Starting phenix.real_space_refine on Tue Sep 15 01:46:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tjv_10513/09_2026/6tjv_10513.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tjv_10513/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6tjv_10513/09_2026/6tjv_10513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tjv_10513/09_2026/6tjv_10513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tjv_10513/09_2026/6tjv_10513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tjv_10513/09_2026/6tjv_10513.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6tjv_10513/09_2026/6tjv_10513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tjv_10513/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 5.76, per 1000 atoms: 0.17 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: 3.13 Conformation dependent library (CDL) restraints added in 1.5 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: 0.64 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: 5.50 Time building geometry restraints manager: 4.04 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 - 24.89: 18938 24.89 - 49.78: 1159 49.78 - 74.67: 145 74.67 - 99.56: 14 99.56 - 124.46: 5 Dihedral angle restraints: 20261 sinusoidal: 7919 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 20258 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: 0.010 Normalize map: mean=0, sd=1: 1.460 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.690 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 15.543 124.455 12353 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/Z covalent geometry : bond 0.01001 / 0.53 (34717) covalent geometry : angle 1.24527 / 0.64 (47319) hydrogen bonds : bond 0.17208 / 11.94 ( 1679) hydrogen bonds : angle 7.14280 / 5.00 ( 4851) metal coordination : bond 0.55812 / 34.01 ( 12) metal coordination : angle 22.59684 / 14.61 ( 36) Misc. bond : bond 0.41878 / 25.25 ( 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 : 0.909 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: 0.2136 time to fit residues: 343.0955 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 : 1.091 ------------------------------------------------------------------------------- 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... 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 = 0.3406 r_free = 0.3406 target = 0.130392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.108110 restraints weight = 46140.133| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.87 r_work: 0.2975 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 34734 Z= 0.160 Angle : 0.885 32.419 47355 Z= 0.389 Chirality : 0.047 0.857 5480 Planarity : 0.006 0.197 5846 Dihedral : 10.589 117.727 4986 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.64 % Favored : 90.06 % Rotamer: Outliers : 3.21 % Allowed : 14.60 % Favored : 82.19 % 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: -2.49 (0.12), residues: 4234 helix: -0.41 (0.10), residues: 2414 sheet: -3.18 (0.33), residues: 199 loop : -3.42 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 310 TYR 0.031 0.002 TYR L 13 PHE 0.024 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/Z covalent geometry : bond 0.00366 / 0.16 (34717) covalent geometry : angle 0.82261 / 0.39 (47319) hydrogen bonds : bond 0.04707 / 3.14 ( 1679) hydrogen bonds : angle 4.91754 / 3.49 ( 4851) metal coordination : bond 0.01936 / 1.05 ( 12) metal coordination : angle 11.89778 / 7.24 ( 36) Misc. bond : bond 0.00505 / 0.25 ( 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 995 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 883 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8797 (m-40) cc_final: 0.7750 (t0) REVERT: A 157 TYR cc_start: 0.7041 (t80) cc_final: 0.6670 (t80) REVERT: A 252 MET cc_start: 0.8537 (tpt) cc_final: 0.8213 (tpt) REVERT: A 301 PHE cc_start: 0.8653 (m-10) cc_final: 0.8395 (m-80) REVERT: B 165 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8448 (mttt) REVERT: B 178 LEU cc_start: 0.9012 (tp) cc_final: 0.8695 (mt) REVERT: B 361 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8380 (mm-30) REVERT: B 431 MET cc_start: 0.9047 (mmt) cc_final: 0.8466 (mmt) REVERT: B 438 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 440 MET cc_start: 0.8984 (mtt) cc_final: 0.8682 (mtm) REVERT: B 466 MET cc_start: 0.8628 (mtm) cc_final: 0.8398 (mtm) REVERT: C 35 LEU cc_start: 0.8714 (tp) cc_final: 0.8461 (tp) REVERT: C 125 ARG cc_start: 0.7709 (tpt-90) cc_final: 0.7386 (tpt170) REVERT: D 17 LEU cc_start: 0.9067 (mt) cc_final: 0.8859 (mp) REVERT: D 325 MET cc_start: 0.8640 (mmm) cc_final: 0.8344 (mmm) REVERT: D 375 SER cc_start: 0.8831 (t) cc_final: 0.8402 (t) REVERT: D 439 ASP cc_start: 0.8524 (t0) cc_final: 0.8197 (t70) REVERT: D 452 GLU cc_start: 0.8273 (tt0) cc_final: 0.8011 (tt0) REVERT: D 484 GLN cc_start: 0.8693 (tt0) cc_final: 0.8451 (tt0) REVERT: E 1 MET cc_start: 0.8790 (tpt) cc_final: 0.7748 (tpt) REVERT: E 56 GLN cc_start: 0.9004 (pt0) cc_final: 0.8777 (pt0) REVERT: E 86 ARG cc_start: 0.8867 (tmm-80) cc_final: 0.8470 (ttt90) REVERT: F 75 ASP cc_start: 0.8748 (p0) cc_final: 0.8260 (t0) REVERT: F 96 MET cc_start: 0.8503 (mtp) cc_final: 0.8219 (mtp) REVERT: F 319 TYR cc_start: 0.8968 (m-80) cc_final: 0.8482 (m-80) REVERT: F 374 ARG cc_start: 0.9077 (ptp90) cc_final: 0.8870 (ptp90) REVERT: F 443 LYS cc_start: 0.9106 (mttp) cc_final: 0.8775 (mttt) REVERT: F 487 LEU cc_start: 0.6626 (mp) cc_final: 0.6152 (tt) REVERT: F 539 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7737 (mtp180) REVERT: G 156 MET cc_start: 0.4466 (ptp) cc_final: 0.4013 (ptp) REVERT: H 29 MET cc_start: 0.8812 (mtp) cc_final: 0.8359 (mtp) REVERT: H 72 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: H 309 TYR cc_start: 0.9001 (m-80) cc_final: 0.8628 (m-10) REVERT: H 310 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8472 (mm-40) REVERT: H 326 GLU cc_start: 0.8020 (pm20) cc_final: 0.7664 (pt0) REVERT: I 20 TYR cc_start: 0.8436 (m-80) cc_final: 0.7501 (m-80) REVERT: I 45 LYS cc_start: 0.9107 (mttt) cc_final: 0.8864 (mtpt) REVERT: I 133 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8043 (mt-10) REVERT: J 23 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6793 (t0) REVERT: J 87 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8446 (t0) REVERT: K 110 TYR cc_start: 0.8453 (m-80) cc_final: 0.8184 (m-80) REVERT: K 172 ASN cc_start: 0.8603 (t0) cc_final: 0.8209 (t0) REVERT: L 59 LEU cc_start: 0.9055 (mt) cc_final: 0.8789 (mt) REVERT: M 19 ASP cc_start: 0.8019 (p0) cc_final: 0.6999 (t0) REVERT: N 40 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8697 (mmmt) REVERT: N 86 TYR cc_start: 0.9344 (t80) cc_final: 0.8795 (t80) REVERT: O 14 GLU cc_start: 0.7819 (pm20) cc_final: 0.7467 (pm20) REVERT: O 37 ARG cc_start: 0.8309 (mtp85) cc_final: 0.7903 (mtp-110) REVERT: O 49 GLN cc_start: 0.8937 (tt0) cc_final: 0.8573 (tt0) REVERT: P 18 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6716 (t-170) REVERT: P 124 MET cc_start: 0.9132 (mtm) cc_final: 0.8744 (mtp) REVERT: P 248 ILE cc_start: 0.8401 (mm) cc_final: 0.8081 (mm) REVERT: P 340 MET cc_start: 0.8868 (ttm) cc_final: 0.8567 (ttp) REVERT: Q 28 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7512 (tm-30) REVERT: Q 60 ASN cc_start: 0.8675 (m-40) cc_final: 0.8369 (m-40) REVERT: Q 87 ILE cc_start: 0.8667 (tt) cc_final: 0.8414 (mm) REVERT: Q 116 ILE cc_start: 0.8225 (mt) cc_final: 0.7998 (mm) REVERT: Q 120 ASN cc_start: 0.6929 (p0) cc_final: 0.6666 (p0) REVERT: S 61 TYR cc_start: 0.8618 (t80) cc_final: 0.8065 (t80) outliers start: 112 outliers final: 70 residues processed: 943 average time/residue: 0.2073 time to fit residues: 320.0687 Evaluate side-chains 877 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 803 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 81 LEU Chi-restraints excluded: chain J residue 87 ASN 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 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: 0.6980 chunk 55 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 268 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 300 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 386 optimal weight: 0.8980 chunk 327 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN F 166 GLN H 113 ASN H 156 ASN H 157 ASN H 267 GLN H 361 ASN H 364 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3402 r_free = 0.3402 target = 0.130255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106992 restraints weight = 46018.967| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.01 r_work: 0.2972 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 34734 Z= 0.151 Angle : 0.817 34.591 47355 Z= 0.365 Chirality : 0.045 0.609 5480 Planarity : 0.006 0.184 5846 Dihedral : 9.772 112.908 4950 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.42 % Favored : 90.29 % Rotamer: Outliers : 4.10 % Allowed : 16.38 % Favored : 79.52 % 