Starting phenix.real_space_refine on Fri Mar 6 21:37:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tjv_10513/03_2026/6tjv_10513.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tjv_10513/03_2026/6tjv_10513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tjv_10513/03_2026/6tjv_10513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tjv_10513/03_2026/6tjv_10513.map" model { file = "/net/cci-nas-00/data/ceres_data/6tjv_10513/03_2026/6tjv_10513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tjv_10513/03_2026/6tjv_10513.cif" } resolution = 3.2 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= 0.004 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: 8 Type Number sf(0) Gaussians Fe 12 7.16 5 Zn 1 6.06 5 P 2 5.49 5 Mg 1 5.21 5 S 170 5.16 5 C 22358 2.51 5 N 5403 2.21 5 O 5891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33838 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2780 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3541 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3615 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 455} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 769 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain: "F" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4587 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 567} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1262 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3153 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 370} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 180} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1278 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain: "K" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1594 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 184} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "M" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "N" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1160 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 11, 'TRANS': 135} Chain: "O" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3496 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 395} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "Q" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1095 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 136} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'PGT': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'BCR': 1, 'CLA': 1, 'SQD': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'SF4': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'DGD': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21442 SG CYS I 103 49.246 52.665 40.882 1.00 40.28 S ATOM 21486 SG CYS I 109 44.489 50.333 36.333 1.00 40.71 S ATOM 21195 SG CYS I 73 42.399 52.392 43.205 1.00 39.24 S ATOM 21467 SG CYS I 106 45.467 46.791 42.412 1.00 42.47 S ATOM 21142 SG CYS I 66 33.780 51.881 32.070 1.00 48.55 S ATOM 21164 SG CYS I 69 39.151 54.232 35.712 1.00 42.88 S ATOM 21123 SG CYS I 63 38.075 57.079 29.652 1.00 52.65 S ATOM 21520 SG CYS I 113 39.997 50.003 29.718 1.00 46.46 S ATOM 24507 SG CYS K 148 51.974 48.622 47.699 1.00 45.35 S ATOM 23783 SG CYS K 53 58.474 49.141 49.919 1.00 48.57 S ATOM 23777 SG CYS K 52 54.568 44.698 53.408 1.00 49.73 S ATOM 24281 SG CYS K 117 52.006 51.666 52.466 1.00 40.88 S Time building chain proxies: 7.03, per 1000 atoms: 0.21 Number of scatterers: 33838 At special positions: 0 Unit cell: (140.4, 98.55, 238.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 12 26.01 S 170 16.00 P 2 15.00 Mg 1 11.99 O 5891 8.00 N 5403 7.00 C 22358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 73 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 103 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 106 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 113 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 66 " pdb=" SF4 K 501 " pdb="FE2 SF4 K 501 " - pdb=" SG CYS K 53 " pdb="FE4 SF4 K 501 " - pdb=" SG CYS K 117 " pdb="FE1 SF4 K 501 " - pdb=" SG CYS K 148 " pdb="FE3 SF4 K 501 " - pdb=" SG CYS K 52 " Number of angles added : 36 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB PRO F 36 " Number of C-beta restraints generated: 7908 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 19 sheets defined 60.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 removed outlier: 4.188A pdb=" N LEU A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.553A pdb=" N ALA A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.989A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.617A pdb=" N LEU A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 113 removed outlier: 3.516A pdb=" N SER A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 removed outlier: 3.698A pdb=" N VAL A 117 " --> pdb=" O TYR A 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 155 through 167 removed outlier: 3.528A pdb=" N GLY A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.711A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.719A pdb=" N THR A 247 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.844A pdb=" N PHE A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 4.030A pdb=" N SER A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 302 through 329 removed outlier: 3.652A pdb=" N LYS A 317 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 366 Processing helix chain 'B' and resid 15 through 19 Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.861A pdb=" N THR B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 57 Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.512A pdb=" N TRP B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 98 removed outlier: 3.541A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.607A pdb=" N VAL B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 removed outlier: 3.973A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.569A pdb=" N ALA B 145 " --> pdb=" O THR B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 188 removed outlier: 3.605A pdb=" N ALA B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.558A pdb=" N ALA B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 199' Processing helix chain 'B' and resid 205 through 224 removed outlier: 3.760A pdb=" N GLY B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 removed outlier: 3.845A pdb=" N GLU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 264 removed outlier: 3.507A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 292 removed outlier: 3.664A pdb=" N ASN B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 315 Processing helix chain 'B' and resid 324 through 354 removed outlier: 3.875A pdb=" N LEU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.755A pdb=" N ALA B 363 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.210A pdb=" N LYS B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.639A pdb=" N THR B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.962A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 435 removed outlier: 3.665A pdb=" N LEU B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 428 " --> pdb=" O TYR B 424 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 429 " --> pdb=" O TYR B 425 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS B 435 " --> pdb=" O MET B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 474 removed outlier: 3.791A pdb=" N MET B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.690A pdb=" N ASN B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 32 through 43 removed outlier: 4.186A pdb=" N ALA C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 97 removed outlier: 4.118A pdb=" N PHE C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.804A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 102' Processing helix chain 'C' and resid 104 through 126 removed outlier: 3.887A pdb=" N GLU C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 25 Proline residue: D 18 - end of helix Processing helix chain 'D' and resid 29 through 54 Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 86 through 103 Processing helix chain 'D' and resid 110 through 128 removed outlier: 3.531A pdb=" N ALA D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 153 removed outlier: 4.229A pdb=" N VAL D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix removed outlier: 3.558A pdb=" N TRP D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 186 removed outlier: 3.526A pdb=" N SER D 172 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 219 Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 239 through 265 Processing helix chain 'D' and resid 266 through 295 removed outlier: 3.621A pdb=" N ALA D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 276 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 318 removed outlier: 3.614A pdb=" N TYR D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL D 313 " --> pdb=" O HIS D 309 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 314 " --> pdb=" O MET D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 354 removed outlier: 3.619A pdb=" N VAL D 326 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.612A pdb=" N SER D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA D 376 " --> pdb=" O PRO D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.829A pdb=" N VAL D 395 " --> pdb=" O LEU D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 434 Processing helix chain 'D' and resid 449 through 452 Processing helix chain 'D' and resid 453 through 469 removed outlier: 3.768A pdb=" N LEU D 461 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 removed outlier: 3.523A pdb=" N VAL D 474 " --> pdb=" O PRO D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 removed outlier: 3.610A pdb=" N SER D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 24 Processing helix chain 'E' and resid 26 through 52 removed outlier: 4.049A pdb=" N VAL E 30 " --> pdb=" O ASN E 26 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 89 removed outlier: 3.619A pdb=" N ALA E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.893A pdb=" N PHE E 96 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 10 No H-bonds generated for 'chain 'F' and resid 8 through 10' Processing helix chain 'F' and resid 11 through 23 removed outlier: 3.917A pdb=" N SER F 16 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 17 " --> pdb=" O PRO F 13 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL F 21 " --> pdb=" O LEU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 27 removed outlier: 3.508A pdb=" N SER F 27 " --> pdb=" O LEU F 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 27' Processing helix chain 'F' and resid 37 through 61 Processing helix chain 'F' and resid 88 through 113 removed outlier: 3.644A pdb=" N GLY F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 139 removed outlier: 3.527A pdb=" N GLY F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 3.728A pdb=" N VAL F 148 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 193 removed outlier: 3.738A pdb=" N ARG F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 199 Processing helix chain 'F' and resid 204 through 212 Processing helix chain 'F' and resid 216 through 235 removed outlier: 3.547A pdb=" N ILE F 220 " --> pdb=" O ASN F 216 " (cutoff:3.500A) Proline residue: F 231 - end of helix Processing helix chain 'F' and resid 241 through 247 removed outlier: 3.666A pdb=" N ASP F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 261 removed outlier: 4.472A pdb=" N ASN F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 273 Processing helix chain 'F' and resid 273 through 278 Processing helix chain 'F' and resid 282 through 304 removed outlier: 3.631A pdb=" N ALA F 304 " --> pdb=" O LEU F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 329 removed outlier: 3.779A pdb=" N VAL F 323 " --> pdb=" O TYR F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 360 removed outlier: 3.707A pdb=" N ALA F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 368 removed outlier: 3.681A pdb=" N LEU F 368 " --> pdb=" O LEU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 388 removed outlier: 3.645A pdb=" N PHE F 382 " --> pdb=" O SER F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 411 removed outlier: 3.525A pdb=" N GLU F 403 " --> pdb=" O PHE F 399 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 404 " --> pdb=" O PRO F 400 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU F 405 " --> pdb=" O GLN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 438 removed