 (mtt-85) cc_final: 0.7565 (mtp180) REVERT: C 169 GLU cc_start: 0.5725 (pp20) cc_final: 0.5325 (pp20) REVERT: C 171 ARG cc_start: 0.7144 (mtm180) cc_final: 0.6700 (pmt170) REVERT: C 303 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 330 GLU cc_start: 0.8228 (tt0) cc_final: 0.7953 (mp0) REVERT: C 358 GLU cc_start: 0.8837 (mp0) cc_final: 0.7923 (tp30) REVERT: D 8 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8547 (mmmm) REVERT: D 38 MET cc_start: 0.8803 (pmm) cc_final: 0.8523 (pmm) REVERT: D 74 TYR cc_start: 0.6381 (t80) cc_final: 0.5779 (t80) REVERT: D 136 ARG cc_start: 0.8514 (ptm-80) cc_final: 0.8174 (tmm160) REVERT: N 27 LYS cc_start: 0.9590 (mttp) cc_final: 0.9270 (ptpt) REVERT: N 51 ASN cc_start: 0.8896 (t0) cc_final: 0.8504 (t0) REVERT: N 52 ASP cc_start: 0.9510 (m-30) cc_final: 0.9230 (t70) REVERT: N 54 LYS cc_start: 0.8989 (tppp) cc_final: 0.8703 (tppp) REVERT: R 49 ILE cc_start: 0.8813 (pt) cc_final: 0.8567 (mm) REVERT: U 33 LYS cc_start: 0.9698 (tppp) cc_final: 0.9366 (tppt) REVERT: U 51 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8043 (mp0) outliers start: 66 outliers final: 43 residues processed: 393 average time/residue: 0.1528 time to fit residues: 91.9450 Evaluate side-chains 390 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 343 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 8 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain R residue 27 TRP Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 215 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 250 optimal weight: 30.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.109681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.079735 restraints weight = 66165.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082573 restraints weight = 32941.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.084441 restraints weight = 21710.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.085621 restraints weight = 16796.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.086305 restraints weight = 14366.826| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21159 Z= 0.162 Angle : 0.652 10.889 28607 Z= 0.329 Chirality : 0.044 0.273 3230 Planarity : 0.004 0.047 3667 Dihedral : 4.705 47.982 2819 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.16 % Allowed : 20.07 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.16), residues: 2584 helix: 1.49 (0.20), residues: 727 sheet: -1.02 (0.20), residues: 663 loop : -1.92 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 15 TYR 0.025 0.001 TYR B1048 PHE 0.017 0.001 PHE D 62 TRP 0.017 0.001 TRP A 533 HIS 0.009 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (21136) covalent geometry : angle 0.64359 / 0.33 (28591) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.27800 / 0.16 ( 2) hydrogen bonds : bond 0.03984 / 2.68 ( 839) hydrogen bonds : angle 4.67840 / 3.38 ( 2397) metal coordination : bond 0.00869 / 0.71 ( 22) metal coordination : angle 4.78608 / 2.27 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 350 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7571 (tp) REVERT: A 148 MET cc_start: 0.8996 (tmm) cc_final: 0.8456 (tmm) REVERT: A 194 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8672 (p0) REVERT: A 251 MET cc_start: 0.8196 (mtm) cc_final: 0.7713 (tpp) REVERT: A 352 VAL cc_start: 0.8074 (p) cc_final: 0.7779 (p) REVERT: A 367 ASP cc_start: 0.9037 (m-30) cc_final: 0.8829 (m-30) REVERT: A 397 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.6852 (t80) REVERT: A 437 MET cc_start: 0.9416 (tpp) cc_final: 0.8853 (tmm) REVERT: A 505 MET cc_start: 0.9033 (mmp) cc_final: 0.8783 (tpp) REVERT: A 527 ILE cc_start: 0.9565 (mm) cc_final: 0.9108 (tp) REVERT: B 361 ASP cc_start: 0.8625 (t0) cc_final: 0.8285 (t0) REVERT: B 437 MET cc_start: 0.9388 (mtm) cc_final: 0.9053 (mtm) REVERT: B 462 ASN cc_start: 0.8896 (t0) cc_final: 0.8548 (p0) REVERT: B 644 LEU cc_start: 0.8553 (mt) cc_final: 0.8186 (pp) REVERT: B 902 GLU cc_start: 0.8613 (tp30) cc_final: 0.8028 (tm-30) REVERT: B 919 ASP cc_start: 0.8338 (p0) cc_final: 0.8102 (m-30) REVERT: B 941 ASN cc_start: 0.8814 (t0) cc_final: 0.8188 (p0) REVERT: B 1054 MET cc_start: 0.8896 (tpt) cc_final: 0.8529 (tpp) REVERT: C 89 MET cc_start: 0.8071 (tpp) cc_final: 0.7732 (tpt) REVERT: C 140 GLU cc_start: 0.7623 (tp30) cc_final: 0.7236 (tm-30) REVERT: C 162 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.7670 (mtp180) REVERT: C 171 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6617 (pmt170) REVERT: C 330 GLU cc_start: 0.8282 (tt0) cc_final: 0.7975 (mp0) REVERT: C 358 GLU cc_start: 0.8806 (mp0) cc_final: 0.8368 (mp0) REVERT: D 74 TYR cc_start: 0.6240 (t80) cc_final: 0.5924 (t80) REVERT: D 112 ASP cc_start: 0.8878 (t0) cc_final: 0.8486 (t0) REVERT: D 136 ARG cc_start: 0.8528 (ptm-80) cc_final: 0.7480 (tmm160) REVERT: D 140 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8400 (mm-30) REVERT: N 27 LYS cc_start: 0.9584 (mttp) cc_final: 0.9261 (ptpt) REVERT: N 51 ASN cc_start: 0.8856 (t0) cc_final: 0.8446 (t0) REVERT: R 49 ILE cc_start: 0.8749 (pt) cc_final: 0.8441 (mm) REVERT: U 18 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8345 (mm-30) REVERT: U 33 LYS cc_start: 0.9693 (tppp) cc_final: 0.9362 (tppt) REVERT: U 51 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8114 (mp0) outliers start: 72 outliers final: 50 residues processed: 388 average time/residue: 0.1492 time to fit residues: 90.0792 Evaluate side-chains 389 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 761 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 930 VAL Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1086 THR Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain R residue 27 TRP Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 155 optimal weight: 0.0980 chunk 144 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 178 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 ASN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** 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 = 0.3909 r_free = 0.3909 target = 0.112633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083182 restraints weight = 64618.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086082 restraints weight = 32190.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087976 restraints weight = 21106.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089140 restraints weight = 16281.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089921 restraints weight = 13880.757| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21159 Z= 0.115 Angle : 0.671 18.179 28607 Z= 0.327 Chirality : 0.044 0.281 3230 Planarity : 0.004 0.069 3667 Dihedral : 4.445 44.753 2819 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.11 % Allowed : 21.56 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2584 helix: 1.58 (0.20), residues: 726 sheet: -0.88 (0.20), residues: 647 loop : -1.87 (0.16), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 330 TYR 0.021 0.001 TYR B1048 PHE 0.022 0.001 PHE R 103 TRP 0.016 0.001 TRP A 533 HIS 0.008 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (21136) covalent geometry : angle 0.66548 / 0.33 (28591) SS BOND : bond 0.00117 / 0.06 ( 1) SS BOND : angle 0.78202 / 0.43 ( 2) hydrogen bonds : bond 0.03442 / 2.33 ( 839) hydrogen bonds : angle 4.43914 / 3.20 ( 2397) metal coordination : bond 0.01405 / 1.21 ( 22) metal coordination : angle 3.86751 / 1.92 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 384 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9004 (tmm) cc_final: 0.8392 (tmm) REVERT: A 251 MET cc_start: 0.8130 (mtm) cc_final: 0.7613 (tpp) REVERT: A 330 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8338 (ttp80) REVERT: A 360 ASP cc_start: 0.7901 (p0) cc_final: 0.7374 (p0) REVERT: A 367 ASP cc_start: 0.9020 (m-30) cc_final: 0.8817 (m-30) REVERT: A 437 MET cc_start: 0.9391 (tpp) cc_final: 0.8834 (tmm) REVERT: A 450 GLU cc_start: 0.9337 (tm-30) cc_final: 0.9055 (pp20) REVERT: A 456 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8415 (t0) REVERT: A 477 SER cc_start: 0.9563 (t) cc_final: 0.9295 (p) REVERT: A 527 ILE cc_start: 0.9523 (mm) cc_final: 0.9090 (tp) REVERT: B 361 ASP cc_start: 0.8525 (t0) cc_final: 0.8206 (t0) REVERT: B 437 MET cc_start: 0.9366 (mtm) cc_final: 0.9124 (mtm) REVERT: B 644 LEU cc_start: 0.8471 (mt) cc_final: 0.8139 (pp) REVERT: B 785 GLU cc_start: 0.8445 (mp0) cc_final: 0.8237 (mm-30) REVERT: B 857 LYS cc_start: 0.8170 (tppt) cc_final: 0.7811 (tppt) REVERT: B 902 GLU cc_start: 0.8649 (tp30) cc_final: 0.8025 (tm-30) REVERT: B 941 ASN cc_start: 0.8934 (t0) cc_final: 0.8379 (p0) REVERT: C 140 GLU cc_start: 0.7528 (tp30) cc_final: 0.6920 (tm-30) REVERT: C 162 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.8161 (mmm160) REVERT: C 171 ARG cc_start: 0.7030 (mtm180) cc_final: 0.6523 (ptt-90) REVERT: C 330 GLU cc_start: 0.8221 (tt0) cc_final: 0.7929 (mp0) REVERT: C 358 GLU cc_start: 0.8370 (mp0) cc_final: 0.8020 (tp30) REVERT: D 8 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8246 (tppt) REVERT: D 38 MET cc_start: 0.8894 (pmm) cc_final: 0.8594 (pmm) REVERT: D 112 ASP cc_start: 0.8863 (t0) cc_final: 0.8484 (t0) REVERT: D 136 ARG cc_start: 0.8606 (ptm-80) cc_final: 0.7518 (tmm160) REVERT: D 140 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8419 (mm-30) REVERT: N 27 LYS cc_start: 0.9572 (mttp) cc_final: 0.9287 (ptpt) REVERT: N 40 GLN cc_start: 0.8765 (mt0) cc_final: 0.8167 (pm20) REVERT: N 51 ASN cc_start: 0.8929 (t0) cc_final: 0.8629 (t0) REVERT: R 49 ILE cc_start: 0.8745 (pt) cc_final: 0.8150 (mm) REVERT: U 18 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8337 (mm-30) REVERT: U 33 LYS cc_start: 0.9686 (tppp) cc_final: 0.9363 (tppt) REVERT: U 51 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8153 (pm20) outliers start: 48 outliers final: 33 residues processed: 406 average time/residue: 0.1547 time to fit residues: 96.7575 Evaluate side-chains 380 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 346 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 59 TYR Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 228 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 182 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 803 HIS ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** 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 = 0.3884 r_free = 0.3884 target = 0.110890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081597 restraints weight = 65121.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084445 restraints weight = 32571.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086289 restraints weight = 21400.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087429 restraints weight = 16549.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088182 restraints weight = 14147.449| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21159 Z= 0.138 Angle : 0.680 13.199 28607 Z= 0.334 Chirality : 0.045 0.416 3230 Planarity : 0.004 0.047 3667 Dihedral : 4.486 44.443 2819 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.02 % Allowed : 22.62 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2584 helix: 1.59 (0.20), residues: 728 sheet: -0.93 (0.20), residues: 654 loop : -1.83 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG U 54 TYR 0.026 0.001 TYR B1048 PHE 0.018 0.001 PHE D 62 TRP 0.012 0.001 TRP R 27 HIS 0.008 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (21136) covalent geometry : angle 0.67345 / 0.33 (28591) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.23592 / 0.14 ( 2) hydrogen bonds : bond 0.03599 / 2.43 ( 839) hydrogen bonds : angle 4.49215 / 3.25 ( 2397) metal coordination : bond 0.00828 / 0.69 ( 22) metal coordination : angle 4.23208 / 1.99 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 355 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9004 (tmm) cc_final: 0.8382 (tmm) REVERT: A 251 MET cc_start: 0.8222 (mtm) cc_final: 0.7687 (tpp) REVERT: A 330 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8428 (ttp80) REVERT: A 360 ASP cc_start: 0.7924 (p0) cc_final: 0.7413 (p0) REVERT: A 367 ASP cc_start: 0.9016 (m-30) cc_final: 0.8794 (m-30) REVERT: A 437 MET cc_start: 0.9393 (tpp) cc_final: 0.8832 (tmm) REVERT: A 450 GLU cc_start: 0.9365 (tm-30) cc_final: 0.9098 (pp20) REVERT: A 477 SER cc_start: 0.9591 (t) cc_final: 0.9347 (p) REVERT: A 753 ASN cc_start: 0.9003 (m-40) cc_final: 0.8748 (p0) REVERT: B 158 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (tmm-80) REVERT: B 361 ASP cc_start: 0.8600 (t0) cc_final: 0.8271 (t0) REVERT: B 437 MET cc_start: 0.9360 (mtm) cc_final: 0.9023 (mtm) REVERT: B 644 LEU cc_start: 0.8481 (mt) cc_final: 0.8166 (pp) REVERT: B 785 GLU cc_start: 0.8435 (mp0) cc_final: 0.8227 (mm-30) REVERT: B 857 LYS cc_start: 0.7991 (tppt) cc_final: 0.7247 (tppt) REVERT: B 902 GLU cc_start: 0.8657 (tp30) cc_final: 0.8067 (tm-30) REVERT: B 941 ASN cc_start: 0.8934 (t0) cc_final: 0.8342 (p0) REVERT: B 1054 MET cc_start: 0.8442 (mmm) cc_final: 0.7938 (mmm) REVERT: C 140 GLU cc_start: 0.7602 (tp30) cc_final: 0.7338 (tm-30) REVERT: C 162 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8184 (mmm160) REVERT: C 171 ARG cc_start: 0.7006 (mtm180) cc_final: 0.6500 (ptt-90) REVERT: C 330 GLU cc_start: 0.8260 (tt0) cc_final: 0.7946 (mp0) REVERT: C 358 GLU cc_start: 0.8330 (mp0) cc_final: 0.8021 (tp30) REVERT: D 8 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8274 (tppt) REVERT: D 38 MET cc_start: 0.8852 (pmm) cc_final: 0.8463 (pmm) REVERT: D 112 ASP cc_start: 0.8875 (t0) cc_final: 0.8485 (t0) REVERT: D 136 ARG cc_start: 0.8588 (ptm-80) cc_final: 0.7445 (tmm160) REVERT: D 139 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8404 (ttm170) REVERT: D 140 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8454 (mm-30) REVERT: N 1 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7259 (ppp) REVERT: N 27 LYS cc_start: 0.9546 (mttp) cc_final: 0.9277 (ptpt) REVERT: N 40 GLN cc_start: 0.8804 (mt0) cc_final: 0.8172 (pm20) REVERT: N 51 ASN cc_start: 0.8943 (t0) cc_final: 0.8644 (t0) REVERT: R 49 ILE cc_start: 0.8837 (pt) cc_final: 0.8306 (mm) REVERT: U 18 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8266 (mm-30) REVERT: U 51 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8326 (pm20) outliers start: 46 outliers final: 37 residues processed: 378 average time/residue: 0.1528 time to fit residues: 89.1650 Evaluate side-chains 376 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 337 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 59 TYR Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 179 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 56 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 250 optimal weight: 30.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 GLN ** 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 = 0.3879 r_free = 0.3879 target = 0.110540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081025 restraints weight = 65474.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083872 restraints weight = 32908.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085747 restraints weight = 21693.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086929 restraints weight = 16752.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.087615 restraints weight = 14314.438| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21159 Z= 0.146 Angle : 0.703 16.991 28607 Z= 0.342 Chirality : 0.045 0.403 3230 Planarity : 0.004 0.047 3667 Dihedral : 4.521 45.358 2819 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.80 % Allowed : 22.79 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 2584 helix: 1.55 (0.20), residues: 730 sheet: -0.96 (0.20), residues: 659 loop : -1.86 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 54 TYR 0.028 0.001 TYR B1048 PHE 0.023 0.001 PHE R 103 TRP 0.016 0.001 TRP R 27 HIS 0.007 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (21136) covalent geometry : angle 0.69629 / 0.34 (28591) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.17139 / 0.10 ( 2) hydrogen bonds : bond 0.03693 / 2.49 ( 839) hydrogen bonds : angle 4.50150 / 3.26 ( 2397) metal coordination : bond 0.01088 / 0.92 ( 22) metal coordination : angle 4.47117 / 2.11 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.8981 (tmm) cc_final: 0.8362 (tmm) REVERT: A 251 MET cc_start: 0.8201 (mtm) cc_final: 0.7593 (tpp) REVERT: A 360 ASP cc_start: 0.7865 (p0) cc_final: 0.7365 (p0) REVERT: A 367 ASP cc_start: 0.9005 (m-30) cc_final: 0.8797 (m-30) REVERT: A 437 MET cc_start: 0.9395 (tpp) cc_final: 0.8845 (tmm) REVERT: A 450 GLU cc_start: 0.9356 (tm-30) cc_final: 0.9095 (pp20) REVERT: A 706 MET cc_start: 0.8947 (tpp) cc_final: 0.8656 (pmm) REVERT: A 720 TYR