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: -1.72 (0.13), residues: 4234 helix: 0.29 (0.11), residues: 2396 sheet: -2.99 (0.34), residues: 189 loop : -3.18 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 578 TYR 0.029 0.002 TYR L 13 PHE 0.027 0.001 PHE K 67 TRP 0.019 0.001 TRP H 70 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (34717) covalent geometry : angle 0.77319 / 0.36 (47319) hydrogen bonds : bond 0.04162 / 2.75 ( 1679) hydrogen bonds : angle 4.58396 / 3.26 ( 4851) metal coordination : bond 0.00557 / 0.36 ( 12) metal coordination : angle 9.64897 / 5.75 ( 36) Misc. bond : bond 0.00530 / 0.26 ( 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 978 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 835 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8689 (m-40) cc_final: 0.7584 (t0) REVERT: A 157 TYR cc_start: 0.6945 (t80) cc_final: 0.6604 (t80) REVERT: A 252 MET cc_start: 0.8640 (tpt) cc_final: 0.8373 (tpt) REVERT: A 271 LEU cc_start: 0.8427 (mt) cc_final: 0.8162 (mm) REVERT: B 165 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8244 (mttt) REVERT: B 340 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8827 (m110) REVERT: B 361 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8149 (mm-30) REVERT: B 431 MET cc_start: 0.8930 (mmt) cc_final: 0.8357 (mmt) REVERT: B 438 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 440 MET cc_start: 0.8914 (mtt) cc_final: 0.8666 (mtm) REVERT: B 468 VAL cc_start: 0.8445 (t) cc_final: 0.8152 (t) REVERT: C 125 ARG cc_start: 0.7705 (tpt-90) cc_final: 0.7391 (tpt170) REVERT: D 17 LEU cc_start: 0.9053 (mt) cc_final: 0.8668 (mt) REVERT: D 36 VAL cc_start: 0.8849 (t) cc_final: 0.8636 (m) REVERT: D 76 LEU cc_start: 0.9381 (tp) cc_final: 0.9107 (tp) REVERT: D 325 MET cc_start: 0.8701 (mmm) cc_final: 0.8480 (mmm) REVERT: D 366 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8309 (p0) REVERT: D 368 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8868 (mm) REVERT: E 1 MET cc_start: 0.8845 (tpt) cc_final: 0.7884 (tpt) REVERT: E 56 GLN cc_start: 0.9024 (pt0) cc_final: 0.8776 (pt0) REVERT: E 86 ARG cc_start: 0.8905 (tmm-80) cc_final: 0.8547 (ttp80) REVERT: E 94 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8702 (mt-10) REVERT: F 17 LEU cc_start: 0.8757 (mm) cc_final: 0.8373 (mp) REVERT: F 75 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8239 (t0) REVERT: F 96 MET cc_start: 0.8386 (mtp) cc_final: 0.8141 (mtp) REVERT: F 319 TYR cc_start: 0.8886 (m-80) cc_final: 0.8501 (m-80) REVERT: F 443 LYS cc_start: 0.8910 (mttp) cc_final: 0.8569 (mttt) REVERT: F 466 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7758 (mp) REVERT: F 487 LEU cc_start: 0.6421 (mp) cc_final: 0.6039 (tt) REVERT: F 539 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7689 (mtp180) REVERT: F 560 PHE cc_start: 0.7803 (m-80) cc_final: 0.7572 (m-80) REVERT: F 592 LEU cc_start: 0.8622 (mt) cc_final: 0.8301 (tp) REVERT: G 6 LEU cc_start: 0.9297 (tp) cc_final: 0.9059 (tt) REVERT: G 114 MET cc_start: 0.9076 (tmm) cc_final: 0.8604 (ttp) REVERT: G 156 MET cc_start: 0.4163 (ptp) cc_final: 0.3758 (ptp) REVERT: H 29 MET cc_start: 0.8708 (mtp) cc_final: 0.8387 (mtp) REVERT: H 267 GLN cc_start: 0.8361 (mt0) cc_final: 0.8141 (mt0) REVERT: H 309 TYR cc_start: 0.8910 (m-80) cc_final: 0.8590 (m-10) REVERT: H 310 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8404 (mm-40) REVERT: H 326 GLU cc_start: 0.8086 (pm20) cc_final: 0.7786 (pt0) REVERT: H 354 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8787 (tmtt) REVERT: H 373 MET cc_start: 0.7129 (mmt) cc_final: 0.6728 (mmt) REVERT: I 20 TYR cc_start: 0.8493 (m-80) cc_final: 0.7581 (m-80) REVERT: I 35 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8409 (ttt-90) REVERT: I 45 LYS cc_start: 0.9058 (mttt) cc_final: 0.8765 (mtpt) REVERT: I 133 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7905 (mt-10) REVERT: I 139 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8932 (m) REVERT: J 23 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6925 (t0) REVERT: J 87 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8362 (t0) REVERT: K 110 TYR cc_start: 0.8453 (m-80) cc_final: 0.8186 (m-80) REVERT: K 172 ASN cc_start: 0.8555 (t0) cc_final: 0.8142 (t0) REVERT: L 59 LEU cc_start: 0.9034 (mt) cc_final: 0.8784 (mt) REVERT: M 19 ASP cc_start: 0.7986 (p0) cc_final: 0.7278 (t0) REVERT: M 34 ASP cc_start: 0.9317 (t0) cc_final: 0.9076 (t70) REVERT: N 40 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8663 (mmmt) REVERT: N 86 TYR cc_start: 0.9296 (t80) cc_final: 0.8719 (t80) REVERT: O 14 GLU cc_start: 0.7905 (pm20) cc_final: 0.7507 (pm20) REVERT: O 34 PHE cc_start: 0.8422 (m-10) cc_final: 0.7975 (m-10) REVERT: O 49 GLN cc_start: 0.8953 (tt0) cc_final: 0.8545 (tt0) REVERT: P 18 HIS cc_start: 0.6963 (OUTLIER) cc_final: 0.6593 (t-170) REVERT: P 83 LYS cc_start: 0.8911 (ttpp) cc_final: 0.8544 (ptmm) REVERT: P 124 MET cc_start: 0.9141 (mtm) cc_final: 0.8682 (mtp) REVERT: P 184 MET cc_start: 0.9406 (mmt) cc_final: 0.8927 (mmt) REVERT: P 301 ASN cc_start: 0.8924 (t0) cc_final: 0.8722 (t0) REVERT: Q 60 ASN cc_start: 0.8550 (m-40) cc_final: 0.8307 (m-40) REVERT: Q 87 ILE cc_start: 0.8669 (tt) cc_final: 0.8394 (mm) REVERT: Q 116 ILE cc_start: 0.8052 (mt) cc_final: 0.7811 (mm) REVERT: Q 120 ASN cc_start: 0.6971 (p0) cc_final: 0.6557 (p0) REVERT: S 49 MET cc_start: 0.8183 (ptm) cc_final: 0.7926 (ptp) REVERT: S 61 TYR cc_start: 0.8677 (t80) cc_final: 0.7976 (t80) REVERT: S 62 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8350 (mm110) outliers start: 143 outliers final: 87 residues processed: 915 average time/residue: 0.1990 time to fit residues: 300.1530 Evaluate side-chains 860 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 763 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 267 VAL Chi-restraints excluded: chain P residue 287 VAL Chi-restraints excluded: chain P residue 309 THR 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 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: 0.9980 chunk 383 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 413 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 304 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 361 ASN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.107481 restraints weight = 45958.150| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.94 r_work: 0.2981 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 34734 Z= 0.150 Angle : 0.742 20.702 47355 Z= 0.343 Chirality : 0.044 0.595 5480 Planarity : 0.006 0.170 5846 Dihedral : 9.108 60.750 4948 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.14 % Favored : 90.60 % Rotamer: Outliers : 4.79 % Allowed : 17.90 % Favored : 77.31 % 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: -1.39 (0.13), residues: 4234 helix: 0.59 (0.11), residues: 2397 sheet: -2.80 (0.35), residues: 189 loop : -3.08 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 578 TYR 0.028 0.001 TYR L 13 PHE 0.028 0.001 PHE K 67 TRP 0.018 0.001 TRP A 280 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (34717) covalent geometry : angle 0.69699 / 0.34 (47319) hydrogen bonds : bond 0.03966 / 2.62 ( 1679) hydrogen bonds : angle 4.43844 / 3.15 ( 4851) metal coordination : bond 0.00589 / 0.36 ( 12) metal coordination : angle 9.28763 / 5.56 ( 36) Misc. bond : bond 0.00123 / 0.07 ( 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: 167 poor density : 805 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8711 (m-40) cc_final: 0.7690 (t0) REVERT: A 157 TYR cc_start: 0.6942 (t80) cc_final: 0.6549 (t80) REVERT: A 252 MET cc_start: 0.8677 (tpt) cc_final: 0.8456 (tpt) REVERT: A 271 LEU cc_start: 0.8400 (mt) cc_final: 0.8122 (mm) REVERT: B 165 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8221 (mttt) REVERT: B 178 LEU cc_start: 0.8933 (tp) cc_final: 0.8675 (mt) REVERT: B 361 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 438 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8170 (tm-30) REVERT: B 440 MET cc_start: 0.8898 (mtt) cc_final: 0.8571 (mtm) REVERT: B 468 VAL cc_start: 0.8434 (t) cc_final: 0.8121 (t) REVERT: C 125 ARG cc_start: 0.7737 (tpt-90) cc_final: 0.7439 (tpt170) REVERT: D 17 LEU cc_start: 0.9043 (mt) cc_final: 0.8653 (mt) REVERT: D 25 MET cc_start: 0.8947 (mmp) cc_final: 0.8607 (mmm) REVERT: D 76 LEU cc_start: 0.9380 (tp) cc_final: 0.9110 (tp) REVERT: D 366 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8362 (p0) REVERT: D 439 ASP cc_start: 0.8479 (t0) cc_final: 0.8136 (t70) REVERT: E 1 MET cc_start: 0.8872 (tpt) cc_final: 0.7912 (tpt) REVERT: E 56 GLN cc_start: 0.8946 (pt0) cc_final: 0.8690 (pt0) REVERT: E 86 ARG cc_start: 0.8878 (tmm-80) cc_final: 0.8462 (ttp80) REVERT: E 89 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: F 17 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8427 (mt) REVERT: F 58 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8243 (m) REVERT: F 75 