outlier: 4.235A pdb=" N GLY F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 424 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA F 427 " --> pdb=" O ASN F 423 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU F 430 " --> pdb=" O ALA F 426 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 437 " --> pdb=" O THR F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 447 Processing helix chain 'F' and resid 453 through 477 removed outlier: 3.831A pdb=" N ILE F 457 " --> pdb=" O PHE F 453 " (cutoff:3.500A) Proline residue: F 459 - end of helix removed outlier: 3.606A pdb=" N LEU F 466 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 467 " --> pdb=" O ASP F 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU F 468 " --> pdb=" O LEU F 464 " (cutoff:3.500A) Proline residue: F 471 - end of helix removed outlier: 3.801A pdb=" N ALA F 475 " --> pdb=" O PRO F 471 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE F 477 " --> pdb=" O LEU F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 509 removed outlier: 3.578A pdb=" N ALA F 490 " --> pdb=" O SER F 486 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA F 492 " --> pdb=" O ALA F 488 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU F 493 " --> pdb=" O THR F 489 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR F 494 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE F 495 " --> pdb=" O ALA F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 529 removed outlier: 3.822A pdb=" N GLN F 525 " --> pdb=" O LEU F 521 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN F 526 " --> pdb=" O PRO F 522 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU F 527 " --> pdb=" O SER F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 532 No H-bonds generated for 'chain 'F' and resid 530 through 532' Processing helix chain 'F' and resid 533 through 542 removed outlier: 3.607A pdb=" N ALA F 540 " --> pdb=" O LYS F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 578 removed outlier: 3.543A pdb=" N TRP F 555 " --> pdb=" O ARG F 551 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL F 561 " --> pdb=" O ASP F 557 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP F 562 " --> pdb=" O ARG F 558 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE F 568 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY F 569 " --> pdb=" O GLY F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 583 Processing helix chain 'F' and resid 586 through 598 Processing helix chain 'G' and resid 2 through 29 removed outlier: 3.639A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 52 removed outlier: 3.766A pdb=" N SER G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 removed outlier: 3.642A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 81 Processing helix chain 'G' and resid 93 through 118 Processing helix chain 'G' and resid 130 through 141 removed outlier: 3.829A pdb=" N THR G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE G 140 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 165 removed outlier: 4.109A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 56 removed outlier: 3.604A pdb=" N GLU H 56 " --> pdb=" O GLU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 68 Proline residue: H 65 - end of helix removed outlier: 4.347A pdb=" N SER H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 91 Proline residue: H 86 - end of helix removed outlier: 3.712A pdb=" N LEU H 89 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 129 through 138 removed outlier: 3.792A pdb=" N PHE H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG H 136 " --> pdb=" O PHE H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 149 removed outlier: 3.580A pdb=" N LEU H 144 " --> pdb=" O TYR H 140 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 147 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 194 Proline residue: H 185 - end of helix removed outlier: 4.098A pdb=" N ASP H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 204 removed outlier: 3.865A pdb=" N LEU H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 218 removed outlier: 3.553A pdb=" N ASN H 217 " --> pdb=" O GLU H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 227 removed outlier: 3.530A pdb=" N ARG H 226 " --> pdb=" O GLY H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 281 removed outlier: 3.695A pdb=" N VAL H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS H 274 " --> pdb=" O ARG H 270 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 302 through 310 removed outlier: 6.599A pdb=" N PHE H 307 " --> pdb=" O TRP H 304 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP H 308 " --> pdb=" O ASN H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 363 removed outlier: 3.849A pdb=" N ASN H 361 " --> pdb=" O PRO H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 371 Processing helix chain 'H' and resid 377 through 385 removed outlier: 3.609A pdb=" N ILE H 385 " --> pdb=" O ILE H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 392 Processing helix chain 'I' and resid 3 through 32 removed outlier: 3.592A pdb=" N GLN I 16 " --> pdb=" O LYS I 12 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 130 through 133 Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 159 through 163 removed outlier: 3.899A pdb=" N LEU I 163 " --> pdb=" O PHE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 193 Processing helix chain 'J' and resid 45 through 56 Processing helix chain 'J' and resid 119 through 129 Processing helix chain 'J' and resid 161 through 165 Processing helix chain 'K' and resid 25 through 41 removed outlier: 3.512A pdb=" N VAL K 34 " --> pdb=" O SER K 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG K 39 " --> pdb=" O TYR K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 62 removed outlier: 4.184A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU K 56 " --> pdb=" O CYS K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 104 removed outlier: 3.786A pdb=" N LEU K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 119 Processing helix chain 'K' and resid 121 through 125 Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.733A pdb=" N LYS K 137 " --> pdb=" O GLY K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 167 removed outlier: 3.591A pdb=" N MET K 156 " --> pdb=" O PRO K 152 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP K 157 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 165 " --> pdb=" O LYS K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 169 No H-bonds generated for 'chain 'K' and resid 168 through 169' Processing helix chain 'K' and resid 170 through 174 removed outlier: 3.781A pdb=" N ARG K 174 " --> pdb=" O ILE K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 208 removed outlier: 3.700A pdb=" N GLN K 208 " --> pdb=" O PRO K 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 22 removed outlier: 3.959A pdb=" N LEU L 10 " --> pdb=" O GLU L 6 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY L 18 " --> pdb=" O GLY L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 40 through 61 Proline residue: L 56 - end of helix removed outlier: 3.746A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 61 " --> pdb=" O GLY L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 65 removed outlier: 3.501A pdb=" N ILE L 65 " --> pdb=" O ALA L 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 62 through 65' Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 66 through 88 removed outlier: 3.603A pdb=" N ASP M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 17 Processing helix chain 'N' and resid 30 through 40 removed outlier: 3.501A pdb=" N LYS N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 90 removed outlier: 3.659A pdb=" N GLU N 89 " --> pdb=" O THR N 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN N 90 " --> pdb=" O TYR N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 108 removed outlier: 3.591A pdb=" N ARG N 107 " --> pdb=" O ASP N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 122 removed outlier: 3.693A pdb=" N THR N 120 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR N 122 " --> pdb=" O GLN N 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 34 removed outlier: 3.742A pdb=" N PHE O 34 " --> pdb=" O PRO O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing helix chain 'P' and resid 20 through 29 removed outlier: 3.936A pdb=" N ARG P 26 " --> pdb=" O ASP P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 68 removed outlier: 3.724A pdb=" N LYS P 43 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE P 44 " --> pdb=" O ASN P 40 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) Proline residue: P 54 - end of helix removed outlier: 3.984A pdb=" N ARG P 60 " --> pdb=" O ASP P 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 63 " --> pdb=" O TRP P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 86 removed outlier: 3.614A pdb=" N PHE P 86 " --> pdb=" O LYS P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 119 Processing helix chain 'P' and resid 125 through 132 Processing helix chain 'P' and resid 138 through 149 Processing helix chain 'P' and resid 156 through 161 removed outlier: 3.697A pdb=" N TYR P 160 " --> pdb=" O GLN P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 178 removed outlier: 3.530A pdb=" N ALA P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 191 removed outlier: 3.557A pdb=" N LEU P 185 " --> pdb=" O ASN P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 229 removed outlier: 4.322A pdb=" N VAL P 214 " --> pdb=" O LEU P 210 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET P 215 " --> pdb=" O PHE P 211 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA P 216 " --> pdb=" O TRP P 212 " (cutoff:3.500A) Proline residue: P 217 - end of helix removed outlier: 3.751A pdb=" N SER P 223 " --> pdb=" O PHE P 219 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 248 Processing helix chain 'P' and resid 268 through 272 removed outlier: 3.501A pdb=" N GLY P 272 " --> pdb=" O LYS P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 279 Processing helix chain 'P' and resid 280 through 288 removed outlier: 3.553A pdb=" N ALA P 286 " --> pdb=" O PRO P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 333 through 340 Processing helix chain 'P' and resid 345 through 354 removed outlier: 3.592A pdb=" N TYR P 351 " --> pdb=" O TYR P 347 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN P 354 " --> pdb=" O ASP P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 361 through 390 removed outlier: 3.567A pdb=" N GLN P 365 " --> pdb=" O ASP P 361 " (cutoff:3.500A) Processing helix chain 'P' and resid 398 through 414 removed outlier: 3.795A pdb=" N ASN P 404 " --> pdb=" O HIS P 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 11 removed outlier: 4.158A pdb=" N THR Q 11 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 24 Processing helix chain 'Q' and resid 50 through 59 removed outlier: 4.114A pdb=" N ILE Q 54 " --> pdb=" O PRO Q 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN Q 59 " --> pdb=" O THR Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 72 Processing helix chain 'Q' and resid 78 through 86 Processing sheet with id=AA1, first strand: chain 'D' and resid 63 through 68 removed outlier: 5.131A pdb=" N THR D 65 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 80 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE D 67 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR D 78 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 69 through 74 removed outlier: 7.056A pdb=" N LEU F 81 " --> pdb=" O TRP F 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 14 removed outlier: 4.028A pdb=" N ASP H 39 " --> pdb=" O THR H 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 159 through 160 Processing sheet with id=AA5, first strand: chain 'H' and resid 327 through 332 removed outlier: 3.519A pdb=" N LEU H 342 " --> pdb=" O HIS H 327 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS H 354 " --> pdb=" O TYR H 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 56 through 58 Processing sheet with id=AA7, first strand: chain 'I' and resid 79 through 82 removed outlier: 6.736A pdb=" N VAL I 79 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR I 96 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP I 81 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE I 98 " --> pdb=" O TYR I 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 30 through 31 removed outlier: 5.977A pdb=" N GLU