Starting phenix.real_space_refine on Mon Sep 14 22:57:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.map" model { file = "/net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6l7p_0850/09_2026/6l7p_0850.cif" } resolution = 3.6 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= 0.001 sd= 0.010 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 12 7.16 5 P 9 5.49 5 S 172 5.16 5 C 21995 2.51 5 N 4929 2.21 5 O 5681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 262 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32798 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2820 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 1 Chain: "B" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3723 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 18, 'TRANS': 473} 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: 4997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 4997 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 613} 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: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1454 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} 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: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1516 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 176} 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: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1550 Classifications: {'peptide': 200} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 180} Chain breaks: 1 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: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} 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: "S" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 366 Unusual residues: {'AJP': 3, 'BCR': 1, 'DGD': 2, 'LHG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 72 Chain: "B" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 483 Unusual residues: {'AJP': 11, 'LHG': 2, 'PQN': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 638 Unresolved non-hydrogen angles: 957 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 264 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: 2 Unresolved non-hydrogen chiralities: 48 Chain: "D" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 606 Unusual residues: {'AJP': 10, 'BCR': 2, 'LHG': 2, 'SQD': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 580 Unresolved non-hydrogen angles: 870 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 240 Chain: "F" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 440 Unusual residues: {'AJP': 9, 'LHG': 2, 'SQD': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 783 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 216 Chain: "G" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 241 Unusual residues: {'AJP': 6, 'LHG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 522 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 144 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: "Q" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'AJP': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 72 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22666 SG CYS I 103 41.406 50.809 51.256 1.00 34.32 S ATOM 22710 SG CYS I 109 37.410 45.086 48.605 1.00 44.55 S ATOM 22415 SG CYS I 73 40.302 44.143 53.740 1.00 38.15 S ATOM 22384 SG CYS I 69 33.105 41.861 50.741 1.00 49.34 S ATOM 22343 SG CYS I 63 25.446 43.586 50.122 1.00 64.42 S ATOM 22362 SG CYS I 66 28.274 37.391 49.649 1.00 61.86 S ATOM 25447 SG CYS K 117 52.703 53.581 56.461 1.00 26.71 S ATOM 24949 SG CYS K 53 54.171 57.049 52.151 1.00 31.57 S ATOM 24943 SG CYS K 52 56.439 53.011 50.020 1.00 34.49 S ATOM 25673 SG CYS K 148 49.442 51.384 51.744 1.00 31.62 S Time building chain proxies: 5.52, per 1000 atoms: 0.17 Number of scatterers: 32798 At special positions: 0 Unit cell: (224.54, 139.52, 175.49, 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 12 26.01 S 172 16.00 P 9 15.00 O 5681 8.00 N 4929 7.00 C 21995 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=22, symmetry=0 Number of additional bonds: simple=22, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 73 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 109 " 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="FE2 SF4 I 202 " - pdb=" SG CYS I 69 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 113 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 117 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 117 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 53 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 148 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 52 " Number of angles added : 39 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 18 sheets defined 61.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.747A pdb=" N LEU A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 4.028A pdb=" N LEU A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 60 " --> pdb=" O SER A 56 " (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 140 removed outlier: 4.065A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.846A pdb=" N GLY A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 removed outlier: 3.755A pdb=" N LEU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 172 " --> pdb=" O GLN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.695A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.529A pdb=" N ILE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 206 removed outlier: 3.736A pdb=" N SER A 206 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.768A pdb=" N ARG A 211 " --> pdb=" O TRP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 removed outlier: 3.571A pdb=" N PHE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 276 removed outlier: 3.867A pdb=" N SER A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.657A pdb=" N ILE A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 330 removed outlier: 4.131A pdb=" N GLN A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TRP A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 366 removed outlier: 4.944A 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: 3.575A pdb=" N THR B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N THR B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 106 removed outlier: 