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8217 (t0) REVERT: F 232 MET cc_start: 0.8778 (ttp) cc_final: 0.8537 (ttp) REVERT: F 319 TYR cc_start: 0.8827 (m-80) cc_final: 0.8474 (m-80) REVERT: F 401 GLN cc_start: 0.8610 (mt0) cc_final: 0.8166 (mt0) REVERT: F 403 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: F 441 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7478 (pm20) REVERT: F 443 LYS cc_start: 0.8852 (mttp) cc_final: 0.8493 (mttt) REVERT: F 466 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7729 (mp) REVERT: F 487 LEU cc_start: 0.6442 (mp) cc_final: 0.6073 (tt) REVERT: F 539 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7733 (mtp180) REVERT: G 6 LEU cc_start: 0.9281 (tp) cc_final: 0.9044 (tt) REVERT: G 114 MET cc_start: 0.9033 (tmm) cc_final: 0.8485 (ttp) REVERT: G 156 MET cc_start: 0.4145 (ptp) cc_final: 0.3689 (ptp) REVERT: H 29 MET cc_start: 0.8684 (mtp) cc_final: 0.8373 (mtp) REVERT: H 309 TYR cc_start: 0.8870 (m-80) cc_final: 0.8547 (m-10) REVERT: H 310 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8432 (mm-40) REVERT: H 326 GLU cc_start: 0.8063 (pm20) cc_final: 0.7790 (pt0) REVERT: H 354 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8781 (tttm) REVERT: H 363 LEU cc_start: 0.8947 (tp) cc_final: 0.8745 (tp) REVERT: H 373 MET cc_start: 0.7061 (mmt) cc_final: 0.6674 (mmt) REVERT: I 20 TYR cc_start: 0.8439 (m-80) cc_final: 0.7594 (m-80) REVERT: I 45 LYS cc_start: 0.9051 (mttt) cc_final: 0.8803 (mtpt) REVERT: I 133 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7862 (mt-10) REVERT: I 139 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8911 (m) REVERT: J 23 ASN cc_start: 0.7525 (OUTLIER) cc_final: 0.7060 (t0) REVERT: J 87 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8358 (t0) REVERT: J 168 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.6189 (p90) REVERT: K 110 TYR cc_start: 0.8409 (m-80) cc_final: 0.8164 (m-80) REVERT: K 172 ASN cc_start: 0.8633 (t0) cc_final: 0.8299 (t0) REVERT: L 29 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: M 19 ASP cc_start: 0.7863 (p0) cc_final: 0.7235 (t0) REVERT: M 34 ASP cc_start: 0.9153 (t0) cc_final: 0.8825 (t70) REVERT: N 40 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8622 (mmmt) REVERT: N 86 TYR cc_start: 0.9270 (t80) cc_final: 0.8650 (t80) REVERT: N 90 ASN cc_start: 0.9116 (m-40) cc_final: 0.8420 (m110) REVERT: N 123 LEU cc_start: 0.7689 (tp) cc_final: 0.7420 (tp) REVERT: N 146 TRP cc_start: 0.9086 (t60) cc_final: 0.8732 (t60) REVERT: O 14 GLU cc_start: 0.7948 (pm20) cc_final: 0.7429 (pm20) REVERT: O 34 PHE cc_start: 0.8379 (m-10) cc_final: 0.7959 (m-10) REVERT: O 49 GLN cc_start: 0.8946 (tt0) cc_final: 0.8522 (tt0) REVERT: P 18 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6599 (t-170) REVERT: P 56 ASP cc_start: 0.8775 (t0) cc_final: 0.8394 (t0) REVERT: P 83 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8566 (ptmm) REVERT: P 120 GLU cc_start: 0.8722 (tp30) cc_final: 0.8304 (mm-30) REVERT: P 124 MET cc_start: 0.9115 (mtm) cc_final: 0.8606 (mtp) REVERT: P 148 MET cc_start: 0.8824 (mtp) cc_final: 0.8440 (mtm) REVERT: P 184 MET cc_start: 0.9427 (mmt) cc_final: 0.8908 (mmt) REVERT: Q 28 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7632 (tm-30) REVERT: Q 60 ASN cc_start: 0.8498 (m-40) cc_final: 0.8259 (m-40) REVERT: Q 87 ILE cc_start: 0.8664 (tt) cc_final: 0.8429 (mm) REVERT: Q 116 ILE cc_start: 0.8041 (mt) cc_final: 0.7816 (mm) REVERT: S 49 MET cc_start: 0.8201 (ptm) cc_final: 0.7953 (ptp) REVERT: S 61 TYR cc_start: 0.8626 (t80) cc_final: 0.7964 (t80) outliers start: 167 outliers final: 112 residues processed: 904 average time/residue: 0.2015 time to fit residues: 299.7013 Evaluate side-chains 893 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 767 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 335 VAL 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 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 472 SER 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 74 TYR 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 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 390 LEU Chi-restraints excluded: chain F residue 403 GLU 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 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 31 THR 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 354 LYS 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 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 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 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 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 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 Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 300 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 414 optimal weight: 0.0870 chunk 245 optimal weight: 3.9990 chunk 322 optimal weight: 0.2980 chunk 218 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 157 ASN H 267 GLN H 361 ASN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.132539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.110116 restraints weight = 45722.803| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.88 r_work: 0.3019 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 34734 Z= 0.138 Angle : 0.711 18.948 47355 Z= 0.333 Chirality : 0.044 0.559 5480 Planarity : 0.005 0.161 5846 Dihedral : 8.775 61.211 4946 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.16 % Favored : 90.60 % Rotamer: Outliers : 4.68 % Allowed : 19.16 % Favored : 76.16 % 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: -1.08 (0.13), residues: 4234 helix: 0.82 (0.11), residues: 2390 sheet: -2.50 (0.38), residues: 171 loop : -2.92 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 578 TYR 0.025 0.001 TYR L 13 PHE 0.027 0.001 PHE K 67 TRP 0.018 0.001 TRP H 70 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (34717) covalent geometry : angle 0.67726 / 0.33 (47319) hydrogen bonds : bond 0.03772 / 2.49 ( 1679) hydrogen bonds : angle 4.34447 / 3.08 ( 4851) metal coordination : bond 0.00516 / 0.33 ( 12) metal coordination : angle 7.88123 / 4.78 ( 36) Misc. bond : bond 0.00107 / 0.06 ( 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 970 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 807 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9004 (mmt) cc_final: 0.8680 (mmm) REVERT: A 93 ASN cc_start: 0.8647 (m-40) cc_final: 0.7790 (t0) REVERT: A 157 TYR cc_start: 0.6974 (t80) cc_final: 0.6537 (t80) REVERT: B 136 PHE cc_start: 0.8034 (t80) cc_final: 0.7803 (t80) REVERT: B 140 GLU cc_start: 0.2381 (OUTLIER) cc_final: 0.2101 (pt0) REVERT: B 165 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8375 (mttt) REVERT: B 178 LEU cc_start: 0.9013 (tp) cc_final: 0.8744 (mt) REVERT: B 361 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8232 (mm-30) REVERT: B 412 LEU cc_start: 0.9267 (mt) cc_final: 0.9023 (mt) REVERT: B 438 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8154 (tm-30) REVERT: B 440 MET cc_start: 0.8900 (mtt) cc_final: 0.8597 (mtm) REVERT: B 468 VAL cc_start: 0.8480 (t) cc_final: 0.8133 (t) REVERT: C 125 ARG cc_start: 0.7811 (tpt-90) cc_final: 0.7538 (tpt170) REVERT: D 17 LEU cc_start: 0.9129 (mt) cc_final: 0.8722 (mt) REVERT: D 76 LEU cc_start: 0.9420 (tp) cc_final: 0.9185 (tp) REVERT: D 439 ASP cc_start: 0.8485 (t0) cc_final: 0.8166 (t70) REVERT: E 1 MET cc_start: 0.8902 (tpt) cc_final: 0.7968 (tpt) REVERT: E 86 ARG cc_start: 0.8757 (tmm-80) cc_final: 0.8480 (ttt180) REVERT: E 89 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8464 (m-30) REVERT: F 17 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8519 (mt) REVERT: F 58 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8601 (m) REVERT: F 75 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (t70) REVERT: F 232 MET cc_start: 0.8916 (ttp) cc_final: 0.8627 (ttp) REVERT: F 319 TYR cc_start: 0.8850 (m-80) cc_final: 0.8577 (m-80) REVERT: F 401 GLN cc_start: 0.8669 (mt0) cc_final: 0.8285 (mt0) REVERT: F 403 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: F 466 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7856 (mp) REVERT: F 487 LEU cc_start: 0.6685 (mp) cc_final: 0.6237 (tt) REVERT: F 539 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7771 (mtp180) REVERT: G 6 LEU cc_start: 0.9349 (tp) cc_final: 0.9122 (tt) REVERT: G 114 MET cc_start: 0.9065 (tmm) cc_final: 0.8509 (ttp) REVERT: G 156 MET cc_start: 0.4281 (ptp) cc_final: 0.3924 (ptp) REVERT: H 8 THR cc_start: 0.9051 (t) cc_final: 0.8847 (p) REVERT: H 29 MET cc_start: 0.8749 (mtp) cc_final: 0.8479 (mtp) REVERT: H 267 GLN cc_start: 0.8432 (mt0) cc_final: 0.8217 (mt0) REVERT: H 292 GLU cc_start: 0.8700 (tp30) cc_final: 0.8389 (mm-30) REVERT: H 309 TYR cc_start: 0.9094 (m-80) cc_final: 0.8767 (m-10) REVERT: H 310 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8534 (mm-40) REVERT: H 363 LEU cc_start: 0.8995 (tp) cc_final: 0.8760 (tp) REVERT: H 373 MET cc_start: 0.7013 (mmt) cc_final: 0.6545 (mmt) REVERT: I 20 TYR cc_start: 0.8412 (m-80) cc_final: 0.7635 (m-80) REVERT: I 35 ARG cc_start: 0.8788 (ttt-90) cc_final: 0.8225 (ttt-90) REVERT: I 45 LYS cc_start: 0.9088 (mttt) cc_final: 0.8864 (mtpt) REVERT: I 133 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7757 (mt-10) REVERT: I 139 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8965 (m) REVERT: J 23 ASN cc_start: 0.7440 (OUTLIER) cc_final: 0.6974 (t0) REVERT: J 31 ARG cc_start: 0.8517 (mmt90) cc_final: 0.8191 (mmm160) REVERT: J 87 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8196 (t0) REVERT: J 106 ARG cc_start: 0.7590 (pmt170) cc_final: 0.7317 (pmt170) REVERT: J 133 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7697 (mm-30) REVERT: J 168 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6606 (p90) REVERT: K 110 TYR cc_start: 0.8366 (m-80) cc_final: 0.8141 (m-80) REVERT: K 172 ASN cc_start: 0.8571 (t0) cc_final: 0.8285 (t0) REVERT: L 29 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: L 59 LEU cc_start: 0.9131 (mt) cc_final: 0.8774 (mt) REVERT: N 40 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8670 (mmmt) REVERT: N 86 TYR cc_start: 0.9257 (t80) cc_final: 0.8891 (t80) REVERT: N 90 ASN cc_start: 0.9113 (m-40) cc_final: 0.8885 (m110) REVERT: N 123 LEU cc_start: 0.7734 (tp) cc_final: 0.7486 (tp) REVERT: N 146 TRP cc_start: 0.9088 (t60) cc_final: 0.8680 (t60) REVERT: O 14 GLU cc_start: 0.7822 (pm20) cc_final: 0.7348 (pm20) REVERT: O 49 GLN cc_start: 0.8968 (tt0) cc_final: 0.8587 (tt0) REVERT: P 18 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6524 (t-170) REVERT: P 56 ASP cc_start: 0.8774 (t0) cc_final: 0.8423 (t0) REVERT: P 83 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8649 (ptmm) REVERT: P 120 GLU cc_start: 0.8682 (tp30) cc_final: 0.8338 (mm-30) REVERT: P 124 MET cc_start: 0.9130 (mtm) cc_final: 0.8614 (mtp) REVERT: P 278 GLU cc_start: 0.8540 (mp0) cc_final: 0.7897 (mm-30) REVERT: Q 28 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7460 (tm-30) REVERT: Q 60 ASN cc_start: 0.8580 (m-40) cc_final: 0.8267 (m-40) REVERT: S 49 MET cc_start: 0.8438 (ptm) cc_final: 0.8179 (ptp) REVERT: S 61 TYR cc_start: 0.8674 (t80) cc_final: 0.8062 (t80) REVERT: S 83 ASN cc_start: 0.8451 (t0) cc_final: 0.8079 (t0) outliers start: 163 outliers final: 116 residues processed: 901 average time/residue: 0.2009 time to fit residues: 300.3808 Evaluate side-chains 903 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 774 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 140 GLU 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 472 SER Chi-restraints excluded: chain B residue 482 PHE 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 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 152 LEU 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 403 GLU 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 31 THR 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 263 ILE Chi-restraints excluded: chain H residue 329 VAL 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 139 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 63 SER 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 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 339 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 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: 0.9980 chunk 355 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 228 optimal weight: 0.9990 chunk 399 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** F 359 ASN ** H 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN J 80 HIS ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 365 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.131699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.109123 restraints weight = 45640.657| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.88 r_work: 0.2989 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 34734 Z= 0.157 Angle : 0.724 20.118 47355 Z= 0.338 Chirality : 0.044 0.559 5480 Planarity : 0.005 0.153 5846 Dihedral : 8.603 61.402 4946 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.61 % Favored : 90.17 % Rotamer: Outliers : 4.99 % Allowed : 20.02 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 4234 helix: 0.91 (0.11), residues: 2394 sheet: -2.41 (0.37), residues: 181 loop : -2.90 (0.14), residues: 1659 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 0.029 0.001 PHE K 67 TRP 0.021 0.001 TRP F 454 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (34717) covalent geometry : angle 0.68602 / 0.34 (47319) hydrogen bonds : bond 0.03832 / 2.53 ( 1679) hydrogen bonds : angle 4.32857 / 3.08 ( 4851) metal coordination : bond 0.00614 / 0.34 ( 12) metal coordination : angle 8.43683 / 5.07 ( 36) Misc. bond : bond 0.00198 / 0.10 ( 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: 174 poor density : 790 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.8661 (m-40) cc_final: 0.7721 (t0) REVERT: A 157 TYR cc_start: 0.6980 (t80) cc_final: 0.6565 (t80) REVERT: B 67 THR cc_start: 0.8321 (p) cc_final: 0.8060 (t) REVERT: B 136 PHE cc_start: 0.8022 (t80) cc_final: 0.7807 (t80) REVERT: B 140 GLU cc_start: 0.2210 (OUTLIER) cc_final: 0.1939 (pt0) REVERT: B 165 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8270 (mttt) REVERT: B 178 LEU cc_start: 0.8918 (tp) cc_final: 0.8632 (mt) REVERT: B 361 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8188 (mm-30) REVERT: B 438 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 440 MET cc_start: 0.8852 (mtt) cc_final: 0.8501 (mtm) REVERT: B 468 VAL cc_start: 0.8442 (t) cc_final: 0.8196 (t) REVERT: C 125 ARG cc_start: 0.7771 (tpt-90) cc_final: 0.7513 (tpt170) REVERT: D 17 LEU cc_start: 0.9033 (mt) cc_final: 0.8637 (mt) REVERT: D 76 LEU cc_start: 0.9410 (tp) cc_final: 0.9162 (tp) REVERT: D 366 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8406 (p0) REVERT: D 439 ASP cc_start: 0.8581 (t0) cc_final: 0.8350 (t70) REVERT: E 1 MET cc_start: 0.8846 (tpt) cc_final: 0.7916 (tpt) REVERT: E 86 ARG cc_start: 0.8781 (tmm-80) cc_final: 0.8437 (ttt180) REVERT: E 89 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: F 17 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8331 (mt) REVERT: F 58 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8575 (m) REVERT: F 75 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8325 (t70) REVERT: F 319 TYR cc_start: 0.8842 (m-80) cc_final: 0.8578 (m-80) REVERT: F 401 GLN cc_start: 0.8692 (mt0) cc_final: 0.8314 (mt0) REVERT: F 403 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: F 464 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6448 (tp) REVERT: F 466 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7732 (mp) REVERT: F 479 TRP cc_start: 0.8342 (t60) cc_final: 0.8042 (t60) REVERT: F 487 LEU cc_start: 0.6588 (mp) cc_final: 0.6172 (tt) REVERT: F 539 ARG cc_start: 0.8057 (mmm-85) cc_final: 0.7767 (mtp180) REVERT: G 114 MET cc_start: 0.9054 (tmm) cc_final: 0.8529 (ttp) REVERT: G 156 MET cc_start: 0.4119 (ptp) cc_final: 0.3839 (ptp) REVERT: H 8 THR cc_start: 0.9085 (t) cc_final: 0.8871 (p) REVERT: H 29 MET cc_start: 0.8766 (mtp) cc_final: 0.8500 (mtp) REVERT: H 267 GLN cc_start: 0.8369 (mt0) cc_final: 0.8124 (mt0) REVERT: H 292 GLU cc_start: 0.8622 (tp30) cc_final: 0.8368 (mm-30) REVERT: H 309 TYR cc_start: 0.9028 (m-80) cc_final: 0.8726 (m-10) REVERT: H 310 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8394 (mm-40) REVERT: H 373 MET cc_start: 0.6956 (mmt) cc_final: 0.6598 (mmt) REVERT: I 20 TYR cc_start: 0.8327 (m-80) cc_final: 0.7549 (m-80) REVERT: I 26 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8372 (p) REVERT: I 35 ARG cc_start: 0.8819 (ttt-90) cc_final: 0.8365 (ttt-90) REVERT: I 45 LYS cc_start: 0.9022 (mttt) cc_final: 0.8785 (mtpt) REVERT: I 133 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7764 (mt-10) REVERT: I 139 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8910 (m) REVERT: J 23 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7042 (t0) REVERT: J 31 ARG cc_start: 0.8465 (mmt90) cc_final: 0.8170 (mmm160) REVERT: J 87 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8242 (t0) REVERT: J 168 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6575 (p90) REVERT: K 110 TYR cc_start: 0.8337 (m-80) cc_final: 0.8105 (m-80) REVERT: K 172 ASN cc_start: 0.8629 (t0) cc_final: 0.8323 (t0) REVERT: L 29 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8296 (m-80) REVERT: L 59 LEU cc_start: 0.9039 (mt) cc_final: 0.8671 (mt) REVERT: M 19 ASP cc_start: 0.7991 (p0) cc_final: 0.6947 (t0) REVERT: N 40 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8605 (mmmt) REVERT: N 86 TYR cc_start: 0.9235 (t80) cc_final: 0.8852 (t80) REVERT: N 90 ASN cc_start: 0.9250 (m-40) cc_final: 0.8977 (m110) REVERT: N 123 LEU cc_start: 0.7689 (tp) cc_final: 0.7432 (tp) REVERT: O 14 GLU cc_start: 0.7843 (pm20) cc_final: 