Starting phenix.real_space_refine on Sat Mar 7 00:58:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l7o_0849/03_2026/6l7o_0849_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l7o_0849/03_2026/6l7o_0849.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/6l7o_0849/03_2026/6l7o_0849_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l7o_0849/03_2026/6l7o_0849_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l7o_0849/03_2026/6l7o_0849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l7o_0849/03_2026/6l7o_0849.map" } 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 14 7.16 5 P 9 5.49 5 S 184 5.16 5 C 23515 2.51 5 N 5205 2.21 5 O 6110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 305 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35037 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2859 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3732 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 18, 'TRANS': 474} Chain: "C" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 978 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "D" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3896 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Chain: "F" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5004 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 614} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1463 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 13, 'TRANS': 178} Chain: "H" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3177 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain: "I" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1525 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 177} 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: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1597 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 184} Chain: "L" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} 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: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 11, 'TRANS': 136} 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: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 321 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 332 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "R" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 748 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "S" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 485 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "V" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 381 Unusual residues: {'AJP': 5, 'BCR': 1, 'DGD': 2, 'LHG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 625 Unresolved non-hydrogen chiralities: 120 Chain: "B" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 618 Unusual residues: {'AJP': 12, 'LHG': 3, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 696 Unresolved non-hydrogen angles: 1044 Unresolved non-hydrogen dihedrals: 1500 Unresolved non-hydrogen chiralities: 288 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 48 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 482 Unusual residues: {'AJP': 12, 'LHG': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 696 Unresolved non-hydrogen angles: 1044 Unresolved non-hydrogen dihedrals: 1500 Unresolved non-hydrogen chiralities: 288 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'AJP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 24 Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 662 Unusual residues: {'AJP': 13, 'BCR': 1, 'LHG': 2, 'SQD': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 754 Unresolved non-hydrogen angles: 1131 Unresolved non-hydrogen dihedrals: 1625 Unresolved non-hydrogen chiralities: 312 Chain: "G" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 224 Unusual residues: {'AJP': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 406 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 875 Unresolved non-hydrogen chiralities: 168 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'SQD': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 256 Unusual residues: {'AJP': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 696 Unresolved non-hydrogen dihedrals: 1000 Unresolved non-hydrogen chiralities: 192 Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22739 SG CYS I 103 55.643 52.477 50.265 1.00 39.26 S ATOM 22783 SG CYS I 109 51.527 46.691 47.807 1.00 50.41 S ATOM 22488 SG CYS I 73 54.151 45.896 53.644 1.00 48.74 S ATOM 22416 SG CYS I 63 39.311 45.723 49.087 1.00 71.75 S ATOM 22435 SG CYS I 66 41.935 40.175 49.035 1.00 61.84 S ATOM 25567 SG CYS K 117 67.001 54.779 55.928 1.00 33.34 S ATOM 25069 SG CYS K 53 68.736 57.832 51.380 1.00 42.53 S ATOM 25063 SG CYS K 52 70.759 53.458 49.683 1.00 47.63 S ATOM 25793 SG CYS K 148 63.834 52.389 51.092 1.00 42.59 S ATOM 30707 SG CYS R 78 40.720 28.949 44.847 1.00117.98 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS R 86 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS R 86 " occ=0.50 Time building chain proxies: 8.09, per 1000 atoms: 0.23 Number of scatterers: 35037 At special positions: 0 Unit cell: (237.62, 138.43, 182.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 14 26.01 S 184 16.00 P 9 15.00 O 6110 8.00 N 5205 7.00 C 23515 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES R 101 " pdb="FE2 FES R 101 " - pdb=" SG CYS R 78 " pdb="FE2 FES R 101 " - pdb=" SG CYS R 48 " pdb="FE1 FES R 101 " - pdb=" SG CYS R 40 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 73 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 103 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 106 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 113 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 148 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " Number of angles added : 40 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7582 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 19 sheets defined 60.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.632A pdb=" N LEU A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.783A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 95 through 113 Proline residue: A 103 - end of helix Proline residue: A 109 - end of helix Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.597A pdb=" N ILE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 4.005A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 172 removed outlier: 3.834A pdb=" N LEU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.578A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.613A pdb=" N ILE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.637A pdb=" N SER A 206 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 Processing helix chain 'A' and resid 250 through 276 removed outlier: 3.649A pdb=" N SER A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.554A pdb=" N ILE A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 330 removed outlier: 3.601A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TRP A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 366 removed outlier: 4.546A pdb=" N LEU A 349 " --> pdb=" O TRP A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 15 through 35 Processing helix chain 'B' and resid 42 through 57 removed outlier: 3.504A pdb=" N THR B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 removed outlier: 3.983A pdb=" N LEU B 61 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 106 removed outlier: 5.332A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.965A pdb=" N PHE B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.818A pdb=" N GLY B 151 " --> pdb=" O TYR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 188 removed outlier: 3.804A pdb=" N LYS B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 205 through 224 removed outlier: 3.515A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.705A pdb=" N HIS B 229 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 removed outlier: 4.361A pdb=" N GLU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 249 through 267 Processing helix chain 'B' and resid 270 through 293 removed outlier: 3.632A pdb=" N TRP B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.822A pdb=" N GLY B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 354 removed outlier: 3.816A pdb=" N ALA B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.818A pdb=" N ALA B 363 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.704A pdb=" N THR B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.775A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.723A pdb=" N VAL B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 456 through 477 removed outlier: 4.243A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.618A pdb=" N PHE B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 43 Proline residue: C 33 - end of helix removed outlier: 3.831A pdb=" N LEU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 97 Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 103 through 126 removed outlier: 3.520A pdb=" N LYS C 126 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 18 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 31 through 57 removed outlier: 4.552A pdb=" N ARG D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 removed outlier: 3.578A pdb=" N ILE D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 133 removed outlier: 3.575A pdb=" N PHE D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.759A pdb=" N PHE D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 157 removed outlier: 4.359A pdb=" N VAL D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 4.303A pdb=" N PHE D 179 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.547A pdb=" N LEU D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 202 " --> pdb=" O MET D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 197 through 202' Processing helix chain 'D' and resid 207 through 226 removed outlier: 3.546A pdb=" N ALA