J 37 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LYS J 97 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE J 39 " --> pdb=" O LYS J 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 66 through 68 removed outlier: 3.583A pdb=" N TYR J 67 " --> pdb=" O VAL J 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 107 through 108 removed outlier: 7.239A pdb=" N VAL J 107 " --> pdb=" O GLU J 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 83 through 87 removed outlier: 6.447A pdb=" N ILE K 84 " --> pdb=" O ILE K 112 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET K 114 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR K 86 " --> pdb=" O MET K 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 182 through 184 removed outlier: 4.393A pdb=" N ARG K 182 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL M 33 " --> pdb=" O ARG K 182 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU M 31 " --> pdb=" O PHE K 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 5 through 7 removed outlier: 3.731A pdb=" N VAL M 10 " --> pdb=" O THR M 7 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.828A pdb=" N GLY M 91 " --> pdb=" O GLU M 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 18 through 19 removed outlier: 6.414A pdb=" N LEU N 98 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL N 129 " --> pdb=" O LEU N 98 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU N 100 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR N 43 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N TRP N 101 " --> pdb=" O THR N 43 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU N 45 " --> pdb=" O TRP N 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 40 through 44 removed outlier: 6.531A pdb=" N GLN O 49 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE O 43 " --> pdb=" O TYR O 47 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR O 47 " --> pdb=" O ILE O 43 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 257 through 259 Processing sheet with id=AB9, first strand: chain 'Q' and resid 38 through 40 Processing sheet with id=AC1, first strand: chain 'S' and resid 86 through 90 removed outlier: 6.749A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) 1679 hydrogen bonds defined for protein. 4851 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: 6.28 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.35: 10376 1.35 - 1.58: 24014 1.58 - 1.81: 287 1.81 - 2.05: 1 2.05 - 2.28: 39 Bond restraints: 34717 Sorted by residual: bond pdb=" N PRO F 376 " pdb=" CA PRO F 376 " ideal model delta sigma weight residual 1.469 1.695 -0.227 1.28e-02 6.10e+03 3.13e+02 bond pdb=" N PRO F 444 " pdb=" CA PRO F 444 " ideal model delta sigma weight residual 1.469 1.693 -0.224 1.28e-02 6.10e+03 3.07e+02 bond pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 1.469 1.657 -0.188 1.28e-02 6.10e+03 2.16e+02 bond pdb=" C6 SQD L 402 " pdb=" S SQD L 402 " ideal model delta sigma weight residual 1.840 1.568 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C LEU D 371 " pdb=" O LEU D 371 " ideal model delta sigma weight residual 1.235 1.174 0.061 4.70e-03 4.53e+04 1.69e+02 ... (remaining 34712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.78: 47279 12.78 - 25.55: 31 25.55 - 38.33: 7 38.33 - 51.10: 1 51.10 - 63.88: 1 Bond angle restraints: 47319 Sorted by residual: angle pdb=" NB CLA F 704 " pdb="MG CLA F 704 " pdb=" ND CLA F 704 " ideal model delta sigma weight residual 176.90 113.02 63.88 3.00e+00 1.11e-01 4.53e+02 angle pdb=" CA ALA H 73 " pdb=" C ALA H 73 " pdb=" N ALA H 74 " ideal model delta sigma weight residual 116.84 87.58 29.26 1.71e+00 3.42e-01 2.93e+02 angle pdb=" C ALA H 73 " pdb=" N ALA H 74 " pdb=" CA ALA H 74 " ideal model delta sigma weight residual 121.54 91.11 30.43 1.91e+00 2.74e-01 2.54e+02 angle pdb=" C ASN D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.84 138.94 -19.10 1.25e+00 6.40e-01 2.34e+02 angle pdb=" C ARG F 375 " pdb=" N PRO F 376 " pdb=" CA PRO F 376 " ideal model delta sigma weight residual 119.84 138.85 -19.01 1.25e+00 6.40e-01 2.31e+02 ... (remaining 47314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.44: 19520 30.44 - 60.88: 816 60.88 - 91.32: 50 91.32 - 121.76: 18 121.76 - 152.20: 5 Dihedral angle restraints: 20409 sinusoidal: 8067 harmonic: 12342 Sorted by residual: dihedral pdb=" CA ILE F 252 " pdb=" C ILE F 252 " pdb=" N PRO F 253 " pdb=" CA PRO F 253 " ideal model delta harmonic sigma weight residual 180.00 117.56 62.44 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA PRO B 387 " pdb=" C PRO B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -120.25 -59.75 0 5.00e+00 4.00e-02 1.43e+02 dihedral pdb=" CA CYS K 148 " pdb=" C CYS K 148 " pdb=" N PRO K 149 " pdb=" CA PRO K 149 " ideal model delta harmonic sigma weight residual -180.00 -126.24 -53.76 0 5.00e+00 4.00e-02 1.16e+02 ... (remaining 20406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.779: 5479 0.779 - 1.558: 0 1.558 - 2.337: 0 2.337 - 3.117: 0 3.117 - 3.896: 1 Chirality restraints: 5480 Sorted by residual: chirality pdb=" CA PRO F 36 " pdb=" N PRO F 36 " pdb=" C PRO F 36 " pdb=" CB PRO F 36 " both_signs ideal model delta sigma weight residual False 2.72 -1.18 3.90 2.00e-01 2.50e+01 3.79e+02 chirality pdb=" CA GLU C 20 " pdb=" N GLU C 20 " pdb=" C GLU C 20 " pdb=" CB GLU C 20 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CA PRO D 372 " pdb=" N PRO D 372 " pdb=" C PRO D 372 " pdb=" CB PRO D 372 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 5477 not shown) Planarity restraints: 5846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CLA F 704 " -0.362 2.00e-02 2.50e+03 4.16e-01 2.16e+03 pdb=" ND CLA F 704 " -0.364 2.00e-02 2.50e+03 pdb=" NA CLA F 704 " -0.034 2.00e-02 2.50e+03 pdb=" NC CLA F 704 " -0.015 2.00e-02 2.50e+03 pdb="MG CLA F 704 " 0.774 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C CLA F 704 " 0.156 2.00e-02 2.50e+03 3.75e-01 1.76e+03 pdb=" C2C CLA F 704 " -0.274 2.00e-02 2.50e+03 pdb=" C4B CLA F 704 " -0.502 2.00e-02 2.50e+03 pdb=" CHC CLA F 704 " 0.593 2.00e-02 2.50e+03 pdb=" NC CLA F 704 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA F 704 " 0.024 2.00e-02 2.50e+03 2.79e-01 1.16e+03 pdb=" C2A CLA F 704 " 0.413 2.00e-02 2.50e+03 pdb=" C4A CLA F 704 " -0.347 2.00e-02 2.50e+03 pdb=" CHA CLA F 704 " -0.295 2.00e-02 2.50e+03 pdb=" NA CLA F 704 " -0.079 2.00e-02 2.50e+03 pdb="MG CLA F 704 " 0.284 2.00e-02 2.50e+03 ... (remaining 5843 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 4224 2.74 - 3.46: 49368 3.46 - 4.18: 82191 4.18 - 4.90: 152152 Nonbonded interactions: 287940 Sorted by model distance: nonbonded pdb=" O PHE A 301 " pdb=" N GLN A 303 " model vdw 1.299 3.120 nonbonded pdb=" O4D DGD A 501 " pdb=" O2D DGD L 401 " model vdw 1.667 3.040 nonbonded pdb=" NH1 ARG F 448 " pdb=" OD1 ASP P 158 " model vdw 1.761 3.120 nonbonded pdb=" O PHE A 301 " pdb=" C LEU A 302 " model vdw 1.906 3.270 nonbonded pdb=" CEB DGD A 501 " pdb=" CHA DGD L 401 " model vdw 1.920 3.840 ... (remaining 287935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.015 0.625 34734 Z= 0.793 Angle : 1.392 63.876 47355 Z= 0.641 Chirality : 0.075 3.896 5480 Planarity : 0.014 0.416 5846 Dihedral : 16.453 152.199 12501 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.64 % Allowed : 11.38 % Favored : 87.98 % Rotamer: Outliers : 1.46 % Allowed : 9.24 % Favored : 89.30 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.11), residues: 4234 helix: -1.80 (0.09), residues: 2388 sheet: -3.59 (0.33), residues: 180 loop : -3.84 (0.13), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG P 357 TYR 0.031 0.002 TYR J 60 PHE 0.036 0.002 PHE K 67 TRP 0.027 0.002 TRP F 482 HIS 0.006 0.001 HIS P 255 Details of bonding type rmsd covalent geometry : bond 0.01001 (34717) covalent geometry : angle 1.24527 (47319) hydrogen bonds : bond 0.17208 ( 1679) hydrogen bonds : angle 7.14280 ( 4851) metal coordination : bond 0.55812 ( 12) metal coordination : angle 22.59684 ( 36) Misc. bond : bond 0.41878 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 964 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8372 (tt0) cc_final: 0.8090 (tt0) REVERT: A 93 ASN cc_start: 0.8436 (m-40) cc_final: 0.7662 (t0) REVERT: A 252 MET cc_start: 0.8020 (tpt) cc_final: 0.7683 (tpt) REVERT: B 100 ARG cc_start: 0.7390 (mmt180) cc_final: 0.7177 (mmt180) REVERT: B 136 PHE cc_start: 0.7766 (t80) cc_final: 0.7486 (t80) REVERT: B 178 LEU cc_start: 0.9144 (tp) cc_final: 0.8873 (mt) REVERT: B 422 ILE cc_start: 0.9081 (mt) cc_final: 0.8660 (tp) REVERT: B 427 ARG cc_start: 0.8475 (ttm170) cc_final: 0.8250 (ttp-170) REVERT: B 431 MET cc_start: 0.8430 (mmt) cc_final: 0.7655 (mmt) REVERT: B 438 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 440 MET cc_start: 0.8782 (mtt) cc_final: 0.8540 (mtm) REVERT: B 466 MET cc_start: 0.7478 (mtm) cc_final: 0.7278 (mtm) REVERT: C 50 MET cc_start: 0.8598 (tpp) cc_final: 0.8382 (tpp) REVERT: C 125 ARG cc_start: 0.7353 (tpt-90) cc_final: 0.6900 (tpt170) REVERT: D 17 LEU cc_start: 0.9117 (mt) cc_final: 0.8646 (mt) REVERT: D 25 MET cc_start: 0.8804 (mmp) cc_final: 0.8515 (mmm) REVERT: D 325 MET cc_start: 0.8010 (mmm) cc_final: 0.7672 (mmm) REVERT: D 484 GLN cc_start: 0.8236 (tt0) cc_final: 0.8019 (tt0) REVERT: E 1 MET cc_start: 0.8604 (tpt) cc_final: 0.7484 (tpt) REVERT: E 86 ARG cc_start: 0.8158 (tmm-80) cc_final: 0.7826 (ttt90) REVERT: F 17 LEU cc_start: 0.8626 (mm) cc_final: 0.8286 (mt) REVERT: F 32 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8577 (mtp85) REVERT: F 238 PHE cc_start: 0.8753 (t80) cc_final: 0.8392 (t80) REVERT: F 319 TYR cc_start: 0.8234 (m-80) cc_final: 0.7812 (m-80) REVERT: F 443 LYS cc_start: 0.8923 (mttp) cc_final: 0.8425 (mttp) REVERT: F 451 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5937 (tt0) REVERT: F 487 LEU cc_start: 0.6657 (mp) cc_final: 0.6352 (tt) REVERT: F 548 MET cc_start: 0.7305 (tpp) cc_final: 0.7061 (tpp) REVERT: G 115 ILE cc_start: 0.9353 (mt) cc_final: 0.9136 (mt) REVERT: H 72 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6048 (m-10) REVERT: H 87 GLU cc_start: 0.7202 (tt0) cc_final: 0.6954 (tt0) REVERT: H 113 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8543 (t0) REVERT: H 278 GLN cc_start: 0.8336 (tt0) cc_final: 0.8114 (tt0) REVERT: H 310 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8483 (mm-40) REVERT: I 20 TYR cc_start: 0.7647 (m-80) cc_final: 0.6883 (m-80) REVERT: I 35 ARG cc_start: 0.8696 (ttt-90) cc_final: 0.8280 (ttt-90) REVERT: I 45 LYS cc_start: 0.9080 (mttt) cc_final: 0.8867 (mtpt) REVERT: I 147 LYS cc_start: 0.9061 (tptt) cc_final: 0.8680 (tppt) REVERT: J 23 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6217 (t0) REVERT: J 87 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8293 (t0) REVERT: K 26 ILE cc_start: 0.8482 (mp) cc_final: 0.8267 (tp) REVERT: K 32 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8497 (t0) REVERT: K 110 TYR cc_start: 0.8000 (m-80) cc_final: 0.7664 (m-80) REVERT: K 200 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8001 (mm-40) REVERT: L 59 LEU cc_start: 0.9007 (mt) cc_final: 0.8732 (mt) REVERT: N 40 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8582 (mmmt) REVERT: N 86 TYR cc_start: 0.9334 (t80) cc_final: 0.8940 (t80) REVERT: N 115 TYR cc_start: 0.8759 (t80) cc_final: 0.8505 (t80) REVERT: N 135 ASP cc_start: 0.8240 (t0) cc_final: 0.7753 (t0) REVERT: N 146 TRP cc_start: 0.7744 (t-100) cc_final: 0.6412 (t-100) REVERT: P 124 MET cc_start: 0.8673 (mtm) cc_final: 0.8447 (mtp) REVERT: P 179 LYS cc_start: 0.8556 (ptmm) cc_final: 0.8334 (ptmt) REVERT: P 248 ILE cc_start: 0.8525 (mm) cc_final: 0.8170 (mm) REVERT: Q 60 ASN cc_start: 0.8594 (m-40) cc_final: 0.8309 (m-40) REVERT: Q 87 ILE cc_start: 0.8642 (tt) cc_final: 0.8419 (mm) REVERT: Q 96 ILE cc_start: 0.8442 (mt) cc_final: 0.8139 (mt) REVERT: Q 116 ILE cc_start: 0.8321 (mt) cc_final: 0.8098 (mm) REVERT: Q 142 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7327 (mt-10) REVERT: S 61 TYR cc_start: 0.8749 (t80) cc_final: 0.8048 (t80) REVERT: S 91 GLN cc_start: 0.9023 (mm110) cc_final: 0.8666 (mm-40) outliers start: 51 outliers final: 22 residues processed: 999 average time/residue: 0.2290 time to fit residues: 365.6834 Evaluate side-chains 845 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 816 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain F residue 32 ARG Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 446 THR Chi-restraints excluded: chain F residue 451 GLU Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 113 ASN Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 184 MET Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 194 LEU Chi-restraints excluded: chain Q residue 108 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 212 GLN A 355 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** F 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 GLN G 8 GLN H 14 ASN H 19 HIS ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN K 168 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN O 65 GLN P 18 HIS P 355 HIS S 62 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.129579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.106779 restraints weight = 46337.726| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.94 r_work: 0.2973 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 34734 Z= 0.163 Angle : 0.890 33.454 47355 Z= 0.391 Chirality : 0.046 0.823 5480 Planarity : 0.006 0.197 5846 Dihedral : 12.139 140.649 5134 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.47 % Favored : 90.22 % Rotamer: Outliers : 3.16 % Allowed : 14.77 % Favored : 82.