0.7352 (pm20) REVERT: O 49 GLN cc_start: 0.8929 (tt0) cc_final: 0.8506 (tt0) REVERT: P 18 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6518 (t-170) REVERT: P 56 ASP cc_start: 0.8798 (t0) cc_final: 0.8407 (t0) REVERT: P 120 GLU cc_start: 0.8661 (tp30) cc_final: 0.8290 (mm-30) REVERT: P 124 MET cc_start: 0.9155 (mtm) cc_final: 0.8593 (mtp) REVERT: P 148 MET cc_start: 0.8502 (mtp) cc_final: 0.8111 (mtm) REVERT: P 278 GLU cc_start: 0.8509 (mp0) cc_final: 0.7858 (mm-30) REVERT: P 339 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8644 (m-30) REVERT: Q 28 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7530 (tm-30) REVERT: Q 60 ASN cc_start: 0.8492 (m-40) cc_final: 0.8219 (m-40) REVERT: S 49 MET cc_start: 0.8354 (ptm) cc_final: 0.8036 (ptp) REVERT: S 61 TYR cc_start: 0.8685 (t80) cc_final: 0.8075 (t80) outliers start: 174 outliers final: 131 residues processed: 897 average time/residue: 0.2021 time to fit residues: 299.0184 Evaluate side-chains 912 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 764 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE 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 140 GLU 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 472 SER 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 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 83 ILE Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 152 LEU 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 390 LEU Chi-restraints excluded: chain F residue 403 GLU 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 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 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 31 THR 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 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 26 SER Chi-restraints excluded: chain I residue 30 ASP 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 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 63 SER 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 33 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 339 ASP Chi-restraints excluded: chain P residue 342 HIS Chi-restraints excluded: chain P residue 365 GLN 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 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: 0.2980 chunk 314 optimal weight: 0.5980 chunk 209 optimal weight: 0.0570 chunk 265 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 308 optimal weight: 0.0980 chunk 315 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 ASN K 181 HIS ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.111196 restraints weight = 45873.172| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.95 r_work: 0.3031 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2580 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= 0.123 Angle : 0.698 19.378 47355 Z= 0.325 Chirality : 0.043 0.536 5480 Planarity : 0.005 0.148 5846 Dihedral : 8.344 60.555 4946 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.09 % Favored : 90.72 % Rotamer: Outliers : 4.42 % Allowed : 20.91 % Favored : 74.67 % 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: -0.80 (0.13), residues: 4234 helix: 1.04 (0.11), residues: 2397 sheet: -2.17 (0.39), residues: 179 loop : -2.82 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 36 TYR 0.024 0.001 TYR L 13 PHE 0.025 0.001 PHE K 67 TRP 0.021 0.001 TRP F 71 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (34717) covalent geometry : angle 0.66245 / 0.32 (47319) hydrogen bonds : bond 0.03524 / 2.32 ( 1679) hydrogen bonds : angle 4.25010 / 3.02 ( 4851) metal coordination : bond 0.00615 / 0.41 ( 12) metal coordination : angle 7.96058 / 4.85 ( 36) Misc. bond : bond 0.00053 / 0.04 ( 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 958 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 804 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: A 93 ASN cc_start: 0.8646 (m-40) cc_final: 0.7776 (t0) REVERT: A 157 TYR cc_start: 0.6898 (t80) cc_final: 0.6593 (t80) REVERT: B 136 PHE cc_start: 0.7998 (t80) cc_final: 0.7765 (t80) REVERT: B 140 GLU cc_start: 0.2191 (OUTLIER) cc_final: 0.1893 (pt0) REVERT: B 165 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8241 (mttt) REVERT: B 166 TYR cc_start: 0.9292 (t80) cc_final: 0.8920 (t80) REVERT: B 178 LEU cc_start: 0.8874 (tp) cc_final: 0.8613 (mt) REVERT: B 313 PHE cc_start: 0.8684 (m-80) cc_final: 0.8428 (m-10) REVERT: B 361 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 438 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 440 MET cc_start: 0.8632 (mtt) cc_final: 0.8283 (mtm) REVERT: B 468 VAL cc_start: 0.8372 (t) cc_final: 0.8103 (t) REVERT: C 125 ARG cc_start: 0.7804 (tpt-90) cc_final: 0.7551 (tpt170) REVERT: D 16 VAL cc_start: 0.7982 (OUTLIER) cc_final: 0.7715 (p) REVERT: D 76 LEU cc_start: 0.9376 (tp) cc_final: 0.9129 (tp) REVERT: D 439 ASP cc_start: 0.8464 (t0) cc_final: 0.8213 (t70) REVERT: D 441 ARG cc_start: 0.7324 (mtm110) cc_final: 0.6743 (mpp80) REVERT: E 1 MET cc_start: 0.8785 (tpt) cc_final: 0.7884 (tpt) REVERT: E 86 ARG cc_start: 0.8750 (tmm-80) cc_final: 0.8460 (ttt180) REVERT: E 89 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8478 (m-30) REVERT: F 17 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8248 (mt) REVERT: F 58 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8288 (m) REVERT: F 75 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8276 (t70) REVERT: F 232 MET cc_start: 0.8856 (ttp) cc_final: 0.8524 (ttp) REVERT: F 319 TYR cc_start: 0.8695 (m-80) cc_final: 0.8469 (m-80) REVERT: F 359 ASN cc_start: 0.8098 (t160) cc_final: 0.7855 (t0) REVERT: F 403 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: F 441 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7649 (pm20) REVERT: F 464 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6602 (tp) REVERT: F 466 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7752 (mp) REVERT: F 479 TRP cc_start: 0.8248 (t60) cc_final: 0.7821 (t60) REVERT: F 487 LEU cc_start: 0.6699 (mp) cc_final: 0.6300 (tt) REVERT: F 539 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7665 (mtp180) REVERT: F 560 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6735 (t80) REVERT: G 114 MET cc_start: 0.8983 (tmm) cc_final: 0.8422 (ttp) REVERT: H 8 THR cc_start: 0.9053 (t) cc_final: 0.8826 (p) REVERT: H 29 MET cc_start: 0.8653 (mtp) cc_final: 0.8359 (mtp) REVERT: H 267 GLN cc_start: 0.8387 (mt0) cc_final: 0.8129 (mt0) REVERT: H 292 GLU cc_start: 0.8586 (tp30) cc_final: 0.8343 (mm-30) REVERT: H 309 TYR cc_start: 0.9014 (m-80) cc_final: 0.8759 (m-10) REVERT: H 310 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8384 (mm-40) REVERT: H 373 MET cc_start: 0.6865 (mmt) cc_final: 0.6308 (mmt) REVERT: I 20 TYR cc_start: 0.8315 (m-80) cc_final: 0.7505 (m-80) REVERT: I 45 LYS cc_start: 0.8971 (mttt) cc_final: 0.8717 (mtpt) REVERT: I 116 ASN cc_start: 0.8535 (m-40) cc_final: 0.8331 (m-40) REVERT: I 133 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7631 (mt-10) REVERT: I 139 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8865 (m) REVERT: J 23 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.6970 (t0) REVERT: J 87 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8213 (t0) REVERT: J 106 ARG cc_start: 0.7385 (pmt170) cc_final: 0.7180 (pmt170) REVERT: J 133 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7881 (mm-30) REVERT: J 168 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6604 (p90) REVERT: K 65 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8159 (p90) REVERT: K 110 TYR cc_start: 0.8290 (m-80) cc_final: 0.8089 (m-80) REVERT: L 29 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: L 59 LEU cc_start: 0.9045 (mt) cc_final: 0.8668 (mt) REVERT: N 40 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8626 (mmmt) REVERT: N 86 TYR cc_start: 0.9159 (t80) cc_final: 0.8784 (t80) REVERT: N 90 ASN cc_start: 0.9102 (m-40) cc_final: 0.8847 (m110) REVERT: N 123 LEU cc_start: 0.7646 (tp) cc_final: 0.7402 (tp) REVERT: O 14 GLU cc_start: 0.7777 (pm20) cc_final: 0.7432 (pm20) REVERT: O 34 PHE cc_start: 0.8440 (m-10) cc_final: 0.7819 (m-10) REVERT: O 35 GLU cc_start: 0.8368 (mp0) cc_final: 0.7563 (mp0) REVERT: O 49 GLN cc_start: 0.8901 (tt0) cc_final: 0.8525 (tt0) REVERT: O 61 LEU cc_start: 0.8757 (mt) cc_final: 0.8544 (mt) REVERT: P 18 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6475 (t-170) REVERT: P 78 LYS cc_start: 0.7204 (ttpt) cc_final: 0.6968 (tttt) REVERT: P 120 GLU cc_start: 0.8563 (tp30) cc_final: 0.8351 (mm-30) REVERT: P 124 MET cc_start: 0.9146 (mtm) cc_final: 0.8576 (mtp) REVERT: P 148 MET cc_start: 0.8396 (mtp) cc_final: 0.7968 (mtm) REVERT: P 278 GLU cc_start: 0.8507 (mp0) cc_final: 0.7885 (mm-30) REVERT: Q 60 ASN cc_start: 0.8431 (m-40) cc_final: 0.8166 (m-40) REVERT: Q 132 MET cc_start: 0.8449 (mpp) cc_final: 0.8146 (mpp) REVERT: S 49 MET cc_start: 0.8392 (ptm) cc_final: 0.8040 (ptp) REVERT: S 69 ARG cc_start: 