D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 4.412A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 removed outlier: 4.294A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 269 removed outlier: 3.587A pdb=" N LYS D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 262 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 removed outlier: 3.672A pdb=" N ALA D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 277' Processing helix chain 'D' and resid 277 through 297 removed outlier: 3.641A pdb=" N ALA D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 322 removed outlier: 3.874A pdb=" N SER D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 355 removed outlier: 3.782A pdb=" N ALA D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL D 333 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 355 " --> pdb=" O GLY D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 removed outlier: 4.034A pdb=" N ALA D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 407 removed outlier: 4.223A pdb=" N VAL D 396 " --> pdb=" O MET D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 430 removed outlier: 4.406A pdb=" N VAL D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 removed outlier: 4.536A pdb=" N LEU D 434 " --> pdb=" O THR D 430 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 454 removed outlier: 3.674A pdb=" N VAL D 451 " --> pdb=" O ASN D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 480 removed outlier: 3.514A pdb=" N ILE D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Proline residue: D 473 - end of helix Processing helix chain 'D' and resid 481 through 503 removed outlier: 3.693A pdb=" N THR D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 23 removed outlier: 3.738A pdb=" N VAL E 6 " --> pdb=" O GLN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 52 removed outlier: 3.731A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 88 removed outlier: 3.819A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 27 removed outlier: 3.518A pdb=" N ILE F 27 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 removed outlier: 4.057A pdb=" N LYS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 36' Processing helix chain 'F' and resid 37 through 66 removed outlier: 3.577A pdb=" N ALA F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS F 66 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 115 removed outlier: 3.512A pdb=" N ILE F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 140 removed outlier: 3.605A pdb=" N VAL F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 163 removed outlier: 3.689A pdb=" N GLY F 163 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 200 removed outlier: 3.815A pdb=" N GLU F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 180 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 218 removed outlier: 3.518A pdb=" N THR F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.590A pdb=" N ALA F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.994A pdb=" N ASP F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 removed outlier: 3.543A pdb=" N SER F 261 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 removed outlier: 4.373A pdb=" N GLY F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 Processing helix chain 'F' and resid 287 through 309 removed outlier: 4.326A pdb=" N MET F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 337 Processing helix chain 'F' and resid 338 through 371 removed outlier: 3.835A pdb=" N MET F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 Processing helix chain 'F' and resid 391 through 407 removed outlier: 3.800A pdb=" N SER F 406 " --> pdb=" O CYS F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 428 removed outlier: 4.037A pdb=" N TRP F 415 " --> pdb=" O PHE F 411 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 454 removed outlier: 3.569A pdb=" N TYR F 445 " --> pdb=" O LEU F 441 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE F 454 " --> pdb=" O TYR F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 493 removed outlier: 4.292A pdb=" N LEU F 490 " --> pdb=" O MET F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 504 removed outlier: 3.675A pdb=" N THR F 498 " --> pdb=" O ALA F 494 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.720A pdb=" N VAL F 513 " --> pdb=" O ASN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 554 removed outlier: 3.526A pdb=" N LEU F 534 " --> pdb=" O LEU F 530 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET F 554 " --> pdb=" O VAL F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 569 removed outlier: 3.799A pdb=" N ILE F 565 " --> pdb=" O SER F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 578 removed outlier: 3.913A pdb=" N SER F 576 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 587 through 629 removed outlier: 4.580A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL F 613 " --> pdb=" O VAL F 609 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN F 614 " --> pdb=" O ASP F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 656 removed outlier: 3.717A pdb=" N TYR F 638 " --> pdb=" O ARG F 634 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 639 " --> pdb=" O ALA F 635 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 29 removed outlier: 3.621A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 54 removed outlier: 3.581A pdb=" N SER G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 Processing helix chain 'G' and resid 69 through 81 Processing helix chain 'G' and resid 93 through 118 Processing helix chain 'G' and resid 132 through 139 Processing helix chain 'G' and resid 144 through 165 removed outlier: 3.889A pdb=" N GLU G 148 " --> pdb=" O LEU G 144 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 69 Processing helix chain 'H' and resid 75 through 91 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 95 through 116 Processing helix chain 'H' and resid 117 through 124 removed outlier: 3.568A pdb=" N PHE H 121 " --> pdb=" O TRP H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 149 removed outlier: 3.710A pdb=" N PHE H 132 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR H 133 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 196 removed outlier: 3.987A pdb=" N LEU H 184 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 3.788A pdb=" N ILE H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN H 196 " --> pdb=" O ARG H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 204 removed outlier: 3.669A pdb=" N LEU H 204 " --> pdb=" O PHE H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 219 Processing helix chain 'H' and resid 222 through 229 removed outlier: 3.548A pdb=" N GLY H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 238 removed outlier: 3.664A pdb=" N VAL H 237 " --> pdb=" O ASP H 233 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP H 238 " --> pdb=" O LEU H 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 233 through 238' Processing helix chain 'H' and resid 257 through 282 removed outlier: 3.575A pdb=" N ARG H 270 " --> pdb=" O ILE H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 358 through 363 removed outlier: 3.642A pdb=" N ASN H 362 " --> pdb=" O PRO H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 370 Processing helix chain 'H' and resid 376 through 385 removed outlier: 4.409A pdb=" N ALA H 380 " --> pdb=" O ALA H 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE H 385 " --> pdb=" O ILE H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 394 Processing helix chain 'I' and resid 3 through 31 removed outlier: 3.604A pdb=" N GLY I 24 " --> pdb=" O TYR I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 183 through 191 removed outlier: 3.558A pdb=" N ILE I 187 " --> pdb=" O ARG I 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 45 through 57 removed outlier: 3.679A pdb=" N ALA J 55 " --> pdb=" O GLN J 51 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP J 56 " --> pdb=" O THR J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 118 removed outlier: 3.935A pdb=" N ASP J 118 " --> pdb=" O LYS J 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 115 through 118' Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'K' and resid 25 through 43 Processing helix chain 'K' and resid 51 through 62 removed outlier: 3.734A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE K 61 " --> pdb=" O PHE K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 71 removed outlier: 3.958A pdb=" N PHE K 70 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 104 Processing helix chain 'K' and resid 115 through 120 removed outlier: 3.542A pdb=" N ILE K 119 " --> pdb=" O GLY K 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 115 through 120' Processing helix chain 'K' and resid 151 through 167 removed outlier: 3.607A pdb=" N ALA K 167 " --> pdb=" O ARG K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 204 through 209 removed outlier: 3.591A pdb=" N ALA K 209 " --> pdb=" O PRO K 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 22 Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.764A pdb=" N ALA L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN L 33 " --> pdb=" O TYR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 54 removed outlier: 3.736A pdb=" N PHE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 62 removed outlier: 3.652A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 60 removed outlier: 3.792A pdb=" N LEU M 46 " --> pdb=" O ASN M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 87 Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 29 through 41 removed outlier: 4.333A pdb=" N TYR N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 60 Processing helix chain 'N' and resid 82 through 90 removed outlier: 3.848A pdb=" N ASN N 90 " --> pdb=" O TYR N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 123 removed outlier: 3.974A pdb=" N TYR N 115 " --> pdb=" O GLN N 111 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 149 Processing