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.12), residues: 4234 helix: -0.38 (0.10), residues: 2404 sheet: -3.18 (0.33), residues: 199 loop : -3.40 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 310 TYR 0.032 0.002 TYR L 13 PHE 0.025 0.001 PHE K 67 TRP 0.021 0.001 TRP F 482 HIS 0.008 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00370 (34717) covalent geometry : angle 0.82889 (47319) hydrogen bonds : bond 0.04643 ( 1679) hydrogen bonds : angle 4.90232 ( 4851) metal coordination : bond 0.02104 ( 12) metal coordination : angle 11.74435 ( 36) Misc. bond : bond 0.00387 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 878 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8802 (m-40) cc_final: 0.7745 (t0) REVERT: A 157 TYR cc_start: 0.7048 (t80) cc_final: 0.6668 (t80) REVERT: A 252 MET cc_start: 0.8542 (tpt) cc_final: 0.8185 (tpt) REVERT: A 301 PHE cc_start: 0.8603 (m-10) cc_final: 0.8254 (m-80) REVERT: B 165 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8436 (mttt) REVERT: B 178 LEU cc_start: 0.9006 (tp) cc_final: 0.8692 (mt) REVERT: B 361 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 431 MET cc_start: 0.9052 (mmt) cc_final: 0.8476 (mmt) REVERT: B 433 VAL cc_start: 0.8642 (m) cc_final: 0.8437 (m) REVERT: B 438 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8158 (tm-30) REVERT: B 440 MET cc_start: 0.8979 (mtt) cc_final: 0.8715 (mtm) REVERT: B 466 MET cc_start: 0.8642 (mtm) cc_final: 0.8402 (mtm) REVERT: C 35 LEU cc_start: 0.8716 (tp) cc_final: 0.8464 (tp) REVERT: C 125 ARG cc_start: 0.7716 (tpt-90) cc_final: 0.7389 (tpt170) REVERT: D 17 LEU cc_start: 0.9063 (mt) cc_final: 0.8855 (mp) REVERT: D 325 MET cc_start: 0.8643 (mmm) cc_final: 0.8348 (mmm) REVERT: D 375 SER cc_start: 0.8827 (t) cc_final: 0.8385 (t) REVERT: D 439 ASP cc_start: 0.8521 (t0) cc_final: 0.8190 (t70) REVERT: D 452 GLU cc_start: 0.8176 (tt0) cc_final: 0.7972 (tt0) REVERT: D 484 GLN cc_start: 0.8699 (tt0) cc_final: 0.8469 (tt0) REVERT: E 1 MET cc_start: 0.8786 (tpt) cc_final: 0.7741 (tpt) REVERT: E 56 GLN cc_start: 0.9011 (pt0) cc_final: 0.8785 (pt0) REVERT: E 86 ARG cc_start: 0.8876 (tmm-80) cc_final: 0.8482 (ttt90) REVERT: F 17 LEU cc_start: 0.8812 (mm) cc_final: 0.8413 (mt) REVERT: F 75 ASP cc_start: 0.8757 (p0) cc_final: 0.8264 (t0) REVERT: F 96 MET cc_start: 0.8404 (mtp) cc_final: 0.8081 (mtp) REVERT: F 319 TYR cc_start: 0.9010 (m-80) cc_final: 0.8568 (m-80) REVERT: F 443 LYS cc_start: 0.9105 (mttp) cc_final: 0.8754 (mttt) REVERT: F 487 LEU cc_start: 0.6614 (mp) cc_final: 0.6139 (tt) REVERT: F 539 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7737 (mtp180) REVERT: G 156 MET cc_start: 0.4443 (ptp) cc_final: 0.4212 (ptp) REVERT: H 29 MET cc_start: 0.8820 (mtp) cc_final: 0.8373 (mtp) REVERT: H 72 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.5892 (m-80) REVERT: H 309 TYR cc_start: 0.9007 (m-80) cc_final: 0.8676 (m-10) REVERT: H 310 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8454 (mm-40) REVERT: H 326 GLU cc_start: 0.8039 (pm20) cc_final: 0.7529 (pt0) REVERT: I 20 TYR cc_start: 0.8447 (m-80) cc_final: 0.7517 (m-80) REVERT: I 45 LYS cc_start: 0.9109 (mttt) cc_final: 0.8862 (mtpt) REVERT: I 133 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8049 (mt-10) REVERT: J 23 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6801 (t0) REVERT: J 31 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8130 (mtt90) REVERT: J 87 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8447 (t0) REVERT: K 32 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8217 (t0) REVERT: K 110 TYR cc_start: 0.8466 (m-80) cc_final: 0.8189 (m-80) REVERT: K 172 ASN cc_start: 0.8590 (t0) cc_final: 0.8185 (t0) REVERT: L 59 LEU cc_start: 0.9058 (mt) cc_final: 0.8792 (mt) REVERT: M 19 ASP cc_start: 0.8041 (p0) cc_final: 0.7026 (t0) REVERT: N 40 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8706 (mmmt) REVERT: N 86 TYR cc_start: 0.9353 (t80) cc_final: 0.8827 (t80) REVERT: O 14 GLU cc_start: 0.7825 (pm20) cc_final: 0.7478 (pm20) REVERT: O 49 GLN cc_start: 0.8937 (tt0) cc_final: 0.8577 (tt0) REVERT: P 18 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6726 (t-170) REVERT: P 124 MET cc_start: 0.9132 (mtm) cc_final: 0.8741 (mtp) REVERT: P 184 MET cc_start: 0.9313 (mmt) cc_final: 0.8921 (mmt) REVERT: P 340 MET cc_start: 0.8916 (ttm) cc_final: 0.8618 (ttp) REVERT: Q 28 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7575 (tm-30) REVERT: Q 60 ASN cc_start: 0.8669 (m-40) cc_final: 0.8368 (m-40) REVERT: Q 87 ILE cc_start: 0.8666 (tt) cc_final: 0.8410 (mm) REVERT: Q 116 ILE cc_start: 0.8163 (mt) cc_final: 0.7931 (mm) REVERT: Q 120 ASN cc_start: 0.6888 (p0) cc_final: 0.6648 (p0) REVERT: S 61 TYR cc_start: 0.8613 (t80) cc_final: 0.8083 (t80) outliers start: 110 outliers final: 69 residues processed: 936 average time/residue: 0.2150 time to fit residues: 327.0836 Evaluate side-chains 871 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 796 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 527 LEU Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 310 ASP Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 437 LEU Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 125 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 300 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 chunk 386 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 chunk 329 optimal weight: 4.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN H 113 ASN H 156 ASN H 157 ASN H 267 GLN H 361 ASN H 364 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 311 GLN P 338 GLN ** P 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.129943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.107199 restraints weight = 46021.801| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.91 r_work: 0.2983 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 34734 Z= 0.151 Angle : 0.825 34.841 47355 Z= 0.367 Chirality : 0.045 0.615 5480 Planarity : 0.006 0.184 5846 Dihedral : 11.185 131.088 5100 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.31 % Favored : 90.39 % Rotamer: Outliers : 4.25 % Allowed : 16.61 % Favored : 79.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % 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: -1.74 (0.13), residues: 4234 helix: 0.29 (0.11), residues: 2389 sheet: -3.01 (0.34), residues: 189 loop : -3.19 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 578 TYR 0.028 0.002 TYR L 13 PHE 0.027 0.001 PHE K 67 TRP 0.022 0.001 TRP F 482 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00353 (34717) covalent geometry : angle 0.78020 (47319) hydrogen bonds : bond 0.04193 ( 1679) hydrogen bonds : angle 4.59738 ( 4851) metal coordination : bond 0.00661 ( 12) metal coordination : angle 9.71294 ( 36) Misc. bond : bond 0.00313 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 831 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8665 (m-40) cc_final: 0.7603 (t0) REVERT: A 157 TYR cc_start: 0.6966 (t80) cc_final: 0.6608 (t80) REVERT: A 252 MET cc_start: 0.8656 (tpt) cc_final: 0.8389 (tpt) REVERT: A 271 LEU cc_start: 0.8484 (mt) cc_final: 0.8201 (mm) REVERT: B 165 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8392 (mttt) REVERT: B 340 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8845 (m110) REVERT: B 361 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8182 (mm-30) REVERT: B 431 MET cc_start: 0.8995 (mmt) cc_final: 0.8433 (mmt) REVERT: B 438 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 440 MET cc_start: 0.8938 (mtt) cc_final: 0.8694 (mtm) REVERT: B 468 VAL cc_start: 0.8565 (t) cc_final: 0.8291 (t) REVERT: C 125 ARG cc_start: 0.7719 (tpt-90) cc_final: 0.7407 (tpt170) REVERT: D 17 LEU cc_start: 0.9083 (mt) cc_final: 0.8679 (mt) REVERT: D 76 LEU cc_start: 0.9371 (tp) cc_final: 0.9121 (tp) REVERT: D 325 MET cc_start: 0.8704 (mmm) cc_final: 0.8475 (mmm) REVERT: D 366 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8339 (p0) REVERT: D 368 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8887 (mm) REVERT: E 1 MET cc_start: 0.8859 (tpt) cc_final: 0.7877 (tpt) REVERT: E 56 GLN cc_start: 0.9038 (pt0) cc_final: 0.8802 (pt0) REVERT: E 86 ARG cc_start: 0.8882 (tmm-80) cc_final: 0.8534 (ttp80) REVERT: F 17 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8393 (mm) REVERT: F 75 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8239 (t0) REVERT: F 96 MET cc_start: 0.8425 (mtp) cc_final: 0.8176 (mtp) REVERT: F 133 MET cc_start: 0.8460 (mmt) cc_final: 0.8147 (mmt) REVERT: F 319 TYR cc_start: 0.8899 (m-80) cc_final: 0.8493 (m-80) REVERT: F 350 MET cc_start: 0.9248 (mmt) cc_final: 0.9024 (mmt) REVERT: F 443 LYS cc_start: 0.8974 (mttp) cc_final: 0.8614 (mttt) REVERT: F 466 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7802 (mp) REVERT: F 487 LEU cc_start: 0.6597 (mp) cc_final: 0.6206 (tt) REVERT: F 539 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7714 (mtp180) REVERT: F 560 PHE cc_start: 0.7838 (m-80) cc_final: 0.7601 (m-80) REVERT: F 592 LEU cc_start: 0.8687 (mt) cc_final: 0.8358 (tp) REVERT: G 6 LEU cc_start: 0.9323 (tp) cc_final: 0.9084 (tt) REVERT: G 114 MET cc_start: 0.9101 (tmm) cc_final: 0.8679 (ttp) REVERT: G 156 MET cc_start: 0.4219 (ptp) cc_final: 0.3924 (ptp) REVERT: H 29 MET cc_start: 0.8735 (mtp) cc_final: 0.8425 (mtp) REVERT: H 309 TYR cc_start: 0.8947 (m-80) cc_final: 0.8617 (m-10) REVERT: H 310 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8397 (mm-40) REVERT: H 326 GLU cc_start: 0.8050 (pm20) cc_final: 0.7809 (pt0) REVERT: H 354 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8792 (tmtt) REVERT: H 373 MET cc_start: 0.7122 (mmt) cc_final: 0.6754 (mmt) REVERT: I 20 TYR cc_start: 0.8498 (m-80) cc_final: 0.7604 (m-80) REVERT: I 45 LYS cc_start: 0.9076 (mttt) cc_final: 0.8791 (mtpt) REVERT: I 133 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7910 (mt-10) REVERT: I 139 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8948 (m) REVERT: J 23 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6862 (t0) REVERT: J 31 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8121 (mtp85) REVERT: J 87 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8359 (t0) REVERT: K 110 TYR cc_start: 0.8457 (m-80) cc_final: 0.8201 (m-80) REVERT: K 172 ASN cc_start: 0.8570 (t0) cc_final: 0.8277 (t0) REVERT: M 19 ASP cc_start: 0.7948 (p0) cc_final: 0.7256 (t0) REVERT: M 34 ASP cc_start: 0.9295 (t0) cc_final: 0.9006 (t70) REVERT: N 40 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8687 (mmmt) REVERT: N 86 TYR cc_start: 0.9298 (t80) cc_final: 0.8733 (t80) REVERT: O 14 GLU cc_start: 0.7889 (pm20) cc_final: 0.7490 (pm20) REVERT: O 34 PHE cc_start: 0.8429 (m-10) cc_final: 0.7996 (m-10) REVERT: O 49 GLN cc_start: 0.8961 (tt0) cc_final: 0.8562 (tt0) REVERT: P 18 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6610 (t-170) REVERT: P 83 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8556 (ptmm) REVERT: P 120 GLU cc_start: 0.8818 (tp30) cc_final: 0.8407 (mm-30) REVERT: P 124 MET cc_start: 0.9119 (mtm) cc_final: 0.8678 (mtp) REVERT: P 301 ASN cc_start: 0.8997 (t0) cc_final: 0.8789 (t0) REVERT: Q 28 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7396 (tm-30) REVERT: Q 60 ASN cc_start: 0.8608 (m-40) cc_final: 0.8361 (m-40) REVERT: Q 87 ILE cc_start: 0.8660 (tt) cc_final: 0.8399 (mm) REVERT: Q 116 ILE cc_start: 0.8117 (mt) cc_final: 0.7877 (mm) REVERT: S 49 MET cc_start: 0.8242 (ptm) cc_final: 0.7964 (ptp) REVERT: S 61 TYR cc_start: 0.8709 (t80) cc_final: 0.8028 (t80) outliers start: 148 outliers final: 92 residues processed: 913 average time/residue: 0.1972 time to fit residues: 296.4976 Evaluate side-chains 867 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 763 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 354 LYS Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 310 ASP Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 173 optimal weight: 1.9990 chunk 383 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 413 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 304 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN F 67 GLN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN H 361 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.109119 restraints weight = 45815.394| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.89 r_work: 0.2998 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 34734 Z= 0.140 Angle : 0.741 21.508 47355 Z= 0.341 Chirality : 0.044 0.608 5480 Planarity : 0.006 0.170 5846 Dihedral : 10.432 126.898 5096 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.16 % Favored : 90.58 % Rotamer: Outliers : 4.70 % Allowed : 17.87 % Favored : 77.