0.8999 (ttm-80) cc_final: 0.8727 (ttm170) outliers start: 154 outliers final: 112 residues processed: 897 average time/residue: 0.2003 time to fit residues: 297.3541 Evaluate side-chains 906 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 776 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE 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 111 PHE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 140 GLU 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 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 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 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 152 LEU 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 403 GLU 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 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 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 81 LEU Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 100 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 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 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 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 232 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 71 optimal weight: 0.7980 chunk 260 optimal weight: 5.9990 chunk 336 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 405 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 ASN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN K 172 ASN K 181 HIS ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN P 201 GLN Q 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.131764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.108240 restraints weight = 45909.457| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.02 r_work: 0.2986 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34734 Z= 0.157 Angle : 0.732 19.482 47355 Z= 0.338 Chirality : 0.044 0.548 5480 Planarity : 0.005 0.143 5846 Dihedral : 8.292 60.997 4944 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.49 % Favored : 90.32 % Rotamer: Outliers : 4.70 % Allowed : 20.85 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.07 % 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: -0.72 (0.13), residues: 4234 helix: 1.09 (0.11), residues: 2390 sheet: -2.02 (0.41), residues: 167 loop : -2.78 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 578 TYR 0.029 0.001 TYR L 13 PHE 0.028 0.001 PHE K 67 TRP 0.019 0.001 TRP F 71 HIS 0.005 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (34717) covalent geometry : angle 0.69093 / 0.34 (47319) hydrogen bonds : bond 0.03724 / 2.45 ( 1679) hydrogen bonds : angle 4.26593 / 3.03 ( 4851) metal coordination : bond 0.00723 / 0.41 ( 12) metal coordination : angle 8.77798 / 5.33 ( 36) Misc. bond : bond 0.00097 / 0.06 ( 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 938 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 774 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: A 93 ASN cc_start: 0.8642 (m-40) cc_final: 0.7773 (t0) REVERT: A 157 TYR cc_start: 0.6981 (t80) cc_final: 0.6500 (t80) REVERT: A 197 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8607 (mm-30) REVERT: B 113 MET cc_start: 0.8463 (mtp) cc_final: 0.7940 (mtm) REVERT: B 136 PHE cc_start: 0.8024 (t80) cc_final: 0.7807 (t80) REVERT: B 140 GLU cc_start: 0.2211 (OUTLIER) cc_final: 0.1913 (pt0) REVERT: B 165 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8273 (mttt) REVERT: B 166 TYR cc_start: 0.9326 (t80) cc_final: 0.8918 (t80) REVERT: B 178 LEU cc_start: 0.8914 (tp) cc_final: 0.8615 (mt) REVERT: B 361 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7986 (mm-30) REVERT: B 438 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 440 MET cc_start: 0.8802 (mtt) cc_final: 0.8480 (mtm) REVERT: B 468 VAL cc_start: 0.8401 (t) cc_final: 0.8129 (t) REVERT: C 125 ARG cc_start: 0.7927 (tpt-90) cc_final: 0.7724 (tpt170) REVERT: D 16 VAL cc_start: 0.7975 (OUTLIER) cc_final: 0.7704 (p) REVERT: D 17 LEU cc_start: 0.9019 (mt) cc_final: 0.8609 (mt) REVERT: D 76 LEU cc_start: 0.9403 (tp) cc_final: 0.9195 (tp) REVERT: D 444 TYR cc_start: 0.9151 (m-80) cc_final: 0.8939 (m-80) REVERT: E 1 MET cc_start: 0.8851 (tpt) cc_final: 0.7964 (tpt) REVERT: E 86 ARG cc_start: 0.8819 (tmm-80) cc_final: 0.8487 (ttt180) REVERT: E 89 ASP cc_start: 0.8974 (t70) cc_final: 0.8554 (m-30) REVERT: F 58 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8652 (m) REVERT: F 75 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8308 (t70) REVERT: F 359 ASN cc_start: 0.8243 (t160) cc_final: 0.7955 (t0) REVERT: F 403 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: F 441 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7589 (pm20) REVERT: F 464 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6571 (tp) REVERT: F 466 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7648 (mp) REVERT: F 479 TRP cc_start: 0.8271 (t60) cc_final: 0.7838 (t60) REVERT: F 487 LEU cc_start: 0.6766 (mp) cc_final: 0.6366 (tt) REVERT: F 539 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.7729 (mtp180) REVERT: G 114 MET cc_start: 0.9036 (tmm) cc_final: 0.8523 (ttp) REVERT: H 8 THR cc_start: 0.9101 (t) cc_final: 0.8868 (p) REVERT: H 29 MET cc_start: 0.8740 (mtp) cc_final: 0.8488 (mtp) REVERT: H 292 GLU cc_start: 0.8614 (tp30) cc_final: 0.8373 (mm-30) REVERT: H 309 TYR cc_start: 0.9024 (m-80) cc_final: 0.8744 (m-10) REVERT: H 310 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8407 (mm-40) REVERT: H 373 MET cc_start: 0.6889 (mmt) cc_final: 0.6567 (mmt) REVERT: I 19 LYS cc_start: 0.8241 (tppt) cc_final: 0.8007 (tppt) REVERT: I 20 TYR cc_start: 0.8341 (m-80) cc_final: 0.7522 (m-80) REVERT: I 45 LYS cc_start: 0.9023 (mttt) cc_final: 0.8788 (mtpt) REVERT: I 84 PHE cc_start: 0.8875 (t80) cc_final: 0.8558 (t80) REVERT: I 133 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7701 (mt-10) REVERT: I 139 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8904 (m) REVERT: J 23 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.7007 (t0) REVERT: J 87 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8225 (t0) REVERT: J 106 ARG cc_start: 0.7423 (pmt170) cc_final: 0.7182 (pmt170) REVERT: J 133 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7771 (mm-30) REVERT: J 168 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6759 (p90) REVERT: K 65 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7923 (p90) REVERT: K 110 TYR cc_start: 0.8347 (m-80) cc_final: 0.8137 (m-80) REVERT: K 114 MET cc_start: 0.8941 (ptm) cc_final: 0.8690 (ttm) REVERT: L 29 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8302 (m-80) REVERT: L 59 LEU cc_start: 0.9024 (mt) cc_final: 0.8651 (mt) REVERT: N 40 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8625 (mmmt) REVERT: N 86 TYR cc_start: 0.9178 (t80) cc_final: 0.8796 (t80) REVERT: N 123 LEU cc_start: 0.7792 (tp) cc_final: 0.7569 (tp) REVERT: O 14 GLU cc_start: 0.7660 (pm20) cc_final: 0.7246 (pm20) REVERT: O 34 PHE cc_start: 0.8504 (m-10) cc_final: 0.8056 (m-10) REVERT: O 49 GLN cc_start: 0.8920 (tt0) cc_final: 0.8482 (tt0) REVERT: P 18 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6547 (t-170) REVERT: P 92 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.4855 (p90) REVERT: P 120 GLU cc_start: 0.8656 (tp30) cc_final: 0.8392 (mm-30) REVERT: P 124 MET cc_start: 0.9165 (mtm) cc_final: 0.8593 (mtp) REVERT: P 248 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7960 (mm) REVERT: P 278 GLU cc_start: 0.8581 (mp0) cc_final: 0.7973 (mm-30) REVERT: P 381 VAL cc_start: 0.9006 (t) cc_final: 0.8579 (p) REVERT: Q 60 ASN cc_start: 0.8488 (m-40) cc_final: 0.8229 (m-40) REVERT: S 49 MET cc_start: 0.8386 (ptm) cc_final: 0.8054 (ptp) outliers start: 164 outliers final: 130 residues processed: 876 average time/residue: 0.1976 time to fit residues: 286.6302 Evaluate side-chains 911 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 764 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 302 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 140 GLU 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 16 VAL Chi-restraints excluded: chain D residue 24 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 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 152 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 390 LEU Chi-restraints excluded: chain F residue 403 GLU 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 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 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 135 ASN 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 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 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 33 VAL Chi-restraints excluded: chain M residue 42 ASN 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 92 TYR 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 232 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 171 