helix chain 'O' and resid 19 through 23 removed outlier: 3.736A pdb=" N ALA O 22 " --> pdb=" O SER O 19 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU O 23 " --> pdb=" O LEU O 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 19 through 23' Processing helix chain 'O' and resid 30 through 35 removed outlier: 3.853A pdb=" N PHE O 34 " --> pdb=" O PRO O 30 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU O 35 " --> pdb=" O PRO O 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 30 through 35' Processing helix chain 'P' and resid 7 through 13 removed outlier: 3.570A pdb=" N ALA P 13 " --> pdb=" O PRO P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 27 removed outlier: 4.202A pdb=" N LEU P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE P 24 " --> pdb=" O LEU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 43 removed outlier: 3.610A pdb=" N ILE Q 21 " --> pdb=" O SER Q 17 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 Processing helix chain 'R' and resid 66 through 73 Processing helix chain 'R' and resid 92 through 97 removed outlier: 3.933A pdb=" N LEU R 96 " --> pdb=" O GLN R 92 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 92 through 97' Processing helix chain 'V' and resid 45 through 63 removed outlier: 3.864A pdb=" N LEU V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Proline residue: V 54 - end of helix removed outlier: 3.912A pdb=" N ALA V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER V 61 " --> pdb=" O LYS V 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA V 62 " --> pdb=" O ASN V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 138 Processing sheet with id=AA1, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA2, first strand: chain 'D' and resid 67 through 70 Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 74 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 15 Processing sheet with id=AA5, first strand: chain 'H' and resid 325 through 332 removed outlier: 3.685A pdb=" N VAL H 329 " --> pdb=" O ILE H 340 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE H 340 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY H 339 " --> pdb=" O ARG H 356 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG H 352 " --> pdb=" O ILE H 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 55 through 58 removed outlier: 7.778A pdb=" N LEU I 118 " --> pdb=" O ASP S 85 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU S 87 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL I 120 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR S 89 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP S 84 " --> pdb=" O GLY S 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY S 81 " --> pdb=" O TRP S 84 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU S 80 " --> pdb=" O GLN S 64 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLN S 64 " --> pdb=" O GLU S 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 79 through 83 removed outlier: 6.798A pdb=" N VAL I 79 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR I 96 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP I 81 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL I 83 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU I 92 " --> pdb=" O VAL I 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 27 through 31 removed outlier: 3.662A pdb=" N GLU J 27 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N MET J 38 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU J 37 " --> pdb=" O ARG J 95 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS J 97 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE J 39 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N PHE J 99 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS J 63 " --> pdb=" O HIS J 80 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE J 82 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LEU J 61 " --> pdb=" O ILE J 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 106 through 108 removed outlier: 3.513A pdb=" N GLU J 133 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'K' and resid 45 through 47 removed outlier: 3.691A pdb=" N ILE K 85 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 143 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA K 113 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 183 through 187 removed outlier: 3.556A pdb=" N ALA K 186 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE M 12 " --> pdb=" O SER M 5 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER M 5 " --> pdb=" O ILE M 12 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 42 through 43 removed outlier: 6.711A pdb=" N THR N 43 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TRP N 101 " --> pdb=" O THR N 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 42 through 43 removed outlier: 6.711A pdb=" N THR N 43 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TRP N 101 " --> pdb=" O THR N 43 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU N 98 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL N 129 " --> pdb=" O LEU N 98 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU N 100 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU N 131 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU N 102 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU N 19 " --> pdb=" O VAL N 130 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL N 132 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU N 21 " --> pdb=" O VAL N 132 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG N 139 " --> pdb=" O PHE N 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 63 through 65 Processing sheet with id=AB7, first strand: chain 'O' and resid 59 through 62 removed outlier: 6.895A pdb=" N TYR O 47 " --> pdb=" O ILE O 43 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE O 43 " --> pdb=" O TYR O 47 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN O 49 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY O 38 " --> pdb=" O VAL O 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 14 through 20 removed outlier: 7.037A pdb=" N LYS R 87 " --> pdb=" O LEU R 53 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 57 through 58 Processing sheet with id=AC1, first strand: chain 'V' and resid 67 through 72 removed outlier: 3.755A pdb=" N TYR V 85 " --> pdb=" O TRP V 80 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN V 86 " --> pdb=" O SER V 105 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER V 105 " --> pdb=" O GLN V 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL V 101 " --> pdb=" O TYR V 90 " (cutoff:3.500A) 1732 hydrogen bonds defined for protein. 5133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 14564 1.44 - 1.66: 21253 1.66 - 1.88: 308 1.88 - 2.11: 0 2.11 - 2.33: 40 Bond restraints: 36165 Sorted by residual: bond pdb=" C12 PQN B 601 " pdb=" C13 PQN B 601 " ideal model delta sigma weight residual 1.334 1.523 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C4 PQN B 601 " pdb=" O4 PQN B 601 " ideal model delta sigma weight residual 1.214 1.401 -0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C1 PQN B 601 " pdb=" O1 PQN B 601 " ideal model delta sigma weight residual 1.214 1.399 -0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C1 PQN B 601 " pdb=" C2 PQN B 601 " ideal model delta sigma weight residual 1.488 1.385 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C1 SQD F 704 " pdb=" O5 SQD F 704 " ideal model delta sigma weight residual 1.500 1.404 0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 36160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 47755 3.00 - 6.00: 1374 6.00 - 8.99: 491 8.99 - 11.99: 170 11.99 - 14.99: 22 Bond angle restraints: 49812 Sorted by residual: angle pdb="FE1 FES R 101 " pdb=" S2 FES R 101 " pdb="FE2 FES R 101 " ideal model delta sigma weight residual 75.66 88.93 -13.27 1.14e+00 7.69e-01 1.36e+02 angle pdb=" S1 FES R 101 " pdb="FE2 FES R 101 " pdb=" S2 FES R 101 " ideal model delta sigma weight residual 104.33 91.06 13.27 1.14e+00 7.69e-01 1.36e+02 angle pdb="FE1 FES R 101 " pdb=" S1 FES R 101 " pdb="FE2 FES R 101 " ideal model delta sigma weight residual 75.66 89.01 -13.35 1.20e+00 6.94e-01 1.24e+02 angle pdb=" S1 FES R 101 " pdb="FE1 FES R 101 " pdb=" S2 FES R 101 " ideal model delta sigma weight residual 104.33 90.99 13.34 1.20e+00 6.94e-01 1.24e+02 angle pdb=" N ILE V 96 " pdb=" CA ILE V 96 " pdb=" C ILE V 96 " ideal model delta sigma weight residual 113.71 107.51 6.20 9.50e-01 1.11e+00 4.26e+01 ... (remaining 49807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 21475 35.99 - 71.98: 1595 71.98 - 107.97: 714 107.97 - 143.96: 1715 143.96 - 179.95: 298 Dihedral angle restraints: 25797 sinusoidal: 13941 harmonic: 11856 Sorted by residual: dihedral pdb=" CA HIS F 578 " pdb=" C HIS F 578 " pdb=" N LYS F 579 " pdb=" CA LYS F 579 " ideal model delta harmonic sigma weight residual 180.00 156.72 23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C12 AJP F 711 " pdb=" C10 AJP F 711 " pdb=" C11 AJP F 711 " pdb=" O82 AJP F 711 " ideal model delta sinusoidal sigma weight residual 287.38 107.43 179.95 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C12 AJP D 607 " pdb=" C10 AJP D 607 " pdb=" C11 AJP D 607 " pdb=" O82 AJP D 607 " ideal model delta sinusoidal sigma weight residual 287.38 107.45 179.93 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 25794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.290: 5348 4.290 - 8.581: 720 8.581 - 12.871: 0 12.871 - 17.161: 0 17.161 - 21.451: 12 Chirality restraints: 6080 Sorted by residual: chirality pdb="FE3 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S4 SF4 I 202 " both_signs ideal model delta sigma weight residual False -10.55 10.90 -21.45 2.00e-01 2.50e+01 1.15e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.83 21.38 2.00e-01 2.50e+01 1.14e+04 chirality pdb="FE3 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.75 -21.31 2.00e-01 2.50e+01 1.13e+04 ... (remaining 6077 