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % 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: -1.41 (0.13), residues: 4234 helix: 0.57 (0.11), residues: 2402 sheet: -2.85 (0.35), residues: 189 loop : -3.08 (0.14), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 578 TYR 0.027 0.001 TYR L 13 PHE 0.028 0.001 PHE K 67 TRP 0.018 0.001 TRP F 482 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00323 (34717) covalent geometry : angle 0.69571 (47319) hydrogen bonds : bond 0.03923 ( 1679) hydrogen bonds : angle 4.43764 ( 4851) metal coordination : bond 0.00534 ( 12) metal coordination : angle 9.27451 ( 36) Misc. bond : bond 0.00098 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 808 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8697 (m-40) cc_final: 0.7740 (t0) REVERT: A 157 TYR cc_start: 0.6950 (t80) cc_final: 0.6541 (t80) REVERT: A 252 MET cc_start: 0.8666 (tpt) cc_final: 0.8448 (tpt) REVERT: A 271 LEU cc_start: 0.8467 (mt) cc_final: 0.8188 (mm) REVERT: A 301 PHE cc_start: 0.8527 (m-80) cc_final: 0.8314 (m-10) REVERT: B 165 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8360 (mttt) REVERT: B 178 LEU cc_start: 0.8977 (tp) cc_final: 0.8675 (mt) REVERT: B 361 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 438 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8141 (tm-30) REVERT: B 440 MET cc_start: 0.8912 (mtt) cc_final: 0.8599 (mtm) REVERT: B 468 VAL cc_start: 0.8485 (t) cc_final: 0.8167 (t) REVERT: C 125 ARG cc_start: 0.7750 (tpt-90) cc_final: 0.7445 (tpt170) REVERT: D 17 LEU cc_start: 0.9069 (mt) cc_final: 0.8672 (mt) REVERT: D 76 LEU cc_start: 0.9373 (tp) cc_final: 0.9105 (tp) REVERT: D 439 ASP cc_start: 0.8482 (t0) cc_final: 0.8140 (t70) REVERT: E 1 MET cc_start: 0.8843 (tpt) cc_final: 0.7884 (tpt) REVERT: E 56 GLN cc_start: 0.8942 (pt0) cc_final: 0.8700 (pt0) REVERT: E 86 ARG cc_start: 0.8867 (tmm-80) cc_final: 0.8465 (ttp80) REVERT: E 89 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: E 94 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8476 (mt-10) REVERT: F 17 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8412 (mm) REVERT: F 58 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8259 (m) REVERT: F 75 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8221 (t0) REVERT: F 133 MET cc_start: 0.8478 (mmt) cc_final: 0.8108 (mmt) REVERT: F 232 MET cc_start: 0.8799 (ttp) cc_final: 0.8553 (ttp) REVERT: F 319 TYR cc_start: 0.8820 (m-80) cc_final: 0.8496 (m-80) REVERT: F 350 MET cc_start: 0.9299 (mmt) cc_final: 0.9033 (mmt) REVERT: F 441 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7525 (pm20) REVERT: F 443 LYS cc_start: 0.8919 (mttp) cc_final: 0.8554 (mttt) REVERT: F 466 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7761 (mp) REVERT: F 487 LEU cc_start: 0.6606 (mp) cc_final: 0.6220 (tt) REVERT: F 539 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7806 (mtp180) REVERT: F 592 LEU cc_start: 0.8590 (mt) cc_final: 0.8386 (tp) REVERT: G 6 LEU cc_start: 0.9314 (tp) cc_final: 0.9073 (tt) REVERT: G 26 VAL cc_start: 0.8782 (t) cc_final: 0.8553 (t) REVERT: G 114 MET cc_start: 0.9054 (tmm) cc_final: 0.8496 (ttp) REVERT: G 156 MET cc_start: 0.4218 (ptp) cc_final: 0.3729 (ptp) REVERT: H 29 MET cc_start: 0.8694 (mtp) cc_final: 0.8381 (mtp) REVERT: H 157 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8638 (t0) REVERT: H 267 GLN cc_start: 0.8366 (mt0) cc_final: 0.8146 (mt0) REVERT: H 309 TYR cc_start: 0.8901 (m-80) cc_final: 0.8600 (m-10) REVERT: H 310 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8457 (mm-40) REVERT: H 363 LEU cc_start: 0.8963 (tp) cc_final: 0.8760 (tp) REVERT: H 373 MET cc_start: 0.7000 (mmt) cc_final: 0.6602 (mmt) REVERT: I 20 TYR cc_start: 0.8445 (m-80) cc_final: 0.7624 (m-80) REVERT: I 45 LYS cc_start: 0.9057 (mttt) cc_final: 0.8818 (mtpt) REVERT: I 133 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7821 (mt-10) REVERT: I 139 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8931 (m) REVERT: J 23 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.6996 (t0) REVERT: J 31 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8082 (mtp85) REVERT: J 87 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8339 (t0) REVERT: K 110 TYR cc_start: 0.8378 (m-80) cc_final: 0.8139 (m-80) REVERT: K 172 ASN cc_start: 0.8641 (t0) cc_final: 0.8359 (t0) REVERT: L 29 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: L 59 LEU cc_start: 0.9044 (mt) cc_final: 0.8842 (mt) REVERT: M 34 ASP cc_start: 0.9214 (t0) cc_final: 0.8872 (t70) REVERT: N 40 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8660 (mmmt) REVERT: N 86 TYR cc_start: 0.9288 (t80) cc_final: 0.8807 (t80) REVERT: N 90 ASN cc_start: 0.9108 (m-40) cc_final: 0.8824 (m110) REVERT: N 123 LEU cc_start: 0.7692 (tp) cc_final: 0.7443 (tp) REVERT: N 146 TRP cc_start: 0.9072 (t60) cc_final: 0.8798 (t60) REVERT: O 14 GLU cc_start: 0.7903 (pm20) cc_final: 0.7386 (pm20) REVERT: O 34 PHE cc_start: 0.8446 (m-10) cc_final: 0.8030 (m-10) REVERT: O 49 GLN cc_start: 0.8950 (tt0) cc_final: 0.8535 (tt0) REVERT: P 18 HIS cc_start: 0.7051 (OUTLIER) cc_final: 0.6620 (t-170) REVERT: P 56 ASP cc_start: 0.8752 (t0) cc_final: 0.8377 (t0) REVERT: P 83 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8561 (ptmm) REVERT: P 120 GLU cc_start: 0.8717 (tp30) cc_final: 0.8331 (mm-30) REVERT: P 124 MET cc_start: 0.9095 (mtm) cc_final: 0.8610 (mtp) REVERT: P 290 ARG cc_start: 0.8448 (mtt180) cc_final: 0.8232 (mtt180) REVERT: P 310 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8122 (p0) REVERT: Q 28 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7682 (tm-30) REVERT: Q 60 ASN cc_start: 0.8541 (m-40) cc_final: 0.8300 (m-40) REVERT: Q 87 ILE cc_start: 0.8686 (tt) cc_final: 0.8470 (mm) REVERT: Q 116 ILE cc_start: 0.8105 (mt) cc_final: 0.7874 (mm) REVERT: S 49 MET cc_start: 0.8266 (ptm) cc_final: 0.8040 (ptp) REVERT: S 61 TYR cc_start: 0.8683 (t80) cc_final: 0.8010 (t80) outliers start: 164 outliers final: 105 residues processed: 903 average time/residue: 0.2060 time to fit residues: 306.4430 Evaluate side-chains 887 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 769 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 418 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 31 HIS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 310 ASP Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 300 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 414 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 322 optimal weight: 0.0770 chunk 218 optimal weight: 0.7980 chunk 260 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 324 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 361 ASN J 80 HIS ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.108762 restraints weight = 45901.510| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.94 r_work: 0.3001 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 34734 Z= 0.141 Angle : 0.716 20.187 47355 Z= 0.334 Chirality : 0.044 0.564 5480 Planarity : 0.005 0.160 5846 Dihedral : 9.894 123.686 5094 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.35 % Favored : 90.41 % Rotamer: Outliers : 4.59 % Allowed : 19.16 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % 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: -1.11 (0.13), residues: 4234 helix: 0.81 (0.11), residues: 2389 sheet: -2.54 (0.37), residues: 171 loop : -2.95 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 578 TYR 0.026 0.001 TYR L 13 PHE 0.027 0.001 PHE K 67 TRP 0.017 0.001 TRP A 280 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00326 (34717) covalent geometry : angle 0.68017 (47319) hydrogen bonds : bond 0.03780 ( 1679) hydrogen bonds : angle 4.34055 ( 4851) metal coordination : bond 0.00711 ( 12) metal coordination : angle 8.16973 ( 36) Misc. bond : bond 0.00395 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 808 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8999 (mmt) cc_final: 0.8700 (mmm) REVERT: A 93 ASN cc_start: 0.8681 (m-40) cc_final: 0.7751 (t0) REVERT: A 157 TYR cc_start: 0.6958 (t80) cc_final: 0.6541 (t80) REVERT: B 136 PHE cc_start: 0.8003 (t80) cc_final: 0.7769 (t80) REVERT: B 165 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8290 (mttt) REVERT: B 178 LEU cc_start: 0.8959 (tp) cc_final: 0.8699 (mt) REVERT: B 361 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 438 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 440 MET cc_start: 0.8886 (mtt) cc_final: 0.8552 (mtm) REVERT: B 468 VAL cc_start: 0.8421 (t) cc_final: 0.8084 (t) REVERT: C 125 ARG cc_start: 0.7762 (tpt-90) cc_final: 0.7472 (tpt170) REVERT: D 17 LEU cc_start: 0.9080 (mt) cc_final: 0.8671 (mt) REVERT: D 76 LEU cc_start: 0.9411 (tp) cc_final: 0.9135 (tp) REVERT: D 78 TYR cc_start: 0.9102 (t80) cc_final: 0.8845 (t80) REVERT: D 439 ASP cc_start: 0.8473 (t0) cc_final: 0.8128 (t70) REVERT: E 1 MET cc_start: 0.8883 (tpt) cc_final: 0.7930 (tpt) REVERT: E 86 ARG cc_start: 0.8770 (tmm-80) cc_final: 0.8468 (ttt180) REVERT: E 89 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: F 17 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8165 (mt) REVERT: F 75 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8367 (t70) REVERT: F 104 MET cc_start: 0.8309 (mtt) cc_final: 0.8104 (mtp) REVERT: F 133 MET cc_start: 0.8465 (mmt) cc_final: 0.7926 (mmt) REVERT: F 232 MET cc_start: 0.8875 (ttp) cc_final: 0.8577 (ttp) REVERT: F 245 ASP cc_start: 0.9094 (t70) cc_final: 0.8828 (t0) REVERT: F 319 TYR cc_start: 0.8814 (m-80) cc_final: 0.8480 (m-80) REVERT: F 350 MET cc_start: 0.9312 (mmt) cc_final: 0.8970 (mmt) REVERT: F 401 GLN cc_start: 0.8642 (mt0) cc_final: 0.8196 (mt0) REVERT: F 466 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7758 (mp) REVERT: F 487 LEU cc_start: 0.6605 (mp) cc_final: 0.6160 (tt) REVERT: F 539 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7771 (mtp180) REVERT: F 592 LEU cc_start: 0.8572 (mt) cc_final: 0.8360 (tp) REVERT: G 6 LEU cc_start: 0.9320 (tp) cc_final: 0.9088 (tt) REVERT: G 114 MET cc_start: 0.9066 (tmm) cc_final: 0.8534 (ttp) REVERT: G 156 MET cc_start: 0.4200 (ptp) cc_final: 0.3810 (ptp) REVERT: H 8 THR cc_start: 0.9080 (t) cc_final: 0.8861 (p) REVERT: H 29 MET cc_start: 0.8700 (mtp) cc_final: 0.8406 (mtp) REVERT: H 292 GLU cc_start: 0.8669 (tp30) cc_final: 0.8363 (mm-30) REVERT: H 309 TYR cc_start: 0.9033 (m-80) cc_final: 0.8712 (m-10) REVERT: H 310 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8466 (mm-40) REVERT: H 373 MET cc_start: 0.6952 (mmt) cc_final: 0.6650 (mmt) REVERT: I 20 TYR cc_start: 0.8372 (m-80) cc_final: 0.7579 (m-80) REVERT: I 45 LYS cc_start: 0.9047 (mttt) cc_final: 0.8817 (mtpt) REVERT: I 133 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7772 (mt-10) REVERT: I 139 VAL cc_start: 0.9139 (OUTLIER) cc_final: 0.8926 (m) REVERT: J 23 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.7023 (t0) REVERT: J 31 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8079 (mtp85) REVERT: J 87 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8218 (t0) REVERT: J 168 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6569 (p90) REVERT: K 65 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8034 (p90) REVERT: K 110 TYR cc_start: 0.8358 (m-80) cc_final: 0.8136 (m-80) REVERT: K 172 ASN cc_start: 0.8638 (t0) cc_final: 0.8357 (t0) REVERT: L 29 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8435 (m-80) REVERT: M 19 ASP cc_start: 0.7929 (p0) cc_final: 0.6916 (t0) REVERT: N 40 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8635 (mmmt) REVERT: N 86 TYR cc_start: 0.9245 (t80) cc_final: 0.8872 (t80) REVERT: N 90 ASN cc_start: 0.9116 (m-40) cc_final: 0.8886 (m110) REVERT: N 123 LEU cc_start: 0.7700 (tp) cc_final: 0.7451 (tp) REVERT: N 146 TRP cc_start: 0.9098 (t60) cc_final: 0.8682 (t60) REVERT: O 14 GLU cc_start: 0.7830 (pm20) cc_final: 0.7340 (pm20) REVERT: O 49 GLN cc_start: 0.8935 (tt0) cc_final: 0.8527 (tt0) REVERT: P 18 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6522 (t-170) REVERT: P 56 ASP cc_start: 0.8769 (t0) cc_final: 0.8423 (t0) REVERT: P 83 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8566 (ptmm) REVERT: P 120 GLU cc_start: 0.8709 (tp30) cc_final: 0.8352 (mm-30) REVERT: P 124 MET cc_start: 0.9157 (mtm) cc_final: 0.8655 (mtp) REVERT: P 148 MET cc_start: 0.8700 (mtp) cc_final: 0.8292 (mtm) REVERT: P 278 GLU cc_start: 0.8545 (mp0) cc_final: 0.7892 (mm-30) REVERT: P 290 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8229 (mtt180) REVERT: Q 28 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7640 (tm-30) REVERT: Q 60 ASN cc_start: 0.8510 (m-40) cc_final: 0.8283 (m-40) REVERT: Q 83 LYS cc_start: 0.8370 (tttp) cc_final: 0.8050 (mtpp) REVERT: Q 87 ILE cc_start: 0.8657 (tt) cc_final: 0.8450 (mm) REVERT: S 49 MET cc_start: 0.8299 (ptm) cc_final: 0.8012 (ptp) REVERT: S 61 TYR cc_start: 0.8668 (t80) cc_final: 0.7992 (t80) outliers start: 160 outliers final: 117 residues processed: 898 average time/residue: 0.2063 time to fit residues: 304.2713 Evaluate side-chains 901 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 772 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 31 HIS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 231 optimal weight: 0.8980 chunk 355 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 289 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 228 optimal weight: 0.0270 chunk 399 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 171 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN H 361 ASN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.141092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119550 restraints weight = 44338.522| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.82 r_work: 0.3042 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 34734 Z= 0.134 Angle : 0.706 19.547 47355 Z= 0.330 Chirality : 0.043 0.553 5480 Planarity : 0.005 0.152 5846 Dihedral : 9.656 121.509 5094 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.14 % Favored : 90.65 % Rotamer: Outliers : 4.70 % Allowed : 19.82 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.13), residues: 4234 helix: 0.94 (0.11), residues: 2402 sheet: -2.38 (0.37), residues: 181 loop : -2.87 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 578 TYR 0.025 0.001 TYR L 13 PHE 0.027 0.001 PHE K 67 TRP 0.021 0.001 TRP D 50 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00309 (34717) covalent geometry : angle 0.67020 (47319) hydrogen bonds : bond 0.03667 ( 1679) hydrogen bonds : angle 4.28870 ( 4851) metal coordination : bond 0.00538 ( 12) metal coordination : angle 8.13336 ( 36) Misc. bond : bond 0.00226 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 800 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8617 (m-40) cc_final: 0.7791 (t0) REVERT: A 157 TYR cc_start: 0.7164 (t80) cc_final: 0.6746 (t80) REVERT: B 165 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8385 (mttt) REVERT: B 166 TYR cc_start: 0.9347 (t80) cc_final: 0.9042 (t80) REVERT: B 178 LEU cc_start: 0.9055 (tp) cc_final: 0.8810 (mt) REVERT: B 361 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 438 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 440 MET cc_start: 0.8859 (mtt) cc_final: 0.8550 (mtm) REVERT: B 468 VAL cc_start: 0.8520 (t) cc_final: 0.8256 (t) REVERT: C 125 ARG cc_start: 0.7798 (tpt-90) cc_final: 0.7519 (tpt170) REVERT: D 17 LEU cc_start: 0.9120 (mt) cc_final: 0.8698 (mt) REVERT: D 76 LEU cc_start: 0.9411 (tp) cc_final: 0.9177 (tp) REVERT: D 439 ASP cc_start: 0.8539 (t0) cc_final: 0.8327 (t70) REVERT: E 1 MET cc_start: 0.8895 (tpt) cc_final: 0.7953 (tpt) REVERT: E 86 ARG cc_start: 0.8777 (tmm-80) cc_final: 0.8500 (ttt180) REVERT: E 89 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8486 (m-30) REVERT: F 17 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8229 (mt) REVERT: F 58 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8921 (m) REVERT: F 75 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8366 (t70) REVERT: F 133 MET cc_start: 0.8557 (mmt) cc_final: 0.8103 (mmt) REVERT: F 232 MET cc_start: 0.8926 (ttp) cc_final: 0.8604 (ttp) REVERT: F 319 TYR cc_start: 0.8838 (m-80) cc_final: 0.8531 (m-80) REVERT: F 401 GLN cc_start: 0.8662 (mt0) cc_final: 0.8274 (mt0) REVERT: F 466 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7830 (mp) REVERT: F 487 LEU cc_start: 0.6766 (mp) cc_final: 0.6354 (tt) REVERT: F 539 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7791 (mtp180) REVERT: F 592 LEU cc_start: 0.8623 (mt) cc_final: 0.8394 (tp) REVERT: G 6 LEU cc_start: 0.9349 (tp) cc_final: 0.9123 (tt) REVERT: G 114 MET cc_start: 0.9071 (tmm) cc_final: 0.8529 (ttp) REVERT: G 156 MET cc_start: 0.4281 (ptp) cc_final: 0.3770 (ptp) REVERT: H 8 THR cc_start: 0.9028 (t) cc_final: 0.8826 (p) REVERT: H 29 MET cc_start: 0.8733 (mtp) cc_final: 0.8473 (mtp) REVERT: H 292 GLU cc_start: 0.8668 (tp30) cc_final: 0.8404 (mm-30) REVERT: H 309 TYR cc_start: 0.9091 (m-80) cc_final: 0.8797 (m-10) REVERT: H 310 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8501 (mm-40) REVERT: H 373 MET cc_start: 0.6943 (mmt) cc_final: 0.6504 (mmt) REVERT: I 20 TYR cc_start: 0.8411 (m-80) cc_final: 0.7624 (m-80) REVERT: I 45 LYS cc_start: 0.9065 (mttt) cc_final: 0.8847 (mtpt) REVERT: I 133 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7717 (mt-10) REVERT: J 23 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6907 (t0) REVERT: J 87 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8179 (t0) REVERT: J 168 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.6777 (p90) REVERT: K 65 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8159 (p90) REVERT: K 110 TYR cc_start: 0.8324 (m-80) cc_final: 0.8106 (m-80) REVERT: K 172 ASN cc_start: 0.8533 (t0) cc_final: 0.8309 (t0) REVERT: L 29 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: L 59 LEU cc_start: 0.9131 (mt) cc_final: 0.8771 (mt) REVERT: N 40 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8688 (mmmt) REVERT: N 86 TYR cc_start: 0.9223 (t80) cc_final: 0.8840 (t80) REVERT: N 90 ASN cc_start: 0.9114 (m-40) cc_final: 0.8876 (m110) REVERT: N 123 LEU cc_start: 0.7725 (tp) cc_final: 0.7479 (tp) REVERT: O 14 GLU cc_start: 0.7753 (pm20) cc_final: 0.7266 (pm20) REVERT: O 34 PHE cc_start: 0.8511 (m-10) cc_final: 0.8171 (m-10) REVERT: O 49 GLN cc_start: 0.8936 (tt0) cc_final: 0.8549 (tt0) REVERT: P 18 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6564 (t-170) REVERT: P 56 ASP cc_start: 0.8765 (t0) cc_final: 0.8375 (t0) REVERT: P 120 GLU cc_start: 0.8618 (tp30) cc_final: 0.8271 (mm-30) REVERT: P 124 MET cc_start: 0.9143 (mtm) cc_final: 0.8671 (mtp) REVERT: P 278 GLU cc_start: 0.8530 (mp0) cc_final: 0.7898 (mm-30) REVERT: P 389 PHE cc_start: 0.9234 (m-80) cc_final: 0.9029 (m-10) REVERT: Q 60 ASN cc_start: 0.8544 (m-40) cc_final: 0.8292 (m-40) REVERT: S 49 MET cc_start: 0.8455 (ptm) cc_final: 0.8166 (ptp) REVERT: S 83 ASN cc_start: 0.8384 (t0) cc_final: 0.8095 (t0) outliers start: 164 outliers final: 123 residues processed: 897 average time/residue: 0.2081 time to fit residues: 308.7482 Evaluate side-chains 896 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 762 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain P residue 435 ASN Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 36 optimal weight: 2.9990 chunk 314 optimal weight: 0.2980 chunk 209 optimal weight: 0.5980 chunk 265 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 308 optimal weight: 2.9990 chunk 315 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN H 267 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.141011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.118910 restraints weight = 44701.395| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.91 r_work: 0.3015 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34734 Z= 0.137 Angle : 0.712 19.509 47355 Z= 0.330 Chirality : 0.044 0.555 5480 Planarity : 0.005 0.146 5846 Dihedral : 9.525 120.293 5094 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.26 % Favored : 90.55 % Rotamer: Outliers : 4.70 % Allowed : 20.80 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % 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: -0.82 (0.13), residues: 4234 helix: 1.04 (0.11), residues: 2393 sheet: -2.23 (0.38), residues: 179 loop : -2.84 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 310 TYR 0.026 0.001 TYR L 13 PHE 0.028 0.001 PHE P 57 TRP 0.019 0.001 TRP F 71 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00321 (34717) covalent geometry : angle 0.67234 (47319) hydrogen bonds : bond 0.03657 ( 1679) hydrogen bonds : angle 4.26081 ( 4851) metal coordination : bond 0.00581 ( 12) metal coordination : angle 8.50571 ( 36) Misc. bond : bond 0.00205 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 796 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8666 (m-40) cc_final: 0.7780 (t0) REVERT: A 157 TYR cc_start: 0.7091 (t80) cc_final: 0.6699 (t80) REVERT: B 165 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8265 (mttt) REVERT: B 166 TYR cc_start: 0.9326 (t80) cc_final: 0.8975 (t80) REVERT: B 178 LEU cc_start: 0.8946 (tp) cc_final: 0.8727 (mt) REVERT: B 361 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 438 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 440 MET cc_start: 0.8660 (mtt) cc_final: 0.8299 (mtm) REVERT: B 468 VAL cc_start: 0.8412 (t) cc_final: 0.8158 (t) REVERT: C 125 ARG cc_start: 0.7824 (tpt-90) cc_final: 0.7544 (tpt170) REVERT: D 16 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7732 (p) REVERT: D 17 LEU cc_start: 0.9030 (mt) cc_final: 0.8634 (mt) REVERT: D 76 LEU cc_start: 0.9384 (tp) cc_final: 0.9137 (tp) REVERT: E 1 MET cc_start: 0.8841 (tpt) cc_final: 0.7916 (tpt) REVERT: E 86 ARG cc_start: 0.8777 (tmm-80) cc_final: 0.8462 (ttt180) REVERT: E 89 ASP cc_start: 0.8935 (t70) cc_final: 0.8505 (m-30) REVERT: F 17 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8013 (mt) REVERT: F 75 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8298 (t70) REVERT: F 133 MET cc_start: 0.8506 (mmt) cc_final: 0.7999 (mmt) REVERT: F 319 TYR cc_start: 0.8829 (m-80) cc_final: 0.8521 (m-80) REVERT: F 401 GLN cc_start: 0.8678 (mt0) cc_final: 0.8301 (mt0) REVERT: F 441 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7419 (pm20) REVERT: F 464 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6561 (tp) REVERT: F 466 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7696 (mp) REVERT: F 479 TRP cc_start: 0.8235 (t60) cc_final: 0.7786 (t60) REVERT: F 487 LEU cc_start: 0.6716 (mp) cc_final: 0.6309 (tt) REVERT: F 539 ARG cc_start: 0.7959 (mmm-85) cc_final: 0.7704 (mtp180) REVERT: F 560 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6754 (t80) REVERT: F 592 LEU cc_start: 0.8418 (mt) cc_final: 0.8209 (tp) REVERT: G 6 LEU cc_start: 0.9287 (tp) cc_final: 0.9064 (tt) REVERT: G 114 MET cc_start: 0.9008 (tmm) cc_final: 0.8472 (ttp) REVERT: H 8 THR cc_start: 0.9057 (t) cc_final: 0.8838 (p) REVERT: H 29 MET cc_start: 0.8714 (mtp) cc_final: 0.8320 (mtp) REVERT: H 116 LEU cc_start: 0.8893 (tp) cc_final: 0.8648 (tp) REVERT: H 292 GLU cc_start: 0.8602 (tp30) cc_final: 0.8340 (mm-30) REVERT: H 309 TYR cc_start: 0.9027 (m-80) cc_final: 0.8746 (m-10) REVERT: H 310 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8375 (mm-40) REVERT: H 373 MET cc_start: 0.6859 (mmt) cc_final: 0.5988 (mmt) REVERT: H 374 LYS cc_start: 0.7690 (mmpt) cc_final: 0.7282 (mmmt) REVERT: I 20 TYR cc_start: 0.8329 (m-80) cc_final: 0.7504 (m-80) REVERT: I 45 LYS cc_start: 0.9004 (mttt) cc_final: 0.8751 (mtpt) REVERT: I 133 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7696 (mt-10) REVERT: J 23 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.6989 (t0) REVERT: J 87 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8217 (t0) REVERT: J 168 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.6748 (p90) REVERT: K 65 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8128 (p90) REVERT: K 110 TYR cc_start: 