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 344 optimal weight: 0.3980 chunk 404 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 319 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 HIS ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 ASN M 109 ASN N 90 ASN Q 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.132707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109647 restraints weight = 45755.490| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.95 r_work: 0.3011 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2665 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= 0.134 Angle : 0.720 19.402 47355 Z= 0.332 Chirality : 0.044 0.537 5480 Planarity : 0.005 0.140 5846 Dihedral : 8.196 60.641 4944 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.12 % Favored : 90.69 % Rotamer: Outliers : 4.42 % Allowed : 21.08 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 1.69 % Twisted General : 0.07 % 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: -0.66 (0.13), residues: 4234 helix: 1.13 (0.11), residues: 2401 sheet: -2.04 (0.39), residues: 179 loop : -2.75 (0.14), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 36 TYR 0.026 0.001 TYR L 13 PHE 0.037 0.001 PHE P 57 TRP 0.020 0.001 TRP F 71 HIS 0.006 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (34717) covalent geometry : angle 0.68023 / 0.33 (47319) hydrogen bonds : bond 0.03595 / 2.37 ( 1679) hydrogen bonds : angle 4.23585 / 3.01 ( 4851) metal coordination : bond 0.00536 / 0.31 ( 12) metal coordination : angle 8.58351 / 5.24 ( 36) Misc. bond : bond 0.00058 / 0.04 ( 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 929 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 775 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: A 93 ASN cc_start: 0.8635 (m-40) cc_final: 0.7818 (t0) REVERT: A 157 TYR cc_start: 0.6760 (t80) cc_final: 0.6393 (t80) REVERT: B 113 MET cc_start: 0.8391 (mtp) cc_final: 0.7854 (mtm) REVERT: B 136 PHE cc_start: 0.8013 (t80) cc_final: 0.7782 (t80) REVERT: B 140 GLU cc_start: 0.2210 (OUTLIER) cc_final: 0.1914 (pt0) REVERT: B 165 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8241 (mttt) REVERT: B 166 TYR cc_start: 0.9308 (t80) cc_final: 0.8898 (t80) REVERT: B 178 LEU cc_start: 0.8893 (tp) cc_final: 0.8601 (mt) REVERT: B 361 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7917 (mm-30) REVERT: B 432 MET cc_start: 0.9049 (ttp) cc_final: 0.8827 (mtp) REVERT: B 438 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 440 MET cc_start: 0.8651 (mtt) cc_final: 0.8288 (mtm) REVERT: B 468 VAL cc_start: 0.8368 (t) cc_final: 0.8100 (t) REVERT: C 60 MET cc_start: 0.8665 (mmm) cc_final: 0.8028 (mmm) REVERT: C 125 ARG cc_start: 0.7921 (tpt-90) cc_final: 0.7711 (tpt170) REVERT: D 16 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7696 (p) REVERT: D 17 LEU cc_start: 0.9014 (mt) cc_final: 0.8613 (mt) REVERT: D 27 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7975 (pp) REVERT: D 76 LEU cc_start: 0.9389 (tp) cc_final: 0.9169 (tp) REVERT: E 1 MET cc_start: 0.8837 (tpt) cc_final: 0.7945 (tpt) REVERT: E 86 ARG cc_start: 0.8761 (tmm-80) cc_final: 0.8420 (ttt180) REVERT: E 89 ASP cc_start: 0.8873 (t70) cc_final: 0.8471 (m-30) REVERT: F 58 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8402 (m) REVERT: F 75 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8313 (t70) REVERT: F 403 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: F 441 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7494 (pm20) REVERT: F 464 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6556 (tp) REVERT: F 466 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7609 (mp) REVERT: F 479 TRP cc_start: 0.8265 (t60) cc_final: 0.7809 (t60) REVERT: F 487 LEU cc_start: 0.6747 (mp) cc_final: 0.6362 (tt) REVERT: F 539 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7755 (mtp180) REVERT: F 560 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.6752 (t80) REVERT: G 114 MET cc_start: 0.8986 (tmm) cc_final: 0.8211 (ttp) REVERT: H 8 THR cc_start: 0.9073 (t) cc_final: 0.8835 (p) REVERT: H 29 MET cc_start: 0.8717 (mtp) cc_final: 0.8463 (mtp) REVERT: H 292 GLU cc_start: 0.8577 (tp30) cc_final: 0.8295 (mm-30) REVERT: H 309 TYR cc_start: 0.9036 (m-80) cc_final: 0.8785 (m-10) REVERT: H 310 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8349 (mm-40) REVERT: H 373 MET cc_start: 0.6859 (mmt) cc_final: 0.6346 (mmt) REVERT: I 19 LYS cc_start: 0.8071 (tppt) cc_final: 0.7798 (tppt) REVERT: I 20 TYR cc_start: 0.8292 (m-80) cc_final: 0.7480 (m-80) REVERT: I 45 LYS cc_start: 0.8971 (mttt) cc_final: 0.8716 (mtpt) REVERT: I 84 PHE cc_start: 0.8865 (t80) cc_final: 0.8555 (t80) REVERT: I 133 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7646 (mt-10) REVERT: I 139 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8898 (m) REVERT: J 23 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7037 (t0) REVERT: J 87 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8217 (t0) REVERT: J 168 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.6791 (p90) REVERT: K 47 MET cc_start: 0.8805 (tpt) cc_final: 0.8591 (tpt) REVERT: K 65 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8105 (p90) REVERT: K 110 TYR cc_start: 0.8314 (m-80) cc_final: 0.8113 (m-80) REVERT: K 114 MET cc_start: 0.8933 (ptm) cc_final: 0.8708 (ttm) REVERT: L 29 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: N 40 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8625 (mmmt) REVERT: N 86 TYR cc_start: 0.9217 (t80) cc_final: 0.8770 (t80) REVERT: N 90 ASN cc_start: 0.9268 (m-40) cc_final: 0.8914 (m-40) REVERT: N 123 LEU cc_start: 0.7661 (tp) cc_final: 0.7422 (tp) REVERT: O 14 GLU cc_start: 0.7605 (pm20) cc_final: 0.7195 (pm20) REVERT: O 34 PHE cc_start: 0.8458 (m-10) cc_final: 0.8074 (m-10) REVERT: O 49 GLN cc_start: 0.8910 (tt0) cc_final: 0.8557 (tt0) REVERT: P 18 HIS cc_start: 0.7212 (OUTLIER) cc_final: 0.6518 (t-170) REVERT: P 78 LYS cc_start: 0.7252 (ttpt) cc_final: 0.6955 (tttt) REVERT: P 92 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.4909 (p90) REVERT: P 120 GLU cc_start: 0.8631 (tp30) cc_final: 0.8385 (mm-30) REVERT: P 124 MET cc_start: 0.9159 (mtm) cc_final: 0.8585 (mtp) REVERT: P 248 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7939 (mm) REVERT: P 278 GLU cc_start: 0.8580 (mp0) cc_final: 0.8013 (mm-30) REVERT: P 381 VAL cc_start: 0.8981 (t) cc_final: 0.8568 (p) REVERT: Q 60 ASN cc_start: 0.8447 (m-40) cc_final: 0.8179 (m-40) REVERT: S 49 MET cc_start: 0.8371 (ptm) cc_final: 0.8087 (ptp) outliers start: 154 outliers final: 124 residues processed: 874 average time/residue: 0.2002 time to fit residues: 290.2549 Evaluate side-chains 903 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 760 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE 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 192 THR Chi-restraints excluded: chain A residue 302 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 140 GLU 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 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 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 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 152 LEU 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 390 LEU Chi-restraints excluded: chain F residue 403 GLU 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 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 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 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 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 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 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 171 ILE 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 33 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 39 VAL Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 82 THR Chi-restraints excluded: chain P residue 92 TYR 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 232 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 202 optimal weight: 4.9990 chunk 281 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 322 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 328 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 175 optimal weight: 0.5980 chunk 311 optimal weight: 0.1980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 ASN K 181 HIS ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.134376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.110832 restraints weight = 45868.785| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.04 r_work: 0.3020 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2794 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= 0.126 Angle : 0.711 18.691 47355 Z= 0.328 Chirality : 0.043 0.513 5480 Planarity : 0.005 0.137 5846 Dihedral : 8.047 60.364 4944 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.19 % Favored : 90.62 % Rotamer: Outliers : 4.39 % Allowed : 21.26 % Favored : 74.35 % 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: -0.58 (0.13), residues: 4234 helix: 1.22 (0.11), residues: 2394 sheet: -2.02 (0.42), residues: 161 loop : -2.73 (0.14), residues: 1679 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 0.025 0.001 PHE K 67 TRP 0.021 0.001 TRP F 71 HIS 0.005 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (34717) covalent geometry : angle 0.67339 / 0.33 (47319) hydrogen bonds : bond 0.03489 / 2.30 ( 1679) hydrogen bonds : angle 4.19865 / 2.98 ( 4851) metal coordination : bond 0.00452 / 0.29 ( 12) metal coordination : angle 8.33944 / 5.11 ( 36) Misc. bond : bond 0.00046 / 0.03 ( 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 938 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 785 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: A 93 ASN cc_start: 0.8635 (m-40) cc_final: 0.7778 (t0) REVERT: A 157 TYR cc_start: 0.6736 (t80) cc_final: 0.6360 (t80) REVERT: B 136 PHE cc_start: 0.7956 (t80) cc_final: 0.7205 (t80) REVERT: B 140 GLU cc_start: 0.2203 (OUTLIER) cc_final: 0.1519 (pm20) REVERT: B 165 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8226 (mttt) REVERT: B 166 TYR cc_start: 0.9290 (t80) cc_final: 0.8870 (t80) REVERT: B 178 LEU cc_start: 0.8871 (tp) cc_final: 0.8609 (mt) REVERT: B 361 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7889 (mm-30) REVERT: B 438 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 440 MET cc_start: 0.8615 (mtt) cc_final: 0.8254 (mtm) REVERT: B 468 VAL cc_start: 0.8425 (t) cc_final: 0.8153 (t) REVERT: C 60 MET cc_start: 0.8655 (mmm) cc_final: 0.8030 (mmm) REVERT: C 125 ARG cc_start: 0.7983 (tpt-90) cc_final: 0.7768 (tpt170) REVERT: D 16 VAL cc_start: 0.7976 (OUTLIER) cc_final: 0.7725 (p) REVERT: D 17 LEU cc_start: 0.9011 (mt) cc_final: 0.8625 (mt) REVERT: D 76 LEU cc_start: 0.9389 (tp) cc_final: 0.9152 (tp) REVERT: D 235 TYR cc_start: 0.9026 (m-10) cc_final: 0.8784 (m-10) REVERT: E 1 MET cc_start: 0.8832 (tpt) cc_final: 0.7931 (tpt) REVERT: E 86 ARG cc_start: 0.8776 (tmm-80) cc_final: 0.8431 (ttt180) REVERT: E 89 ASP cc_start: 0.8853 (t70) cc_final: 0.8426 (m-30) REVERT: F 58 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8372 (m) REVERT: F 75 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8268 (t70) REVERT: F 403 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: F 441 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7511 (pm20) REVERT: F 464 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6589 (tp) REVERT: F 466 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7667 (mp) REVERT: F 478 ASP cc_start: 0.7872 (m-30) cc_final: 0.7587 (m-30) REVERT: F 479 TRP cc_start: 0.8260 (t60) cc_final: 0.7897 (t60) REVERT: F 487 LEU cc_start: 0.6736 (mp) cc_final: 0.6365 (tt) REVERT: F 539 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.7790 (mtp-110) REVERT: F 560 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6869 (t80) REVERT: G 114 MET cc_start: 0.8972 (tmm) cc_final: 0.8229 (ttp) REVERT: H 8 THR cc_start: 0.9041 (t) cc_final: 0.8790 (p) REVERT: H 29 MET cc_start: 0.8687 (mtp) cc_final: 0.8414 (mtp) REVERT: H 41 GLU cc_start: 0.8441 (tt0) cc_final: 0.8137 (tt0) REVERT: H 78 ASN cc_start: 0.8974 (OUTLIER) cc_final: 0.8751 (m110) REVERT: H 292 GLU cc_start: 0.8564 (tp30) cc_final: 0.8298 (mm-30) REVERT: H 309 TYR cc_start: 0.9025 (m-80) cc_final: 0.8793 (m-10) REVERT: H 310 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8311 (mm-40) REVERT: H 374 LYS cc_start: 0.7466 (mmpt) cc_final: 0.7182 (mmmt) REVERT: I 19 LYS cc_start: 0.8099 (tppt) cc_final: 0.7849 (tppt) REVERT: I 20 TYR cc_start: 0.8249 (m-80) cc_final: 0.7465 (m-80) REVERT: I 45 LYS cc_start: 0.8942 (mttt) cc_final: 0.8682 (mtpt) REVERT: I 84 PHE cc_start: 0.8844 (t80) cc_final: 0.8550 (t80) REVERT: I 133 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7590 (mt-10) REVERT: I 139 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8902 (m) REVERT: J 23 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7039 (t0) REVERT: J 87 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8180 (t0) REVERT: J 106 ARG cc_start: 0.7388 (pmt170) cc_final: 0.7088 (pmt170) REVERT: J 168 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.6822 (p90) REVERT: K 47 MET cc_start: 0.8857 (tpt) cc_final: 0.8628 (tpt) REVERT: K 156 MET cc_start: 0.8739 (mtm) cc_final: 0.8336 (mtm) REVERT: L 29 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: L 59 LEU cc_start: 0.9009 (mt) cc_final: 0.8617 (mt) REVERT: M 27 GLU cc_start: 0.6774 (pm20) cc_final: 0.6573 (pm20) REVERT: N 86 TYR cc_start: 0.9170 (t80) cc_final: 0.8741 (t80) REVERT: N 90 ASN cc_start: 0.9263 (m-40) cc_final: 0.8871 (m-40) REVERT: N 123 LEU cc_start: 0.7640 (tp) cc_final: 0.7421 (tp) REVERT: O 14 GLU cc_start: 0.7541 (pm20) cc_final: 0.7146 (pm20) REVERT: O 27 HIS cc_start: 0.7614 (t70) cc_final: 0.7232 (t70) REVERT: O 34 PHE cc_start: 0.8491 (m-10) cc_final: 0.8057 (m-10) REVERT: O 49 GLN cc_start: 0.8896 (tt0) cc_final: 0.8470 (tt0) REVERT: P 18 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6496 (t-170) REVERT: P 78 LYS cc_start: 0.7138 (ttpt) cc_final: 0.6883 (tttt) REVERT: P 92 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.5085 (p90) REVERT: P 120 GLU cc_start: 0.8657 (tp30) cc_final: 0.8413 (mm-30) REVERT: P 124 MET cc_start: 0.9158 (mtm) cc_final: 0.8570 (mtp) REVERT: P 248 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7938 (mm) REVERT: P 278 GLU cc_start: 0.8560 (mp0) cc_final: 0.8001 (mm-30) REVERT: P 310 ASP cc_start: 0.8190 (p0) cc_final: 0.7917 (p0) REVERT: P 313 ASP cc_start: 0.9203 (m-30) cc_final: 0.8975 (m-30) REVERT: P 381 VAL cc_start: 0.8973 (t) cc_final: 0.8576 (p) REVERT: Q 60 ASN cc_start: 0.8433 (m-40) cc_final: 0.8189 (m-40) REVERT: S 49 MET cc_start: 0.8411 (ptm) cc_final: 0.8133 (ptp) outliers start: 153 outliers final: 124 residues processed: 880 average time/residue: 0.2094 time to fit residues: 305.0907 Evaluate side-chains 903 residues out of total 3534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 761 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE 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 192 THR Chi-restraints excluded: chain A residue 302 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 140 GLU 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 462 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 484 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 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 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 152 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 390 LEU Chi-restraints excluded: chain F residue 403 GLU 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 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 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 135 ASN 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 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 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 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 92 TYR 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 232 THR 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 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: 3.9990 chunk 173 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 297 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 299 optimal weight: 0.6980 chunk 130 optimal weight: 0.0980 chunk 20 optimal weight: 0.0570 chunk 314 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 157 ASN ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 HIS ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.122344 restraints weight = 44483.278| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.85 r_work: 0.3067 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2903 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= 0.122 Angle : 0.711 18.127 47355 Z= 0.328 Chirality : 0.043 0.498 5480 Planarity : 0.005 0.132 5846 Dihedral : 7.958 60.209 4942 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.12 % Favored : 90.69 % Rotamer: Outliers : 4.10 % Allowed : 21.94 % Favored : 73.95 % 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: -0.52 (0.14), residues: 4234 helix: 1.29 (0.11), residues: 2385 sheet: -1.99 (0.43), residues: 161 loop : -2.72 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 36 TYR 0.027 0.001 TYR L 13 PHE 0.024 0.001 PHE K 67 TRP 0.020 0.001 TRP F 454 HIS 0.005 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (34717) covalent geometry : angle 0.67548 / 0.33 (47319) hydrogen bonds : bond 0.03419 / 2.25 ( 1679) hydrogen bonds : angle 4.18323 / 2.97 ( 4851) metal coordination : bond 0.00481 / 0.33 ( 12) metal coordination : angle 8.09983 / 4.95 ( 36) Misc. bond : bond 0.00059 / 0.04 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9356.26 seconds wall clock time: 160 minutes 37.65 seconds (9637.65 seconds total)