not shown) Planarity restraints: 5682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 PQN B 601 " -0.081 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C12 PQN B 601 " 0.237 2.00e-02 2.50e+03 pdb=" C13 PQN B 601 " -0.363 2.00e-02 2.50e+03 pdb=" C14 PQN B 601 " 0.147 2.00e-02 2.50e+03 pdb=" C15 PQN B 601 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR P 101 " 0.197 2.00e-02 2.50e+03 1.64e-01 3.36e+02 pdb=" C21 BCR P 101 " -0.258 2.00e-02 2.50e+03 pdb=" C22 BCR P 101 " -0.077 2.00e-02 2.50e+03 pdb=" C23 BCR P 101 " 0.150 2.00e-02 2.50e+03 pdb=" C37 BCR P 101 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR P 101 " -0.118 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C11 BCR P 101 " 0.099 2.00e-02 2.50e+03 pdb=" C12 BCR P 101 " 0.148 2.00e-02 2.50e+03 pdb=" C13 BCR P 101 " -0.129 2.00e-02 2.50e+03 ... (remaining 5679 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 6 2.06 - 2.77: 6501 2.77 - 3.48: 46845 3.48 - 4.19: 78123 4.19 - 4.90: 139702 Nonbonded interactions: 271177 Sorted by model distance: nonbonded pdb=" OH TYR F 629 " pdb=" C18 AJP F 712 " model vdw 1.354 3.440 nonbonded pdb=" OH TYR F 629 " pdb=" C19 AJP F 712 " model vdw 1.525 3.470 nonbonded pdb=" CZ TYR F 629 " pdb=" C19 AJP F 712 " model vdw 1.851 3.690 nonbonded pdb=" CD2 LEU D 413 " pdb=" C80 AJP D 608 " model vdw 2.025 3.880 nonbonded pdb=" CZ TYR F 629 " pdb=" C18 AJP F 712 " model vdw 2.042 2.928 ... (remaining 271172 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.330 Find NCS groups from input model: 0.350 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 : 0.017 0.974 36208 Z= 1.103 Angle : 1.465 63.011 49852 Z= 0.525 Chirality : 2.044 21.451 6080 Planarity : 0.007 0.210 5682 Dihedral : 50.049 179.955 18215 Min Nonbonded Distance : 1.354 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.12), residues: 4078 helix: -0.50 (0.10), residues: 2244 sheet: -1.06 (0.31), residues: 244 loop : -3.71 (0.12), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 44 TYR 0.015 0.001 TYR F 445 PHE 0.025 0.001 PHE C 112 TRP 0.007 0.000 TRP H 248 HIS 0.003 0.000 HIS N 63 Details of bonding type rmsd covalent geometry : bond 0.00782 (36165) covalent geometry : angle 1.35124 (49812) hydrogen bonds : bond 0.13758 ( 1732) hydrogen bonds : angle 5.19259 ( 5133) metal coordination : bond 0.60094 ( 15) metal coordination : angle 20.04432 ( 40) Misc. bond : bond 0.35038 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 860 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ASP cc_start: 0.6001 (m-30) cc_final: 0.5740 (m-30) REVERT: A 204 ILE cc_start: 0.7426 (mm) cc_final: 0.7065 (mm) REVERT: D 311 ILE cc_start: 0.8291 (mt) cc_final: 0.7936 (mt) REVERT: E 81 ILE cc_start: 0.6785 (mm) cc_final: 0.6545 (mt) REVERT: E 91 VAL cc_start: 0.6878 (p) cc_final: 0.6601 (p) REVERT: F 60 TRP cc_start: 0.5934 (t-100) cc_final: 0.5151 (t60) REVERT: F 421 LEU cc_start: 0.7780 (mt) cc_final: 0.7553 (mt) REVERT: F 546 MET cc_start: 0.7719 (ttp) cc_final: 0.7455 (ttm) REVERT: F 586 TYR cc_start: 0.7010 (t80) cc_final: 0.6246 (t80) REVERT: F 605 ASP cc_start: 0.7866 (t70) cc_final: 0.7572 (t0) REVERT: F 649 PHE cc_start: 0.7246 (m-80) cc_final: 0.6983 (m-80) REVERT: H 3 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6680 (pttt) REVERT: H 320 PHE cc_start: 0.7119 (p90) cc_final: 0.6657 (p90) REVERT: I 116 ASN cc_start: 0.7991 (p0) cc_final: 0.7593 (m-40) REVERT: I 168 MET cc_start: 0.3870 (mmp) cc_final: 0.3374 (mmp) REVERT: J 123 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6873 (tt0) REVERT: K 169 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6662 (mt-10) REVERT: M 4 LYS cc_start: 0.7806 (pttp) cc_final: 0.7472 (pttp) REVERT: O 10 LYS cc_start: 0.7308 (tttt) cc_final: 0.6934 (ttmm) outliers start: 0 outliers final: 0 residues processed: 860 average time/residue: 0.2222 time to fit residues: 307.0201 Evaluate side-chains 600 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 208 ASN A 291 ASN B 9 GLN B 340 ASN B 358 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 60 ASN D 65 GLN D 127 GLN D 288 ASN ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 66 HIS F 146 GLN F 247 HIS F 312 GLN F 349 HIS F 600 GLN H 78 ASN I 5 ASN I 76 ASN I 108 ASN J 120 GLN ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN N 8 GLN N 69 HIS N 94 ASN N 118 GLN O 65 GLN P 40 ASN S 55 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.190862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162422 restraints weight = 46326.613| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.79 r_work: 0.3803 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.263 36208 Z= 0.309 Angle : 3.491 54.108 49852 Z= 1.405 Chirality : 0.448 6.784 6080 Planarity : 0.004 0.049 5682 Dihedral : 45.402 179.985 10943 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.03 % Allowed : 11.66 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 4078 helix: 0.62 (0.11), residues: 2286 sheet: -0.59 (0.32), residues: 248 loop : -3.33 (0.13), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 95 TYR 0.023 0.001 TYR K 35 PHE 0.029 0.001 PHE D 277 TRP 0.017 0.001 TRP V 80 HIS 0.010 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00834 (36165) covalent geometry : angle 3.38526 (49812) hydrogen bonds : bond 0.03757 ( 1732) hydrogen bonds : angle 3.92750 ( 5133) metal coordination : bond 0.04468 ( 15) metal coordination : angle 30.23640 ( 40) Misc. bond : bond 0.00544 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 628 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 PHE cc_start: 0.6327 (t80) cc_final: 0.6088 (t80) REVERT: A 111 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 204 ILE cc_start: 0.7652 (mm) cc_final: 0.7332 (mm) REVERT: B 365 LEU cc_start: 0.8157 (mt) cc_final: 0.7822 (mt) REVERT: C 84 PHE cc_start: 0.7530 (m-80) cc_final: 0.7317 (m-80) REVERT: D 384 LEU cc_start: 0.8998 (mt) cc_final: 0.8600 (mm) REVERT: E 44 ASN cc_start: 0.8142 (t0) cc_final: 0.7932 (t0) REVERT: E 91 VAL cc_start: 0.7496 (p) cc_final: 0.7087 (p) REVERT: F 7 TYR cc_start: 0.7846 (m-80) cc_final: 0.7478 (m-80) REVERT: F 60 TRP cc_start: 0.6721 (t-100) cc_final: 0.5607 (t60) REVERT: F 64 GLN cc_start: 0.6550 (tp40) cc_final: 0.5745 (tt0) REVERT: F 280 MET cc_start: 0.8743 (mmm) cc_final: 0.7992 (mmt) REVERT: F 421 LEU cc_start: 0.8004 (mt) cc_final: 0.7791 (mt) REVERT: F 546 MET cc_start: 0.8074 (ttp) cc_final: 0.7794 (ttm) REVERT: F 586 TYR cc_start: 0.7281 (t80) cc_final: 0.6663 (t80) REVERT: G 116 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6592 (mm) REVERT: G 142 ASP cc_start: 0.8108 (m-30) cc_final: 0.7866 (m-30) REVERT: H 320 PHE cc_start: 0.7320 (p90) cc_final: 0.6923 (p90) REVERT: I 108 ASN cc_start: 0.8339 (t160) cc_final: 0.8022 (t0) REVERT: I 116 ASN cc_start: 0.8543 (p0) cc_final: 0.7929 (m-40) REVERT: I 146 TYR cc_start: 0.6880 (t80) cc_final: 0.6631 (t80) REVERT: J 73 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6994 (mm-40) REVERT: J 93 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6645 (pt0) REVERT: J 123 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7405 (tm-30) REVERT: N 139 ARG cc_start: 0.7086 (ptt90) cc_final: 0.6820 (ptt-90) REVERT: O 10 LYS cc_start: 0.7786 (tttt) cc_final: 0.7568 (tttp) REVERT: P 28 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.8020 (mmt90) REVERT: P 29 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7437 (m-40) REVERT: V 80 TRP cc_start: 0.6689 (t60) cc_final: 0.6235 (t60) REVERT: V 115 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6020 (pm20) outliers start: 69 outliers final: 42 residues processed: 658 average time/residue: 0.2050 time to fit residues: 224.4569 Evaluate side-chains 618 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 571 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 56 LEU Chi-restraints excluded: chain V residue 115 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 402 optimal weight: 8.9990 chunk 286 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 299 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 385 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** D 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN F 54 HIS ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS I 95 HIS I 108 ASN J 23 ASN ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 HIS M 11 HIS O 65 GLN P 29 ASN S 64 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115673 restraints weight = 44561.197| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.91 r_work: 0.3159 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.283 36208 Z= 0.444 Angle : 3.542 55.886 49852 Z= 1.448 Chirality : 0.443 6.460 6080 Planarity : 0.007 0.099 5682 Dihedral : 44.946 179.998 10943 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.84 % Favored : 93.06 % Rotamer: Outliers : 4.09 % Allowed : 15.22 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 4078 helix: 0.57 (0.11), residues: 2308 sheet: -0.53 (0.31), residues: 270 loop : -3.23 (0.13), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 69 TYR 0.045 0.003 TYR B 166 PHE 0.061 0.003 PHE F 29 TRP 0.036 0.003 TRP H 70 HIS 0.009 0.002 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.01128 (36165) covalent geometry : angle 3.43165 (49812) hydrogen bonds : bond 0.09445 ( 1732) hydrogen bonds : angle 4.53621 ( 5133) metal coordination : bond 0.03561 ( 15) metal coordination : angle 31.17114 ( 40) Misc. bond : bond 0.00790 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 586 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.7838 (m-30) cc_final: 0.7551 (m-30) REVERT: A 130 MET cc_start: 0.7836 (mtp) cc_final: 0.7588 (mtp) REVERT: A 204 ILE cc_start: 0.8502 (mm) cc_final: 0.8229 (mt) REVERT: A 271 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8322 (mp) REVERT: B 168 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8314 (tt) REVERT: C 110 LEU cc_start: 0.8366 (mt) cc_final: 0.8067 (mp) REVERT: D 161 LYS cc_start: 0.8825 (pttt) cc_final: 0.8582 (ptmm) REVERT: D 253 