0.8312 (m-80) cc_final: 0.8098 (m-80) REVERT: K 114 MET cc_start: 0.8946 (ptm) cc_final: 0.8568 (ttm) REVERT: L 29 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: L 59 LEU cc_start: 0.9038 (mt) cc_final: 0.8674 (mt) REVERT: M 19 ASP cc_start: 0.7854 (p0) cc_final: 0.7015 (t0) REVERT: N 40 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8631 (mmmt) REVERT: N 86 TYR cc_start: 0.9177 (t80) cc_final: 0.8818 (t80) REVERT: N 90 ASN cc_start: 0.9124 (m-40) cc_final: 0.8884 (m110) REVERT: N 123 LEU cc_start: 0.7673 (tp) cc_final: 0.7424 (tp) REVERT: O 14 GLU cc_start: 0.7839 (pm20) cc_final: 0.7504 (pm20) REVERT: O 49 GLN cc_start: 0.8910 (tt0) cc_final: 0.8554 (tt0) REVERT: P 18 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6515 (t-170) REVERT: P 120 GLU cc_start: 0.8652 (tp30) cc_final: 0.8393 (mm-30) REVERT: P 124 MET cc_start: 0.9170 (mtm) cc_final: 0.8646 (mtp) REVERT: P 278 GLU cc_start: 0.8501 (mp0) cc_final: 0.7863 (mm-30) REVERT: Q 60 ASN cc_start: 0.8449 (m-40) cc_final: 0.8200 (m-40) REVERT: Q 132 MET cc_start: 0.8458 (mpp) cc_final: 0.8166 (mpp) REVERT: S 49 MET cc_start: 0.8400 (ptm) cc_final: 0.8110 (ptp) REVERT: S 69 ARG cc_start: 0.8990 (ttm-80) cc_final: 0.8687 (ttm170) REVERT: S 83 ASN cc_start: 0.8341 (t0) cc_final: 0.8130 (t0) outliers start: 164 outliers final: 127 residues processed: 894 average time/residue: 0.2084 time to fit residues: 307.0975 Evaluate side-chains 906 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 767 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain P residue 435 ASN Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 108 ASN Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 71 optimal weight: 0.0060 chunk 260 optimal weight: 2.9990 chunk 336 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 405 optimal weight: 0.9980 chunk 305 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 309 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN K 172 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.112224 restraints weight = 45504.938| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.89 r_work: 0.3019 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 34734 Z= 0.138 Angle : 0.714 19.377 47355 Z= 0.331 Chirality : 0.044 0.546 5480 Planarity : 0.005 0.142 5846 Dihedral : 9.414 118.939 5094 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.42 % Favored : 90.39 % Rotamer: Outliers : 4.73 % Allowed : 20.80 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % 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: -0.75 (0.13), residues: 4234 helix: 1.09 (0.11), residues: 2396 sheet: -2.16 (0.39), residues: 179 loop : -2.81 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 310 TYR 0.026 0.001 TYR L 13 PHE 0.034 0.001 PHE P 57 TRP 0.019 0.001 TRP F 71 HIS 0.005 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00324 (34717) covalent geometry : angle 0.67542 (47319) hydrogen bonds : bond 0.03637 ( 1679) hydrogen bonds : angle 4.25613 ( 4851) metal coordination : bond 0.00537 ( 12) metal coordination : angle 8.43365 ( 36) Misc. bond : bond 0.00281 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 789 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: A 93 ASN cc_start: 0.8625 (m-40) cc_final: 0.7798 (t0) REVERT: A 157 TYR cc_start: 0.6940 (t80) cc_final: 0.6457 (t80) REVERT: B 165 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8321 (mttt) REVERT: B 166 TYR cc_start: 0.9333 (t80) cc_final: 0.8964 (t80) REVERT: B 361 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 438 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8103 (tm-30) REVERT: B 440 MET cc_start: 0.8666 (mtt) cc_final: 0.8303 (mtm) REVERT: B 468 VAL cc_start: 0.8500 (t) cc_final: 0.8236 (t) REVERT: C 125 ARG cc_start: 0.7921 (tpt-90) cc_final: 0.7716 (tpt170) REVERT: D 16 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7763 (p) REVERT: D 17 LEU cc_start: 0.9062 (mt) cc_final: 0.8694 (mt) REVERT: D 27 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7804 (pp) REVERT: D 76 LEU cc_start: 0.9392 (tp) cc_final: 0.9162 (tp) REVERT: D 439 ASP cc_start: 0.8374 (t0) cc_final: 0.8054 (t70) REVERT: E 1 MET cc_start: 0.8858 (tpt) cc_final: 0.7938 (tpt) REVERT: E 86 ARG cc_start: 0.8799 (tmm-80) cc_final: 0.8359 (ttt90) REVERT: E 89 ASP cc_start: 0.8863 (t70) cc_final: 0.8471 (m-30) REVERT: F 17 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8074 (mt) REVERT: F 58 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8954 (m) REVERT: F 75 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8293 (t70) REVERT: F 133 MET cc_start: 0.8575 (mmt) cc_final: 0.8095 (mmt) REVERT: F 166 GLN cc_start: 0.8953 (tt0) cc_final: 0.8748 (tt0) REVERT: F 319 TYR cc_start: 0.8735 (m-80) cc_final: 0.8403 (m-80) REVERT: F 464 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6639 (tp) REVERT: F 466 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7656 (mp) REVERT: F 479 TRP cc_start: 0.8261 (t60) cc_final: 0.7862 (t60) REVERT: F 487 LEU cc_start: 0.6803 (mp) cc_final: 0.6405 (tt) REVERT: F 537 LEU cc_start: 0.8162 (tp) cc_final: 0.7952 (tp) REVERT: F 539 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7703 (mtp180) REVERT: F 560 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6785 (t80) REVERT: F 592 LEU cc_start: 0.8483 (mt) cc_final: 0.8276 (tp) REVERT: G 6 LEU cc_start: 0.9320 (tp) cc_final: 0.9095 (tt) REVERT: G 114 MET cc_start: 0.9024 (tmm) cc_final: 0.8492 (ttp) REVERT: H 8 THR cc_start: 0.9067 (t) cc_final: 0.8842 (p) REVERT: H 29 MET cc_start: 0.8767 (mtp) cc_final: 0.8378 (mtp) REVERT: H 292 GLU cc_start: 0.8616 (tp30) cc_final: 0.8312 (mm-30) REVERT: H 309 TYR cc_start: 0.9060 (m-80) cc_final: 0.8769 (m-10) REVERT: H 310 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8419 (mm-40) REVERT: H 373 MET cc_start: 0.6943 (mmt) cc_final: 0.6477 (mmt) REVERT: I 20 TYR cc_start: 0.8335 (m-80) cc_final: 0.7543 (m-80) REVERT: I 33 ARG cc_start: 0.8199 (ptt90) cc_final: 0.7759 (ptt90) REVERT: I 45 LYS cc_start: 0.9023 (mttt) cc_final: 0.8780 (mtpt) REVERT: I 84 PHE cc_start: 0.8868 (t80) cc_final: 0.8562 (t80) REVERT: I 133 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7683 (mt-10) REVERT: J 23 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.6948 (t0) REVERT: J 87 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8214 (t0) REVERT: J 168 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6797 (p90) REVERT: K 65 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8160 (p90) REVERT: K 110 TYR cc_start: 0.8313 (m-80) cc_final: 0.8109 (m-80) REVERT: L 29 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: L 59 LEU cc_start: 0.9058 (mt) cc_final: 0.8687 (mt) REVERT: M 19 ASP cc_start: 0.7810 (p0) cc_final: 0.7010 (t0) REVERT: N 40 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8661 (mmmt) REVERT: N 86 TYR cc_start: 0.9176 (t80) cc_final: 0.8823 (t80) REVERT: N 90 ASN cc_start: 0.9129 (m-40) cc_final: 0.8889 (m110) REVERT: N 123 LEU cc_start: 0.7741 (tp) cc_final: 0.7515 (tp) REVERT: O 14 GLU cc_start: 0.7762 (pm20) cc_final: 0.7428 (pm20) REVERT: O 49 GLN cc_start: 0.8920 (tt0) cc_final: 0.8506 (tt0) REVERT: P 18 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6501 (t-170) REVERT: P 120 GLU cc_start: 0.8635 (tp30) cc_final: 0.8400 (mm-30) REVERT: P 124 MET cc_start: 0.9160 (mtm) cc_final: 0.8654 (mtp) REVERT: P 278 GLU cc_start: 0.8565 (mp0) cc_final: 0.7978 (mm-30) REVERT: P 381 VAL cc_start: 0.9052 (t) cc_final: 0.8635 (p) REVERT: Q 60 ASN cc_start: 0.8511 (m-40) cc_final: 0.8258 (m-40) REVERT: S 49 MET cc_start: 0.8440 (ptm) cc_final: 0.8176 (ptp) outliers start: 165 outliers final: 132 residues processed: 889 average time/residue: 0.2037 time to fit residues: 299.0870 Evaluate side-chains 924 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 777 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 235 CYS Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 65 PHE Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 172 ASN Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain P residue 435 ASN Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 171 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 344 optimal weight: 1.9990 chunk 404 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 212 optimal weight: 0.5980 chunk 202 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 319 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN H 78 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN K 168 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Q 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.132934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.109394 restraints weight = 45679.121| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.03 r_work: 0.3004 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 34734 Z= 0.137 Angle : 0.717 19.151 47355 Z= 0.332 Chirality : 0.044 0.530 5480 Planarity : 0.005 0.139 5846 Dihedral : 9.314 117.422 5092 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.33 % Favored : 90.48 % Rotamer: Outliers : 4.50 % Allowed : 21.26 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % 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: -0.69 (0.13), residues: 4234 helix: 1.13 (0.11), residues: 2397 sheet: -2.09 (0.39), residues: 179 loop : -2.80 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 310 TYR 0.027 0.001 TYR L 13 PHE 0.040 0.001 PHE P 57 TRP 0.020 0.001 TRP F 71 HIS 0.005 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00320 (34717) covalent geometry : angle 0.67912 (47319) hydrogen bonds : bond 0.03627 ( 1679) hydrogen bonds : angle 4.24584 ( 4851) metal coordination : bond 0.00540 ( 12) metal coordination : angle 8.36114 ( 36) Misc. bond : bond 0.00053 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 775 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: A 93 ASN cc_start: 0.8642 (m-40) cc_final: 0.7770 (t0) REVERT: A 157 TYR cc_start: 0.6787 (t80) cc_final: 0.6414 (t80) REVERT: B 97 MET cc_start: 0.9200 (ptm) cc_final: 0.8992 (ptt) REVERT: B 165 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8253 (mttt) REVERT: B 166 TYR cc_start: 0.9324 (t80) cc_final: 0.8927 (t80) REVERT: B 361 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7928 (mm-30) REVERT: B 438 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8097 (tm-30) REVERT: B 440 MET cc_start: 0.8652 (mtt) cc_final: 0.8295 (mtm) REVERT: B 468 VAL cc_start: 0.8459 (t) cc_final: 0.8197 (t) REVERT: C 125 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7704 (tpt170) REVERT: D 16 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7704 (p) REVERT: D 17 LEU cc_start: 0.9019 (mt) cc_final: 0.8666 (mt) REVERT: D 27 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7866 (pp) REVERT: D 76 LEU cc_start: 0.9396 (tp) cc_final: 0.9163 (tp) REVERT: D 439 ASP cc_start: 0.8342 (t0) cc_final: 0.8109 (t0) REVERT: D 441 ARG cc_start: 0.7102 (mtm110) cc_final: 0.6737 (mpp80) REVERT: E 1 MET cc_start: 0.8836 (tpt) cc_final: 0.7924 (tpt) REVERT: E 86 ARG cc_start: 0.8759 (tmm-80) cc_final: 0.8474 (tmm-80) REVERT: E 89 ASP cc_start: 0.8854 (t70) cc_final: 0.8431 (m-30) REVERT: F 17 LEU cc_start: 0.8522 (mm) cc_final: 0.8051 (mt) REVERT: F 58 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8923 (m) REVERT: F 75 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8311 (t70) REVERT: F 133 MET cc_start: 0.8482 (mmt) cc_final: 0.8028 (mmt) REVERT: F 166 GLN cc_start: 0.8956 (tt0) cc_final: 0.8728 (tt0) REVERT: F 319 TYR cc_start: 0.8722 (m-80) cc_final: 0.8397 (m-80) REVERT: F 441 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7477 (pm20) REVERT: F 466 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7576 (mp) REVERT: F 479 TRP cc_start: 0.8238 (t60) cc_final: 0.7831 (t60) REVERT: F 487 LEU cc_start: 0.6766 (mp) cc_final: 0.6382 (tt) REVERT: F 539 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7773 (mtp180) REVERT: F 560 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6773 (t80) REVERT: F 592 LEU cc_start: 0.8400 (mt) cc_final: 0.8199 (tp) REVERT: G 6 LEU cc_start: 0.9292 (tp) cc_final: 0.9069 (tt) REVERT: G 114 MET cc_start: 0.8994 (tmm) cc_final: 0.8489 (ttp) REVERT: H 8 THR cc_start: 0.9076 (t) cc_final: 0.8853 (p) REVERT: H 29 MET cc_start: 0.8756 (mtp) cc_final: 0.8335 (mtp) REVERT: H 41 GLU cc_start: 0.8462 (tt0) cc_final: 0.8132 (tt0) REVERT: H 78 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8792 (m110) REVERT: H 292 GLU cc_start: 0.8589 (tp30) cc_final: 0.8307 (mm-30) REVERT: H 309 TYR cc_start: 0.9049 (m-80) cc_final: 