cc_start: 0.8631 (m-80) cc_final: 0.8403 (m-10) REVERT: A 753 ASN cc_start: 0.9082 (m-40) cc_final: 0.8827 (p0) REVERT: B 158 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8320 (tmm-80) REVERT: B 361 ASP cc_start: 0.8602 (t0) cc_final: 0.8255 (t0) REVERT: B 437 MET cc_start: 0.9358 (mtm) cc_final: 0.9022 (mtm) REVERT: B 644 LEU cc_start: 0.8506 (mt) cc_final: 0.8198 (pp) REVERT: B 785 GLU cc_start: 0.8437 (mp0) cc_final: 0.8227 (mm-30) REVERT: B 902 GLU cc_start: 0.8659 (tp30) cc_final: 0.8067 (tm-30) REVERT: B 941 ASN cc_start: 0.8942 (t0) cc_final: 0.8336 (p0) REVERT: B 1054 MET cc_start: 0.8431 (mmm) cc_final: 0.7869 (mmm) REVERT: C 140 GLU cc_start: 0.7566 (tp30) cc_final: 0.7297 (tm-30) REVERT: C 162 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.8117 (mmm160) REVERT: C 171 ARG cc_start: 0.7018 (mtm180) cc_final: 0.6522 (ptt-90) REVERT: C 330 GLU cc_start: 0.8307 (tt0) cc_final: 0.7964 (mp0) REVERT: C 358 GLU cc_start: 0.8342 (mp0) cc_final: 0.8036 (tp30) REVERT: D 8 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8250 (tppt) REVERT: D 38 MET cc_start: 0.8770 (pmm) cc_final: 0.8379 (pmm) REVERT: D 112 ASP cc_start: 0.8865 (t0) cc_final: 0.8473 (t0) REVERT: D 136 ARG cc_start: 0.8562 (ptm-80) cc_final: 0.7863 (tmm160) REVERT: D 139 ARG cc_start: 0.8893 (ttm-80) cc_final: 0.8434 (ttm170) REVERT: D 140 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8728 (mm-30) REVERT: N 1 MET cc_start: 0.8149 (ptm) cc_final: 0.7269 (ppp) REVERT: N 27 LYS cc_start: 0.9537 (mttp) cc_final: 0.9278 (ptpt) REVERT: N 40 GLN cc_start: 0.8790 (mt0) cc_final: 0.8161 (pm20) REVERT: N 51 ASN cc_start: 0.8984 (t0) cc_final: 0.8680 (t0) REVERT: N 54 LYS cc_start: 0.8734 (tppp) cc_final: 0.8327 (tppt) REVERT: R 49 ILE cc_start: 0.8801 (pt) cc_final: 0.8156 (mm) REVERT: U 18 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8286 (mm-30) REVERT: U 51 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8347 (pm20) outliers start: 41 outliers final: 37 residues processed: 361 average time/residue: 0.1459 time to fit residues: 81.9870 Evaluate side-chains 370 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 332 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 962 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain N residue 12 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 59 TYR Chi-restraints excluded: chain U residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 163 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 34 optimal weight: 0.0170 chunk 187 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 HIS ** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN U 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.111873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.082725 restraints weight = 64356.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085606 restraints weight = 32040.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.087496 restraints weight = 21024.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.088672 restraints weight = 16190.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089414 restraints weight = 13793.740| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21159 Z= 0.118 Angle : 0.694 14.096 28607 Z= 0.336 Chirality : 0.045 0.418 3230 Planarity : 0.004 0.047 3667 Dihedral : 4.389 43.821 2819 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.02 % Allowed : 22.75 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2584 helix: 1.61 (0.20), residues: 729 sheet: -0.87 (0.20), residues: 650 loop : -1.83 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 54 TYR 0.024 0.001 TYR B1048 PHE 0.017 0.001 PHE D 50 TRP 0.014 0.001 TRP R 27 HIS 0.007 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (21136) covalent geometry : angle 0.68901 / 0.34 (28591) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 0.65719 / 0.37 ( 2) hydrogen bonds : bond 0.03425 / 2.34 ( 839) hydrogen bonds : angle 4.39700 / 3.18 ( 2397) metal coordination : bond 0.01100 / 0.97 ( 22) metal coordination : angle 3.94158 / 1.89 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5333.28 seconds wall clock time: 92 minutes 17.85 seconds (5537.85 seconds total)