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7969 (mp) REVERT: D 254 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8732 (mp) REVERT: D 336 MET cc_start: 0.8657 (mtm) cc_final: 0.8293 (mtp) REVERT: D 379 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8667 (t80) REVERT: D 456 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7966 (pp) REVERT: E 1 MET cc_start: 0.7871 (tpp) cc_final: 0.7421 (ttp) REVERT: E 94 GLU cc_start: 0.8077 (pt0) cc_final: 0.7857 (tp30) REVERT: E 100 LYS cc_start: 0.8089 (mttt) cc_final: 0.7856 (mttm) REVERT: F 7 TYR cc_start: 0.8574 (m-80) cc_final: 0.7696 (m-80) REVERT: F 45 MET cc_start: 0.8338 (mmp) cc_final: 0.7972 (mmm) REVERT: F 56 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8058 (mp) REVERT: F 64 GLN cc_start: 0.7919 (tp40) cc_final: 0.7146 (tt0) REVERT: F 85 MET cc_start: 0.8030 (mtt) cc_final: 0.7705 (mtp) REVERT: F 351 TYR cc_start: 0.7976 (m-80) cc_final: 0.7587 (m-10) REVERT: F 367 MET cc_start: 0.8326 (tpp) cc_final: 0.7869 (mmm) REVERT: F 379 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6656 (mt0) REVERT: F 419 GLU cc_start: 0.6299 (tp30) cc_final: 0.6044 (tp30) REVERT: F 546 MET cc_start: 0.7990 (ttp) cc_final: 0.7739 (ttm) REVERT: F 586 TYR cc_start: 0.7296 (t80) cc_final: 0.6598 (t80) REVERT: G 24 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7940 (mm) REVERT: G 166 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7980 (mtm-85) REVERT: H 51 MET cc_start: 0.8851 (mmt) cc_final: 0.8588 (mmt) REVERT: H 105 MET cc_start: 0.8382 (mmt) cc_final: 0.8102 (mmt) REVERT: I 19 LYS cc_start: 0.6905 (tttt) cc_final: 0.6383 (tttt) REVERT: I 116 ASN cc_start: 0.9022 (p0) cc_final: 0.8204 (m-40) REVERT: I 171 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.6606 (t-90) REVERT: J 64 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8643 (tm-30) REVERT: J 145 GLU cc_start: 0.8221 (mp0) cc_final: 0.7890 (mp0) REVERT: K 48 TYR cc_start: 0.8555 (t80) cc_final: 0.7253 (t80) REVERT: K 105 MET cc_start: 0.9110 (mtp) cc_final: 0.8823 (mtp) REVERT: K 168 ASN cc_start: 0.8816 (t0) cc_final: 0.8544 (t0) REVERT: M 38 GLU cc_start: 0.8113 (tp30) cc_final: 0.7291 (tt0) REVERT: M 46 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (mt) REVERT: N 110 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8321 (mptt) REVERT: O 5 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8220 (mtpp) REVERT: O 10 LYS cc_start: 0.7939 (tttt) cc_final: 0.7733 (ttmm) REVERT: P 20 LEU cc_start: 0.8471 (mm) cc_final: 0.8188 (mp) REVERT: R 23 GLU cc_start: 0.5370 (tt0) cc_final: 0.4857 (tm-30) REVERT: R 93 GLU cc_start: 0.6812 (tt0) cc_final: 0.6564 (tt0) REVERT: S 99 VAL cc_start: 0.5750 (OUTLIER) cc_final: 0.5489 (t) REVERT: V 80 TRP cc_start: 0.6967 (t60) cc_final: 0.6569 (t60) REVERT: V 141 LYS cc_start: 0.8342 (mttt) cc_final: 0.7823 (mtmm) outliers start: 139 outliers final: 74 residues processed: 683 average time/residue: 0.2271 time to fit residues: 250.7838 Evaluate side-chains 579 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 493 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 379 GLN Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain K residue 119 ILE Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 99 VAL Chi-restraints excluded: chain V residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 80 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 396 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 67 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 HIS B 230 GLN B 290 ASN C 71 ASN D 127 GLN D 339 HIS D 486 GLN E 87 ASN F 312 GLN F 345 HIS H 14 ASN H 364 GLN K 32 ASN K 104 GLN P 44 HIS S 64 GLN V 140 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124111 restraints weight = 45282.887| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.91 r_work: 0.3249 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.255 36208 Z= 0.301 Angle : 3.448 53.174 49852 Z= 1.399 Chirality : 0.438 6.385 6080 Planarity : 0.005 0.053 5682 Dihedral : 44.813 179.976 10943 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.15 % Allowed : 18.02 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.45 (0.13), residues: 4078 helix: 1.31 (0.11), residues: 2298 sheet: -0.37 (0.31), residues: 274 loop : -3.01 (0.13), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 25 TYR 0.090 0.002 TYR F 629 PHE 0.030 0.001 PHE F 352 TRP 0.018 0.001 TRP H 70 HIS 0.007 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00825 (36165) covalent geometry : angle 3.33761 (49812) hydrogen bonds : bond 0.05046 ( 1732) hydrogen bonds : angle 3.93011 ( 5133) metal coordination : bond 0.02426 ( 15) metal coordination : angle 30.69439 ( 40) Misc. bond : bond 0.00474 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 557 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7427 (mtt) cc_final: 0.7144 (mtm) REVERT: A 47 VAL cc_start: 0.8724 (t) cc_final: 0.8518 (t) REVERT: A 71 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8431 (pp) REVERT: A 79 ASP cc_start: 0.7905 (m-30) cc_final: 0.7557 (m-30) REVERT: A 130 MET cc_start: 0.7571 (mtp) cc_final: 0.7302 (mtp) REVERT: A 316 ILE cc_start: 0.8525 (pt) cc_final: 0.8163 (mt) REVERT: B 302 MET cc_start: 0.8895 (ttp) cc_final: 0.8675 (ttp) REVERT: B 444 VAL cc_start: 0.7996 (t) cc_final: 0.7718 (t) REVERT: B 449 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5660 (tm-30) REVERT: C 125 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7098 (tmm160) REVERT: D 64 MET cc_start: 0.7796 (mtt) cc_final: 0.7099 (mtt) REVERT: D 336 MET cc_start: 0.8289 (mtm) cc_final: 0.7876 (mtp) REVERT: D 372 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8124 (ptm) REVERT: E 1 MET cc_start: 0.7782 (tpp) cc_final: 0.7335 (ttp) REVERT: E 39 ASN cc_start: 0.8281 (m-40) cc_final: 0.7853 (m110) REVERT: E 93 MET cc_start: 0.7765 (mtp) cc_final: 0.7362 (mtp) REVERT: E 94 GLU cc_start: 0.7377 (pt0) cc_final: 0.6962 (tp30) REVERT: E 100 LYS cc_start: 0.8040 (mttt) cc_final: 0.7751 (mttm) REVERT: F 7 TYR cc_start: 0.8466 (m-80) cc_final: 0.7588 (m-80) REVERT: F 45 MET cc_start: 0.8319 (mmp) cc_final: 0.8050 (mmm) REVERT: F 60 TRP cc_start: 0.7404 (t-100) cc_final: 0.5929 (t60) REVERT: F 64 GLN cc_start: 0.7822 (tp40) cc_final: 0.6951 (tt0) REVERT: F 85 MET cc_start: 0.7662 (mtt) cc_final: 0.7396 (mtp) REVERT: F 367 MET cc_start: 0.7939 (tpp) cc_final: 0.7367 (mmm) REVERT: F 546 MET cc_start: 0.7880 (ttp) cc_final: 0.7601 (ttm) REVERT: F 586 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6615 (t80) REVERT: G 24 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8134 (mm) REVERT: G 166 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7868 (mtm-85) REVERT: H 22 MET cc_start: 0.7442 (tpp) cc_final: 0.7220 (tpp) REVERT: H 27 ARG cc_start: 0.8473 (ttt180) cc_final: 0.8135 (ttt-90) REVERT: H 105 MET cc_start: 0.8267 (mmt) cc_final: 0.7989 (mmt) REVERT: H 109 ASN cc_start: 0.8272 (m-40) cc_final: 0.8019 (m-40) REVERT: I 19 LYS cc_start: 0.6863 (tttt) cc_final: 0.6392 (tttt) REVERT: I 116 ASN cc_start: 0.8870 (p0) cc_final: 0.8041 (m-40) REVERT: I 168 MET cc_start: 0.7114 (mmp) cc_final: 0.6696 (mmp) REVERT: I 171 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6409 (t-90) REVERT: J 64 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8613 (tm-30) REVERT: J 145 GLU cc_start: 0.8101 (mp0) cc_final: 0.7736 (mp0) REVERT: K 32 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7738 (t0) REVERT: K 48 TYR cc_start: 0.8489 (t80) cc_final: 0.7313 (t80) REVERT: N 58 TYR cc_start: 0.8229 (m-80) cc_final: 0.7996 (m-80) REVERT: N 110 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8450 (mptt) REVERT: N 136 ARG cc_start: 0.7523 (ttt90) cc_final: 0.7311 (mtp85) REVERT: O 10 LYS cc_start: 0.7837 (tttt) cc_final: 0.7482 (ttmt) REVERT: P 20 LEU cc_start: 0.8419 (mm) cc_final: 0.8122 (mp) REVERT: R 54 GLU cc_start: 0.5638 (pm20) cc_final: 0.5391 (pm20) REVERT: R 93 GLU cc_start: 0.7019 (tt0) cc_final: 0.6771 (tt0) REVERT: V 80 TRP cc_start: 0.6729 (t60) cc_final: 0.6225 (t60) REVERT: V 141 LYS cc_start: 0.8092 (mttt) cc_final: 0.7652 (mtmm) outliers start: 107 outliers final: 67 residues processed: 621 average time/residue: 0.2152 time to fit residues: 221.2864 Evaluate side-chains 587 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 512 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 312 GLN Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 374 ASN Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain F residue 652 PHE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 388 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 317 optimal weight: 0.9980 chunk 402 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 300 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 396 optimal weight: 8.9990 chunk 267 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 127 GLN E 87 ASN F 460 ASN ** G 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 267 GLN H 361 ASN K 32 ASN S 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.151851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116781 restraints weight = 44993.386| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.00 r_work: 0.3096 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.252 36208 Z= 0.340 Angle : 3.456 51.256 49852 Z= 1.406 Chirality : 0.438 6.415 6080 Planarity : 0.005 0.056 5682 Dihedral : 44.894 179.982 10943 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 4.12 % Allowed : 18.78 % Favored : 77.