0.8773 (m-10) REVERT: H 310 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8379 (mm-40) REVERT: H 373 MET cc_start: 0.6853 (mmt) cc_final: 0.5963 (mmt) REVERT: H 374 LYS cc_start: 0.7737 (mmpt) cc_final: 0.7227 (mmmt) REVERT: I 19 LYS cc_start: 0.8072 (tppt) cc_final: 0.7843 (tppt) REVERT: I 20 TYR cc_start: 0.8304 (m-80) cc_final: 0.7493 (m-80) REVERT: I 45 LYS cc_start: 0.8991 (mttt) cc_final: 0.8740 (mtpt) REVERT: I 84 PHE cc_start: 0.8873 (t80) cc_final: 0.8562 (t80) REVERT: I 133 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7678 (mt-10) REVERT: J 23 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7023 (t0) REVERT: J 87 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8218 (t0) REVERT: J 168 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.6777 (p90) REVERT: K 110 TYR cc_start: 0.8333 (m-80) cc_final: 0.8132 (m-80) REVERT: L 29 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: L 59 LEU cc_start: 0.9020 (mt) cc_final: 0.8646 (mt) REVERT: M 19 ASP cc_start: 0.7851 (p0) cc_final: 0.7025 (t0) REVERT: N 86 TYR cc_start: 0.9155 (t80) cc_final: 0.8801 (t80) REVERT: N 90 ASN cc_start: 0.9130 (m-40) cc_final: 0.8884 (m110) REVERT: N 123 LEU cc_start: 0.7682 (tp) cc_final: 0.7445 (tp) REVERT: O 14 GLU cc_start: 0.7569 (pm20) cc_final: 0.7179 (pm20) REVERT: O 27 HIS cc_start: 0.7739 (t70) cc_final: 0.7339 (t70) REVERT: O 49 GLN cc_start: 0.8912 (tt0) cc_final: 0.8560 (tt0) REVERT: P 18 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6469 (t-170) REVERT: P 120 GLU cc_start: 0.8671 (tp30) cc_final: 0.8433 (mm-30) REVERT: P 124 MET cc_start: 0.9177 (mtm) cc_final: 0.8641 (mtp) REVERT: P 278 GLU cc_start: 0.8590 (mp0) cc_final: 0.8022 (mm-30) REVERT: P 381 VAL cc_start: 0.8990 (t) cc_final: 0.8582 (p) REVERT: Q 60 ASN cc_start: 0.8469 (m-40) cc_final: 0.8211 (m-40) REVERT: S 49 MET cc_start: 0.8413 (ptm) cc_final: 0.8120 (ptp) outliers start: 157 outliers final: 129 residues processed: 870 average time/residue: 0.1981 time to fit residues: 285.5215 Evaluate side-chains 905 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 763 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 450 TRP Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 42 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 22 LYS Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 202 optimal weight: 1.9990 chunk 281 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 322 optimal weight: 0.2980 chunk 96 optimal weight: 0.7980 chunk 328 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 175 optimal weight: 0.0070 chunk 311 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN H 78 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 267 GLN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN K 172 ASN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Q 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.136066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.113585 restraints weight = 45561.987| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.89 r_work: 0.3040 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34734 Z= 0.127 Angle : 0.715 18.709 47355 Z= 0.330 Chirality : 0.044 0.510 5480 Planarity : 0.005 0.135 5846 Dihedral : 9.197 117.104 5092 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.09 % Favored : 90.72 % Rotamer: Outliers : 4.16 % Allowed : 21.89 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.05 % 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: -0.62 (0.13), residues: 4234 helix: 1.21 (0.11), residues: 2387 sheet: -2.12 (0.39), residues: 183 loop : -2.76 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 310 TYR 0.026 0.001 TYR L 13 PHE 0.026 0.001 PHE K 67 TRP 0.021 0.001 TRP F 71 HIS 0.007 0.001 HIS K 181 Details of bonding type rmsd covalent geometry : bond 0.00291 (34717) covalent geometry : angle 0.67440 (47319) hydrogen bonds : bond 0.03525 ( 1679) hydrogen bonds : angle 4.23216 ( 4851) metal coordination : bond 0.00522 ( 12) metal coordination : angle 8.63760 ( 36) Misc. bond : bond 0.00051 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8468 Ramachandran restraints generated. 4234 Oldfield, 0 Emsley, 4234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 782 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: A 93 ASN cc_start: 0.8584 (m-40) cc_final: 0.7786 (t0) REVERT: A 157 TYR cc_start: 0.6742 (t80) cc_final: 0.6339 (t80) REVERT: B 165 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8323 (mttt) REVERT: B 166 TYR cc_start: 0.9330 (t80) cc_final: 0.8921 (t80) REVERT: B 361 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 438 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8100 (tm-30) REVERT: B 440 MET cc_start: 0.8625 (mtt) cc_final: 0.8267 (mtm) REVERT: B 468 VAL cc_start: 0.8484 (t) cc_final: 0.8223 (t) REVERT: C 125 ARG cc_start: 0.7931 (tpt-90) cc_final: 0.7711 (tpt170) REVERT: D 16 VAL cc_start: 0.8001 (OUTLIER) cc_final: 0.7734 (p) REVERT: D 17 LEU cc_start: 0.9060 (mt) cc_final: 0.8734 (mt) REVERT: D 25 MET cc_start: 0.8557 (mmm) cc_final: 0.8306 (tpp) REVERT: D 27 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8070 (pp) REVERT: D 76 LEU cc_start: 0.9380 (tp) cc_final: 0.9168 (tp) REVERT: D 439 ASP cc_start: 0.8322 (t0) cc_final: 0.8120 (t0) REVERT: D 441 ARG cc_start: 0.7129 (mtm110) cc_final: 0.6795 (mpp80) REVERT: E 1 MET cc_start: 0.8858 (tpt) cc_final: 0.7948 (tpt) REVERT: E 86 ARG cc_start: 0.8755 (tmm-80) cc_final: 0.8181 (ptm160) REVERT: E 89 ASP cc_start: 0.8792 (t70) cc_final: 0.8399 (m-30) REVERT: F 58 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8907 (m) REVERT: F 133 MET cc_start: 0.8510 (mmt) cc_final: 0.8073 (mmt) REVERT: F 441 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7742 (pm20) REVERT: F 466 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7641 (mp) REVERT: F 478 ASP cc_start: 0.7804 (m-30) cc_final: 0.7516 (m-30) REVERT: F 479 TRP cc_start: 0.8281 (t60) cc_final: 0.7898 (t60) REVERT: F 487 LEU cc_start: 0.6777 (mp) cc_final: 0.6403 (tt) REVERT: F 539 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7801 (mtp-110) REVERT: F 560 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.6898 (t80) REVERT: F 592 LEU cc_start: 0.8429 (mt) cc_final: 0.8210 (tp) REVERT: G 114 MET cc_start: 0.8971 (tmm) cc_final: 0.8188 (ttp) REVERT: H 8 THR cc_start: 0.9049 (t) cc_final: 0.8822 (p) REVERT: H 29 MET cc_start: 0.8719 (mtp) cc_final: 0.8324 (mtp) REVERT: H 41 GLU cc_start: 0.8467 (tt0) cc_final: 0.8146 (tt0) REVERT: H 292 GLU cc_start: 0.8588 (tp30) cc_final: 0.8303 (mm-30) REVERT: H 309 TYR cc_start: 0.9066 (m-80) cc_final: 0.8825 (m-10) REVERT: H 310 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8399 (mm-40) REVERT: H 373 MET cc_start: 0.6880 (mmt) cc_final: 0.6394 (mmt) REVERT: I 19 LYS cc_start: 0.8132 (tppt) cc_final: 0.7892 (tppt) REVERT: I 20 TYR cc_start: 0.8274 (m-80) cc_final: 0.7501 (m-80) REVERT: I 45 LYS cc_start: 0.8987 (mttt) cc_final: 0.8734 (mtpt) REVERT: I 84 PHE cc_start: 0.8815 (t80) cc_final: 0.8529 (t80) REVERT: I 133 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7617 (mt-10) REVERT: J 23 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.7023 (t0) REVERT: J 87 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8183 (t0) REVERT: J 168 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6792 (p90) REVERT: K 156 MET cc_start: 0.8836 (mtm) cc_final: 0.8419 (mtm) REVERT: L 29 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: L 59 LEU cc_start: 0.9038 (mt) cc_final: 0.8666 (mt) REVERT: N 40 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8655 (mmmt) REVERT: N 86 TYR cc_start: 0.9129 (t80) cc_final: 0.8861 (t80) REVERT: N 90 ASN cc_start: 0.9117 (m-40) cc_final: 0.8877 (m110) REVERT: N 123 LEU cc_start: 0.7664 (tp) cc_final: 0.7447 (tp) REVERT: O 14 GLU cc_start: 0.7505 (pm20) cc_final: 0.7118 (pm20) REVERT: O 27 HIS cc_start: 0.7571 (t70) cc_final: 0.7202 (t70) REVERT: O 34 PHE cc_start: 0.8513 (m-10) cc_final: 0.8268 (m-10) REVERT: O 49 GLN cc_start: 0.8914 (tt0) cc_final: 0.8577 (tt0) REVERT: O 61 LEU cc_start: 0.8799 (mt) cc_final: 0.8591 (mt) REVERT: P 18 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6525 (t-170) REVERT: P 78 LYS cc_start: 0.7156 (ttpt) cc_final: 0.6904 (tttt) REVERT: P 120 GLU cc_start: 0.8621 (tp30) cc_final: 0.8385 (mm-30) REVERT: P 124 MET cc_start: 0.9147 (mtm) cc_final: 0.8634 (mtp) REVERT: P 248 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7991 (mm) REVERT: P 278 GLU cc_start: 0.8562 (mp0) cc_final: 0.7985 (mm-30) REVERT: P 381 VAL cc_start: 0.9031 (t) cc_final: 0.8626 (p) REVERT: Q 60 ASN cc_start: 0.8500 (m-40) cc_final: 0.8235 (m-40) REVERT: S 49 MET cc_start: 0.8445 (ptm) cc_final: 0.8184 (ptp) REVERT: S 69 ARG cc_start: 0.9010 (ttm-80) cc_final: 0.8712 (ttm170) outliers start: 145 outliers final: 121 residues processed: 867 average time/residue: 0.2036 time to fit residues: 292.6867 Evaluate side-chains 899 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 766 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 408 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 484 GLN Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 201 TRP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 274 THR Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 449 SER Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 519 PHE Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 560 PHE Chi-restraints excluded: chain F residue 562 ASP Chi-restraints excluded: chain F residue 587 SER Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain H residue 19 HIS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 70 TRP Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 148 VAL Chi-restraints excluded: chain J residue 168 TYR Chi-restraints excluded: chain K residue 52 CYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 105 MET Chi-restraints excluded: chain K residue 172 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 29 TYR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 22 VAL Chi-restraints excluded: chain M residue 109 ASN Chi-restraints excluded: chain N residue 47 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain P residue 18 HIS Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 157 LEU Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 233 SER Chi-restraints excluded: chain P residue 248 ILE Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 259 ILE Chi-restraints excluded: chain P residue 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 429 ARG Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain Q residue 22 LYS Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 39 PHE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 123 ILE Chi-restraints excluded: chain Q residue 126 ILE Chi-restraints excluded: chain Q residue 130 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 312 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 222 optimal weight: 0.5980 chunk 297 optimal weight: 0.5980 chunk 88 optimal weight: 0.0050 chunk 299 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 20 optimal weight: 0.0270 chunk 314 optimal weight: 0.0030 chunk 123 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN Q 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.135377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.112325 restraints weight = 45689.514| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.96 r_work: 0.3054 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 34734 Z= 0.121 Angle : 0.713 17.988 47355 Z= 0.327 Chirality : 0.043 0.495 5480 Planarity : 0.005 0.131 5846 Dihedral : 9.101 117.194 5090 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.95 % Favored : 90.86 % Rotamer: Outliers : 3.84 % Allowed : 22.32 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.02 % 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: -0.54 (0.14), residues: 4234 helix: 1.28 (0.11), residues: 2388 sheet: -2.14 (0.40), residues: 173 loop : -2.74 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 36 TYR 0.027 0.001 TYR L 13 PHE 0.032 0.001 PHE B 136 TRP 0.025 0.001 TRP F 71 HIS 0.015 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00270 (34717) covalent geometry : angle 0.67327 (47319) hydrogen bonds : bond 0.03421 ( 1679) hydrogen bonds : angle 4.19601 ( 4851) metal coordination : bond 0.00742 ( 12) metal coordination : angle 8.51176 ( 36) Misc. bond : bond 0.00071 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10035.08 seconds wall clock time: 172 minutes 1.27 seconds (10321.27 seconds total)