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.38 (0.13), residues: 4078 helix: 1.32 (0.11), residues: 2317 sheet: -0.14 (0.32), residues: 265 loop : -2.95 (0.13), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 131 TYR 0.063 0.002 TYR F 629 PHE 0.033 0.002 PHE K 67 TRP 0.019 0.002 TRP A 330 HIS 0.009 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00919 (36165) covalent geometry : angle 3.34738 (49812) hydrogen bonds : bond 0.06581 ( 1732) hydrogen bonds : angle 4.03074 ( 5133) metal coordination : bond 0.02764 ( 15) metal coordination : angle 30.54030 ( 40) Misc. bond : bond 0.00405 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 503 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8614 (pp) REVERT: A 79 ASP cc_start: 0.7886 (m-30) cc_final: 0.7560 (m-30) REVERT: A 258 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.5904 (m-80) REVERT: B 168 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8103 (tt) REVERT: B 335 VAL cc_start: 0.8741 (t) cc_final: 0.8323 (m) REVERT: C 92 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7460 (t80) REVERT: C 125 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7174 (tmm160) REVERT: D 336 MET cc_start: 0.8322 (mtm) cc_final: 0.7962 (mtp) REVERT: D 379 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8635 (t80) REVERT: D 500 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7002 (mtp85) REVERT: E 1 MET cc_start: 0.7814 (tpp) cc_final: 0.7458 (ttp) REVERT: E 93 MET cc_start: 0.8188 (mtp) cc_final: 0.7853 (mtp) REVERT: E 94 GLU cc_start: 0.7547 (pt0) cc_final: 0.7300 (tp30) REVERT: E 100 LYS cc_start: 0.8133 (mttt) cc_final: 0.7705 (mttm) REVERT: F 7 TYR cc_start: 0.8624 (m-80) cc_final: 0.7686 (m-80) REVERT: F 45 MET cc_start: 0.8439 (mmp) cc_final: 0.8228 (mmm) REVERT: F 64 GLN cc_start: 0.7879 (tp40) cc_final: 0.7087 (tt0) REVERT: F 85 MET cc_start: 0.8006 (mtt) cc_final: 0.7640 (mtp) REVERT: F 334 MET cc_start: 0.8795 (tpp) cc_final: 0.8574 (ttm) REVERT: F 367 MET cc_start: 0.8123 (tpp) cc_final: 0.7458 (mmm) REVERT: F 376 ASP cc_start: 0.8170 (t70) cc_final: 0.7776 (t70) REVERT: F 446 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8267 (tpp) REVERT: F 586 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6614 (t80) REVERT: G 24 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8003 (mm) REVERT: G 166 ARG cc_start: 0.8303 (mtm180) cc_final: 0.8048 (mtm-85) REVERT: H 51 MET cc_start: 0.8709 (mmt) cc_final: 0.8487 (mmt) REVERT: H 105 MET cc_start: 0.8356 (mmt) cc_final: 0.8011 (mmt) REVERT: H 109 ASN cc_start: 0.8507 (m-40) cc_final: 0.8273 (m-40) REVERT: I 19 LYS cc_start: 0.6778 (tttt) cc_final: 0.6283 (tttt) REVERT: I 116 ASN cc_start: 0.8841 (p0) cc_final: 0.7910 (m-40) REVERT: J 64 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8738 (tm-30) REVERT: J 145 GLU cc_start: 0.8209 (mp0) cc_final: 0.7902 (mp0) REVERT: N 58 TYR cc_start: 0.8239 (m-80) cc_final: 0.8027 (m-80) REVERT: N 110 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8459 (mptt) REVERT: N 136 ARG cc_start: 0.7760 (ttt90) cc_final: 0.7440 (mtp85) REVERT: O 10 LYS cc_start: 0.7825 (tttt) cc_final: 0.7463 (ttmt) REVERT: P 20 LEU cc_start: 0.8462 (mm) cc_final: 0.8155 (mp) REVERT: R 54 GLU cc_start: 0.5920 (pm20) cc_final: 0.5631 (pm20) REVERT: R 93 GLU cc_start: 0.6881 (tt0) cc_final: 0.6598 (tt0) REVERT: V 80 TRP cc_start: 0.6615 (t60) cc_final: 0.6259 (t60) REVERT: V 141 LYS cc_start: 0.8031 (mttt) cc_final: 0.7545 (mtmm) outliers start: 140 outliers final: 96 residues processed: 592 average time/residue: 0.2151 time to fit residues: 211.9600 Evaluate side-chains 595 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 490 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 388 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 374 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 330 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 378 optimal weight: 0.9990 chunk 382 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN E 87 ASN H 14 ASN H 19 HIS S 64 GLN V 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.158298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122838 restraints weight = 44332.972| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.02 r_work: 0.3197 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.253 36208 Z= 0.296 Angle : 3.429 52.675 49852 Z= 1.392 Chirality : 0.436 6.382 6080 Planarity : 0.004 0.053 5682 Dihedral : 44.925 179.973 10943 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 3.65 % Allowed : 19.84 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.00 (0.13), residues: 4078 helix: 1.65 (0.11), residues: 2302 sheet: 0.02 (0.33), residues: 255 loop : -2.79 (0.13), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 500 TYR 0.051 0.001 TYR F 629 PHE 0.027 0.001 PHE R 64 TRP 0.020 0.001 TRP C 124 HIS 0.009 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00820 (36165) covalent geometry : angle 3.31840 (49812) hydrogen bonds : bond 0.04702 ( 1732) hydrogen bonds : angle 3.79602 ( 5133) metal coordination : bond 0.02108 ( 15) metal coordination : angle 30.72839 ( 40) Misc. bond : bond 0.00378 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 514 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7524 (mtt) cc_final: 0.7215 (mtm) REVERT: A 47 VAL cc_start: 0.8606 (t) cc_final: 0.8405 (t) REVERT: A 71 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8524 (pp) REVERT: A 258 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: C 92 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7364 (t80) REVERT: D 136 MET cc_start: 0.8906 (tpt) cc_final: 0.8349 (tpt) REVERT: D 172 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: D 254 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8228 (mp) REVERT: D 336 MET cc_start: 0.8040 (mtm) cc_final: 0.7776 (mtp) REVERT: D 379 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8639 (t80) REVERT: D 387 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7579 (mt) REVERT: E 1 MET cc_start: 0.7831 (tpp) cc_final: 0.7456 (ttp) REVERT: E 93 MET cc_start: 0.7998 (mtp) cc_final: 0.7588 (mtp) REVERT: E 94 GLU cc_start: 0.7539 (pt0) cc_final: 0.7188 (tp30) REVERT: E 100 LYS cc_start: 0.7953 (mttt) cc_final: 0.7375 (mmtt) REVERT: F 7 TYR cc_start: 0.8504 (m-80) cc_final: 0.7562 (m-80) REVERT: F 60 TRP cc_start: 0.7475 (t-100) cc_final: 0.5830 (t60) REVERT: F 64 GLN cc_start: 0.7612 (tp40) cc_final: 0.6747 (tt0) REVERT: F 85 MET cc_start: 0.7939 (mtt) cc_final: 0.7599 (mtp) REVERT: F 367 MET cc_start: 0.7798 (tpp) cc_final: 0.7182 (mmm) REVERT: F 586 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6731 (t80) REVERT: G 24 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7791 (mm) REVERT: G 166 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7883 (mtm180) REVERT: H 27 ARG cc_start: 0.8471 (ttt180) cc_final: 0.8204 (mmm-85) REVERT: H 105 MET cc_start: 0.8296 (mmt) cc_final: 0.8027 (mmt) REVERT: H 109 ASN cc_start: 0.8434 (m-40) cc_final: 0.8178 (m-40) REVERT: I 19 LYS cc_start: 0.6702 (tttt) cc_final: 0.6302 (tttt) REVERT: I 148 VAL cc_start: 0.8311 (t) cc_final: 0.8109 (p) REVERT: I 168 MET cc_start: 0.7478 (mmp) cc_final: 0.6226 (mmm) REVERT: I 171 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.6680 (t-90) REVERT: J 64 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8753 (tm-30) REVERT: K 156 MET cc_start: 0.8761 (mmm) cc_final: 0.8480 (mtt) REVERT: N 26 GLU cc_start: 0.8721 (pp20) cc_final: 0.8120 (pp20) REVERT: N 131 GLU cc_start: 0.7797 (mp0) cc_final: 0.7441 (mp0) REVERT: O 10 LYS cc_start: 0.7707 (tttt) cc_final: 0.7370 (ttmt) REVERT: P 20 LEU cc_start: 0.8416 (mm) cc_final: 0.8093 (mp) REVERT: R 6 THR cc_start: 0.5062 (OUTLIER) cc_final: 0.4789 (t) REVERT: R 54 GLU cc_start: 0.5650 (pm20) cc_final: 0.5338 (pm20) REVERT: R 56 GLU cc_start: 0.5523 (mm-30) cc_final: 0.5063 (pp20) REVERT: R 85 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6198 (t70) REVERT: R 93 GLU cc_start: 0.6965 (tt0) cc_final: 0.6714 (tt0) REVERT: V 52 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.5079 (m-80) REVERT: V 80 TRP cc_start: 0.6477 (t60) cc_final: 0.6127 (t60) REVERT: V 141 LYS cc_start: 0.8027 (mttt) cc_final: 0.7623 (mtmm) outliers start: 124 outliers final: 81 residues processed: 592 average time/residue: 0.2099 time to fit residues: 206.6879 Evaluate side-chains 585 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 491 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 330 MET Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 388 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 105 SER Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 327 optimal weight: 0.9990 chunk 137 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 236 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN A 208 ASN B 230 GLN C 71 ASN D 127 GLN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN J 23 ASN S 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121536 restraints weight = 44750.116| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.96 r_work: 0.3228 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.253 36208 Z= 0.295 Angle : 3.425 51.491 49852 Z= 1.390 Chirality : 0.435 6.379 6080 Planarity : 0.004 0.053 5682 Dihedral : 44.998 179.880 10943 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.70 % Rotamer: Outliers : 3.47 % Allowed : 20.25 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.20 (0.13), residues: 4078 helix: 1.80 (0.11), residues: 2304 sheet: 0.26 (0.35), residues: 233 loop : -2.67 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 500 TYR 0.037 0.001 TYR F 629 PHE 0.027 0.001 PHE F 29 TRP 0.017 0.001 TRP B 62 HIS 0.008 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00821 (36165) covalent geometry : angle 3.31443 (49812) hydrogen bonds : bond 0.04534 ( 1732) hydrogen bonds : angle 3.71584 ( 5133) metal coordination : bond 0.01998 ( 15) metal coordination : angle 30.62865 ( 40) Misc. bond : bond 0.00367 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 506 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7511 (mtt) cc_final: 0.7174 (mtt) REVERT: A 45 VAL cc_start: 0.7006 (OUTLIER) cc_final: 0.6712 (t) REVERT: A 71 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8471 (pp) REVERT: A 258 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6061 (m-10) REVERT: C 125 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7777 (tpt90) REVERT: D 44 ILE cc_start: 0.8141 (pt) cc_final: 0.7748 (mt) REVERT: D 172 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: D 254 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8202 (mp) REVERT: D 336 MET cc_start: 0.7933 (mtm) cc_final: 0.7688 (mtp) REVERT: D 379 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8657 (t80) REVERT: D 387 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7701 (mt) REVERT: E 1 MET cc_start: 0.7837 (tpp) cc_final: 0.7416 (ttp) REVERT: E 94 GLU cc_start: 0.7576 (pt0) cc_final: 0.7336 (tp30) REVERT: E 100 LYS cc_start: 0.8023 (mttt) cc_final: 0.7471 (mmtt) REVERT: F 7 TYR cc_start: 0.8567 (m-80) cc_final: 0.7617 (m-80) REVERT: F 45 MET cc_start: 0.8200 (mmp) cc_final: 0.7602 (mmt) REVERT: F 60 TRP cc_start: 0.7523 (t-100) cc_final: 0.5890 (t60) REVERT: F 64 GLN cc_start: 0.7714 (tp40) cc_final: 0.6837 (tt0) REVERT: F 85 MET cc_start: 0.8000 (mtt) cc_final: 0.7686 (mtp) REVERT: F 367 MET cc_start: 0.7827 (tpp) cc_final: 0.7217 (mmm) REVERT: F 376 ASP cc_start: 0.8146 (t70) cc_final: 0.7707 (t70) REVERT: F 402 CYS cc_start: 0.8233 (m) cc_final: 0.7940 (m) REVERT: F 445 TYR cc_start: 0.7841 (p90) cc_final: 0.7410 (p90) REVERT: F 586 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.6839 (t80) REVERT: G 24 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7914 (mm) REVERT: G 166 ARG cc_start: 0.8259 (mtm180) cc_final: 0.7983 (mtm180) REVERT: H 27 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8262 (mmm-85) REVERT: H 105 MET cc_start: 0.8346 (mmt) cc_final: 0.8073 (mmt) REVERT: H 109 ASN cc_start: 0.8474 (m-40) cc_final: 0.8244 (m-40) REVERT: I 19 LYS cc_start: 0.6630 (tttt) cc_final: 0.6219 (tttt) REVERT: I 168 MET cc_start: 0.7422 (mmp) cc_final: 0.6236 (mmm) REVERT: I 171 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.6687 (t-90) REVERT: J 64 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8755 (tm-30) REVERT: K 156 MET cc_start: 0.8790 (mmm) cc_final: 0.8567 (mtt) REVERT: N 26 GLU cc_start: 0.8702 (pp20) cc_final: 0.8117 (pp20) REVERT: N 47 MET cc_start: 0.7860 (tpt) cc_final: 0.7283 (mtt) REVERT: N 131 GLU cc_start: 0.7904 (mp0) cc_final: 0.7554 (mp0) REVERT: P 20 LEU cc_start: 0.8469 (mm) cc_final: 0.8150 (mp) REVERT: R 6 THR cc_start: 0.5130 (OUTLIER) cc_final: 0.4791 (t) REVERT: R 56 GLU cc_start: 0.5341 (mm-30) cc_final: 0.5029 (pp20) REVERT: R 93 GLU cc_start: 0.6980 (tt0) cc_final: 0.6737 (tt0) REVERT: V 52 PHE cc_start: 0.6311 (OUTLIER) cc_final: 0.5303 (m-80) REVERT: V 80 TRP cc_start: 0.6464 (t60) cc_final: 0.6105 (t60) REVERT: V 140 GLN cc_start: 0.8319 (mt0) cc_final: 0.8020 (mt0) REVERT: V 141 LYS cc_start: 0.8043 (mttt) cc_final: 0.7588 (mtmm) outliers start: 118 outliers final: 83 residues processed: 582 average time/residue: 0.2018 time to fit residues: 197.0220 Evaluate side-chains 589 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 494 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 388 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 111 optimal weight: 1.9990 chunk 384 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 363 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 400 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 127 GLN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN S 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119990 restraints weight = 44591.135| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.95 r_work: 0.3196 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 36208 Z= 0.299 Angle : 3.428 51.065 49852 Z= 1.392 Chirality : 0.434 6.387 6080 Planarity : 0.004 0.054 5682 Dihedral : 45.038 179.970 10943 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 3.56 % Allowed : 20.25 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.26 (0.13), residues: 4078 helix: 1.81 (0.11), residues: 2310 sheet: 0.37 (0.35), residues: 230 loop : -2.61 (0.14), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 73 TYR 0.037 0.001 TYR F 629 PHE 0.034 0.001 PHE F 24 TRP 0.017 0.001 TRP B 62 HIS 0.005 0.001 HIS N 63 Details of bonding type rmsd covalent geometry : bond 0.00830 (36165) covalent geometry : angle 3.31795 (49812) hydrogen bonds : bond 0.04890 ( 1732) hydrogen bonds : angle 3.74414 ( 5133) metal coordination : bond 0.02103 ( 15) metal coordination : angle 30.57390 ( 40) Misc. bond : bond 0.00263 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 500 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8500 (pp) REVERT: A 258 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6044 (m-10) REVERT: B 64 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: C 92 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7440 (t80) REVERT: C 125 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7815 (tpt90) REVERT: D 44 ILE cc_start: 0.8132 (pt) cc_final: 0.7776 (mt) REVERT: D 136 MET cc_start: 0.8907 (tpt) cc_final: 0.8478 (tpt) REVERT: D 172 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: D 254 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8180 (mp) REVERT: D 379 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8702 (t80) REVERT: E 1 MET cc_start: 0.7926 (tpp) cc_final: 0.7541 (ttp) REVERT: E 93 MET cc_start: 0.8002 (mtp) cc_final: 0.7662 (mtp) REVERT: E 94 GLU cc_start: 0.7675 (pt0) cc_final: 0.7448 (tp30) REVERT: E 100 LYS cc_start: 0.8010 (mttt) cc_final: 0.7440 (mmtt) REVERT: F 7 TYR cc_start: 0.8591 (m-80) cc_final: 0.7555 (m-80) REVERT: F 45 MET cc_start: 0.8225 (mmp) cc_final: 0.7607 (mmt) REVERT: F 60 TRP cc_start: 0.7560 (t-100) cc_final: 0.5974 (t60) REVERT: F 64 GLN cc_start: 0.7675 (tp40) cc_final: 0.6771 (tt0) REVERT: F 85 MET cc_start: 0.8124 (mtt) cc_final: 0.7793 (mtp) REVERT: F 334 MET cc_start: 0.8617 (ttm) cc_final: 0.8380 (tpp) REVERT: F 367 MET cc_start: 0.7859 (tpp) cc_final: 0.7257 (mmm) REVERT: F 376 ASP cc_start: 0.8195 (t70) cc_final: 0.7727 (t70) REVERT: F 402 CYS cc_start: 0.8252 (m) cc_final: 0.7771 (m) REVERT: F 446 MET cc_start: 0.8141 (tpp) cc_final: 0.7867 (tpp) REVERT: F 586 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6801 (t80) REVERT: G 24 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7904 (mm) REVERT: G 166 ARG cc_start: 0.8296 (mtm180) cc_final: 0.8003 (mtm180) REVERT: H 27 ARG cc_start: 0.8509 (ttt180) cc_final: 0.8278 (mmm-85) REVERT: H 105 MET cc_start: 0.8366 (mmt) cc_final: 0.8103 (mmt) REVERT: H 109 ASN cc_start: 0.8474 (m-40) cc_final: 0.8249 (m-40) REVERT: I 19 LYS cc_start: 0.6678 (tttt) cc_final: 0.6258 (tttt) REVERT: I 131 ARG cc_start: 0.8799 (ptt-90) cc_final: 0.8397 (tmm160) REVERT: I 168 MET cc_start: 0.7547 (mmp) cc_final: 0.6299 (mmm) REVERT: I 171 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.6595 (t-90) REVERT: J 64 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8758 (tm-30) REVERT: J 106 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7464 (mtm180) REVERT: K 156 MET cc_start: 0.8752 (mmm) cc_final: 0.8520 (mtt) REVERT: N 26 GLU cc_start: 0.8726 (pp20) cc_final: 0.8130 (pp20) REVERT: N 47 MET cc_start: 0.7886 (tpt) cc_final: 0.7299 (mtt) REVERT: N 106 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7892 (ttmm) REVERT: N 131 GLU cc_start: 0.7906 (mp0) cc_final: 0.7473 (mp0) REVERT: P 20 LEU cc_start: 0.8453 (mm) cc_final: 0.8120 (mp) REVERT: R 6 THR cc_start: 0.5243 (OUTLIER) cc_final: 0.4903 (t) REVERT: R 56 GLU cc_start: 0.5415 (mm-30) cc_final: 0.5158 (pp20) REVERT: R 93 GLU cc_start: 0.7043 (tt0) cc_final: 0.6799 (tt0) REVERT: V 52 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.5221 (m-80) REVERT: V 80 TRP cc_start: 0.6673 (t60) cc_final: 0.6328 (t60) REVERT: V 93 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6233 (mm-30) REVERT: V 141 LYS cc_start: 0.8025 (mttt) cc_final: 0.7518 (mtmm) outliers start: 121 outliers final: 89 residues processed: 578 average time/residue: 0.2031 time to fit residues: 196.6518 Evaluate side-chains 593 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 490 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 388 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 171 HIS Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 93 GLU Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 230 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 356 optimal weight: 0.4980 chunk 178 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 311 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 127 GLN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN S 64 GLN V 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.119801 restraints weight = 44217.026| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.95 r_work: 0.3195 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 36208 Z= 0.297 Angle : 3.427 50.929 49852 Z= 1.392 Chirality : 0.434 6.382 6080 Planarity : 0.004 0.054 5682 Dihedral : 45.062 179.981 10943 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 3.41 % Allowed : 20.61 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.34 (0.14), residues: 4078 helix: 1.86 (0.11), residues: 2313 sheet: 0.51 (0.34), residues: 244 loop : -2.59 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 73 TYR 0.035 0.001 TYR F 629 PHE 0.026 0.001 PHE F 352 TRP 0.019 0.001 TRP C 124 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00827 (36165) covalent geometry : angle 3.31690 (49812) hydrogen bonds : bond 0.04828 ( 1732) hydrogen bonds : angle 3.73727 ( 5133) metal coordination : bond 0.02072 ( 15) metal coordination : angle 30.57918 ( 40) Misc. bond : bond 0.00280 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 503 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.7040 (t) cc_final: 0.6722 (t) REVERT: A 71 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8494 (pp) REVERT: A 258 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6070 (m-10) REVERT: B 64 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: C 92 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7447 (t80) REVERT: C 125 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7780 (tpt90) REVERT: D 44 ILE cc_start: 0.8103 (pt) cc_final: 0.7778 (mt) REVERT: D 136 MET cc_start: 0.8939 (tpt) cc_final: 0.8479 (tpt) REVERT: D 172 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: D 254 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8151 (mp) REVERT: D 336 MET cc_start: 0.7917 (mtm) cc_final: 0.7669 (mtp) REVERT: D 379 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8639 (t80) REVERT: E 1 MET cc_start: 0.7934 (tpp) cc_final: 0.7559 (ttp) REVERT: E 100 LYS cc_start: 0.8001 (mttt) cc_final: 0.7436 (mmtt) REVERT: F 7 TYR cc_start: 0.8611 (m-80) cc_final: 0.7581 (m-80) REVERT: F 45 MET cc_start: 0.8189 (mmp) cc_final: 0.7574 (mmt) REVERT: F 64 GLN cc_start: 0.7661 (tp40) cc_final: 0.6850 (tt0) REVERT: F 85 MET cc_start: 0.8142 (mtt) cc_final: 0.7807 (mtp) REVERT: F 334 MET cc_start: 0.8605 (ttm) cc_final: 0.8388 (tpp) REVERT: F 367 MET cc_start: 0.7817 (tpp) cc_final: 0.7236 (mmm) REVERT: F 376 ASP cc_start: 0.8216 (t70) cc_final: 0.7761 (t70) REVERT: F 402 CYS cc_start: 0.8193 (m) cc_final: 0.7855 (m) REVERT: F 586 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6796 (t80) REVERT: G 24 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7884 (mm) REVERT: G 166 ARG cc_start: 0.8335 (mtm180) cc_final: 0.8033 (mtm180) REVERT: H 27 ARG cc_start: 0.8514 (ttt180) cc_final: 0.8271 (mmm-85) REVERT: H 105 MET cc_start: 0.8337 (mmt) cc_final: 0.8068 (mmt) REVERT: H 109 ASN cc_start: 0.8425 (m-40) cc_final: 0.8186 (m-40) REVERT: I 19 LYS cc_start: 0.6800 (tttt) cc_final: 0.6380 (tttt) REVERT: I 131 ARG cc_start: 0.8762 (ptt-90) cc_final: 0.8401 (tmm160) REVERT: J 64 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8769 (tm-30) REVERT: J 106 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7435 (mtm110) REVERT: K 156 MET cc_start: 0.8736 (mmm) cc_final: 0.8505 (mtt) REVERT: N 26 GLU cc_start: 0.8728 (pp20) cc_final: 0.8131 (pp20) REVERT: N 47 MET cc_start: 0.7923 (tpt) cc_final: 0.7346 (mtt) REVERT: N 106 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7870 (ttmm) REVERT: P 20 LEU cc_start: 0.8457 (mm) cc_final: 0.8110 (mp) REVERT: R 6 THR cc_start: 0.5242 (OUTLIER) cc_final: 0.4913 (t) REVERT: R 56 GLU cc_start: 0.5568 (mm-30) cc_final: 0.5157 (pp20) REVERT: R 93 GLU cc_start: 0.7034 (tt0) cc_final: 0.6777 (tt0) REVERT: S 80 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7515 (tp30) REVERT: V 52 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5015 (m-80) REVERT: V 80 TRP cc_start: 0.6683 (t60) cc_final: 0.6345 (t60) REVERT: V 141 LYS cc_start: 0.8002 (mttt) cc_final: 0.7516 (mtmm) outliers start: 116 outliers final: 91 residues processed: 576 average time/residue: 0.2034 time to fit residues: 195.8248 Evaluate side-chains 597 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 492 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 553 LEU Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 388 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 40 ASN Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 260 optimal weight: 0.7980 chunk 379 optimal weight: 1.9990 chunk 389 optimal weight: 10.0000 chunk 401 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 172 optimal weight: 0.4980 chunk 298 optimal weight: 20.0000 chunk 195 optimal weight: 0.0270 chunk 130 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 127 GLN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 HIS ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN S 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122815 restraints weight = 44802.312| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.96 r_work: 0.3234 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.252 36208 Z= 0.291 Angle : 3.422 51.838 49852 Z= 1.389 Chirality : 0.433 6.371 6080 Planarity : 0.004 0.053 5682 Dihedral : 45.097 179.972 10943 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.06 % Allowed : 21.22 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.46 (0.14), residues: 4078 helix: 1.95 (0.11), residues: 2311 sheet: 0.63 (0.35), residues: 242 loop : -2.53 (0.14), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 235 TYR 0.032 0.001 TYR F 629 PHE 0.025 0.001 PHE F 352 TRP 0.023 0.001 TRP H 248 HIS 0.006 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00813 (36165) covalent geometry : angle 3.31094 (49812) hydrogen bonds : bond 0.04206 ( 1732) hydrogen bonds : angle 3.67213 ( 5133) metal coordination : bond 0.01822 ( 15) metal coordination : angle 30.65335 ( 40) Misc. bond : bond 0.00239 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8156 Ramachandran restraints generated. 4078 Oldfield, 0 Emsley, 4078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 510 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.7003 (OUTLIER) cc_final: 0.6708 (t) REVERT: A 258 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6197 (m-10) REVERT: B 64 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: C 92 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7391 (t80) REVERT: D 44 ILE cc_start: 0.8025 (pt) cc_final: 0.7756 (mt) REVERT: D 136 MET cc_start: 0.8874 (tpt) cc_final: 0.8413 (tpt) REVERT: D 172 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: D 379 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8663 (t80) REVERT: D 392 MET cc_start: 0.7967 (mpt) cc_final: 0.7411 (mpt) REVERT: E 1 MET cc_start: 0.7918 (tpp) cc_final: 0.7543 (ttp) REVERT: E 100 LYS cc_start: 0.7939 (mttt) cc_final: 0.7374 (mmtt) REVERT: F 7 TYR cc_start: 0.8595 (m-80) cc_final: 0.7568 (m-80) REVERT: F 45 MET cc_start: 0.8212 (mmp) cc_final: 0.7627 (mmt) REVERT: F 64 GLN cc_start: 0.7685 (tp40) cc_final: 0.6889 (tt0) REVERT: F 85 MET cc_start: 0.8061 (mtt) cc_final: 0.7727 (mtp) REVERT: F 367 MET cc_start: 0.7773 (tpp) cc_final: 0.7246 (mmm) REVERT: F 376 ASP cc_start: 0.8178 (t70) cc_final: 0.7726 (t70) REVERT: F 402 CYS cc_start: 0.8158 (m) cc_final: 0.7673 (m) REVERT: F 419 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6734 (tp30) REVERT: F 586 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6773 (t80) REVERT: G 24 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7856 (mm) REVERT: G 121 GLN cc_start: 0.7542 (mp10) cc_final: 0.7122 (tp40) REVERT: G 166 ARG cc_start: 0.8285 (mtm180) cc_final: 0.8029 (mtm180) REVERT: H 27 ARG cc_start: 0.8486 (ttt180) cc_final: 0.8258 (mmm-85) REVERT: H 335 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8275 (mmtm) REVERT: I 19 LYS cc_start: 0.6773 (tttt) cc_final: 0.6357 (tttt) REVERT: I 131 ARG cc_start: 0.8703 (ptt-90) cc_final: 0.8369 (tmm160) REVERT: J 64 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8765 (tm-30) REVERT: J 106 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7426 (mtm110) REVERT: K 60 MET cc_start: 0.8480 (ttp) cc_final: 0.8098 (ttp) REVERT: K 156 MET cc_start: 0.8704 (mmm) cc_final: 0.8465 (mtt) REVERT: N 47 MET cc_start: 0.7900 (tpt) cc_final: 0.7352 (mtt) REVERT: N 106 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7867 (ttmm) REVERT: O 10 LYS cc_start: 0.7802 (tttt) cc_final: 0.7549 (ttmm) REVERT: P 20 LEU cc_start: 0.8437 (mm) cc_final: 0.8086 (mp) REVERT: R 6 THR cc_start: 0.5224 (OUTLIER) cc_final: 0.4891 (t) REVERT: R 56 GLU cc_start: 0.5670 (mm-30) cc_final: 0.5304 (pp20) REVERT: R 93 GLU cc_start: 0.7027 (tt0) cc_final: 0.6778 (tt0) REVERT: S 80 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7506 (tp30) REVERT: V 52 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5166 (m-80) REVERT: V 80 TRP cc_start: 0.6628 (t60) cc_final: 0.6296 (t60) REVERT: V 141 LYS cc_start: 0.7935 (mttt) cc_final: 0.7473 (mtmm) outliers start: 104 outliers final: 82 residues processed: 575 average time/residue: 0.2088 time to fit residues: 199.3418 Evaluate side-chains 592 residues out of total 3399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 498 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 280 TRP Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 446 ASN Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 480 HIS Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 388 ILE Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 93 GLU Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 114 MET Chi-restraints excluded: chain K residue 130 SER Chi-restraints excluded: chain K residue 136 ASP Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 5 SER Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 96 SER Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 106 LYS Chi-restraints excluded: chain N residue 140 TRP Chi-restraints excluded: chain P residue 14 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain V residue 52 PHE Chi-restraints excluded: chain V residue 53 LEU Chi-restraints excluded: chain V residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 168 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 291 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 336 optimal weight: 0.9990 chunk 87 optimal weight: 0.0970 chunk 133 optimal weight: 3.9990 chunk 401 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN C 71 ASN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122531 restraints weight = 44684.009| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.95 r_work: 0.3232 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.251 36208 Z= 0.291 Angle : 3.422 51.280 49852 Z= 1.389 Chirality : 0.433 6.376 6080 Planarity : 0.004 0.057 5682 Dihedral : 45.124 179.997 10943 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.06 % Allowed : 21.49 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.52 (0.14), residues: 4078 helix: 1.99 (0.11), residues: 2311 sheet: 0.66 (0.34), residues: 243 loop : -2.51 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 500 TYR 0.030 0.001 TYR H 182 PHE 0.026 0.001 PHE R 64 TRP 0.022 0.001 TRP F 60 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00813 (36165) covalent geometry : angle 3.31162 (49812) hydrogen bonds : bond 0.04252 ( 1732) hydrogen bonds : angle 3.65236 ( 5133) metal coordination : bond 0.01851 ( 15) metal coordination : angle 30.58751 ( 40) Misc. bond : bond 0.00231 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12293.36 seconds wall clock time: 209 minutes 42.49 seconds (12582.49 seconds total)