5.380A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR B 101 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.926A pdb=" N PHE B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 Processing helix chain 'B' and resid 156 through 188 removed outlier: 3.731A pdb=" N ASN B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.676A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.596A pdb=" N PHE B 228 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 229 " --> pdb=" O VAL B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 229' Processing helix chain 'B' and resid 231 through 239 removed outlier: 4.334A pdb=" N GLU B 237 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 3.783A 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: 3.760A pdb=" N TRP B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.770A pdb=" N GLY B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 354 removed outlier: 3.598A pdb=" N SER B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 4.029A pdb=" N ALA B 363 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.732A pdb=" N THR B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.771A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 397 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.747A pdb=" N VAL B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 removed outlier: 3.772A pdb=" N VAL B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 4.236A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 487 removed outlier: 3.731A 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 Processing helix chain 'C' and resid 72 through 97 removed outlier: 3.545A pdb=" N PHE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Proline residue: C 93 - end of helix Processing helix chain 'C' and resid 103 through 126 removed outlier: 3.788A 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: 3.555A pdb=" N ALA D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 105 removed outlier: 3.588A pdb=" N ILE D 92 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 133 removed outlier: 3.632A pdb=" N PHE D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 128 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.695A pdb=" N PHE D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 157 removed outlier: 4.030A pdb=" N TYR D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 178 removed outlier: 3.881A pdb=" N ALA D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 167 " --> pdb=" O GLN D 163 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.944A pdb=" N MET D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 202 removed outlier: 3.721A pdb=" N ALA D 202 " --> pdb=" O MET D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 226 removed outlier: 3.693A pdb=" N ALA D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 240 removed outlier: 4.512A pdb=" N ASP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 removed outlier: 4.169A pdb=" N LEU D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 removed outlier: 3.700A pdb=" N LYS D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 261 " --> pdb=" O MET D 257 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 262 " --> pdb=" O GLY D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 299 removed outlier: 3.907A pdb=" N ALA D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 322 removed outlier: 4.084A pdb=" N SER D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 317 " --> pdb=" O HIS D 313 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 355 removed outlier: 3.780A pdb=" N ALA D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL D 333 " --> pdb=" O MET D 329 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 355 " --> pdb=" O GLY D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 removed outlier: 4.311A pdb=" N ALA D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 407 removed outlier: 4.325A pdb=" N VAL D 396 " --> pdb=" O MET D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 430 removed outlier: 4.587A pdb=" N VAL D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 442 removed outlier: 3.610A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 442 " --> pdb=" O LEU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 454 removed outlier: 3.695A pdb=" N VAL D 451 " --> pdb=" O ASN D 447 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 480 removed outlier: 3.588A pdb=" N VAL D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 466 " --> pdb=" O ARG D 462 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 467 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 3.692A 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: 3.663A pdb=" N THR D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR D 491 " --> pdb=" O ILE D 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 23 removed outlier: 3.822A pdb=" N VAL E 6 " --> pdb=" O GLN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 52 removed outlier: 3.924A pdb=" N LEU E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 88 removed outlier: 3.871A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.610A pdb=" N LYS E 95 " --> pdb=" O ASP E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 13 through 27 removed outlier: 3.563A pdb=" N GLY F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE F 27 " --> pdb=" O GLY F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 65 removed outlier: 3.607A pdb=" N ALA F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 115 removed outlier: 3.659A pdb=" N ILE F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 140 removed outlier: 3.701A pdb=" N VAL F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 163 removed outlier: 3.711A pdb=" N GLY F 163 " --> pdb=" O TYR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 200 removed outlier: 3.642A pdb=" N GLU F 173 " --> pdb=" O LYS F 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 180 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 218 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.605A pdb=" N ALA F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 3.981A 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: 4.145A pdb=" N ASP F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU F 255 " --> pdb=" O PRO F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 265 removed outlier: 3.537A pdb=" N SER F 261 " --> pdb=" O PRO F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 280 removed outlier: 4.243A pdb=" N GLY F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.831A 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 288 through 309 Processing helix chain 'F' and resid 314 through 337 Processing helix chain 'F' and resid 338 through 371 removed outlier: 3.957A pdb=" N MET F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 405 Processing helix chain 'F' and resid 411 through 428 removed outlier: 4.123A pdb=" N TRP F 415 " --> pdb=" O PHE F 411 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 454 removed outlier: 3.552A pdb=" N GLY F 440 " --> pdb=" O TRP F 436 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 3.559A 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: 4.164A pdb=" N LEU F 490 " --> pdb=" O MET F 486 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL F 491 " --> pdb=" O THR F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 504 removed outlier: 4.495A pdb=" N GLY F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE F 502 " --> pdb=" O THR F 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 515 removed outlier: 3.673A pdb=" N VAL F 513 " --> pdb=" O ASN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 554 removed outlier: 3.573A pdb=" N LEU F 534 " --> pdb=" O LEU F 530 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 554 " --> pdb=" O VAL F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 569 removed outlier: 3.783A pdb=" N ILE F 565 " --> pdb=" O SER F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 578 removed outlier: 3.756A pdb=" N SER F 576 " --> pdb=" O LEU F 572 " (cutoff:3.500A) removed outlier: 4.551A 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: 4.761A pdb=" N VAL F 609 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASP F 610 " --> pdb=" O TYR F 606 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N VAL F 613 " --> pdb=" O VAL F 609 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN F 614 " --> pdb=" O ASP F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 655 removed outlier: 3.748A pdb=" N TYR F 638 " --> pdb=" O ARG F 634 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA F 639 " --> pdb=" O ALA F 635 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 650 " --> pdb=" O VAL F 646 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 29 removed outlier: 3.664A pdb=" N VAL G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU G 29 " --> pdb=" O GLY G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 54 removed outlier: 3.533A pdb=" N SER G 35 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.861A 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: 3.829A pdb=" N GLU G 148 " --> pdb=" O LEU G 144 " (cutoff:3.500A) removed outlier: 4.065A 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 83 Processing helix chain 'H' and resid 84 through 90 Processing helix chain 'H' and resid 95 through 116 removed outlier: 3.538A pdb=" N ALA H 112 " --> pdb=" O LEU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 124 removed outlier: 3.586A pdb=" N PHE H 121 " --> pdb=" O TRP H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 149 removed outlier: 3.677A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 193 removed outlier: 4.214A pdb=" N LEU H 184 " --> pdb=" O CYS H 180 " (cutoff:3.500A) Proline residue: H 185 - end of helix Processing helix chain 'H' and resid 199 through 204 removed outlier: 3.690A 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: 3.573A pdb=" N ARG H 226 " --> pdb=" O GLY H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 257 through 282 removed outlier: 3.672A pdb=" N ARG H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 270 " --> pdb=" O ILE H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 298 removed outlier: 3.505A pdb=" N GLU H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 363 removed outlier: 4.197A pdb=" N ASN H 361 " --> pdb=" O PRO H 357 " (cutoff:3.500A) removed outlier: 3.829A 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 377 through 385 removed outlier: 3.680A pdb=" N ILE H 385 " --> pdb=" O ILE H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 393 Processing helix chain 'I' and resid 4 through 32 removed outlier: 3.534A pdb=" N MET I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 73 removed outlier: 3.663A pdb=" N VAL I 72 " --> pdb=" O VAL I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 142 Processing helix chain 'I' and resid 186 through 191 Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 45 through 55 removed outlier: 3.684A pdb=" N ALA J 55 " --> pdb=" O GLN J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 118 removed outlier: 3.936A 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 removed outlier: 3.571A pdb=" N ARG K 39 " --> pdb=" O TYR K 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 62 removed outlier: 3.791A pdb=" N ILE K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE K 61 " --> pdb=" O PHE K 57 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 71 removed outlier: 3.856A 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: 3.503A pdb=" N THR K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 167 removed outlier: 3.799A pdb=" N ALA K 167 " --> pdb=" O ARG K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 22 removed outlier: 3.523A pdb=" N LEU L 8 " --> pdb=" O SER L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.825A pdb=" N ALA L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE L 27 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN L 33 " --> pdb=" O TYR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 54 removed outlier: 3.933A pdb=" N PHE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 62 removed outlier: 3.530A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 60 Processing helix chain 'M' and resid 66 through 87 removed outlier: 3.618A pdb=" N LEU M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 16 Processing helix chain 'N' and resid 29 through 41 removed outlier: 4.488A 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: 3.948A pdb=" N ASN N 90 " --> pdb=" O TYR N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 123 removed outlier: 4.331A pdb=" N ALA N 114 " --> pdb=" O LYS N 110 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR N 115 " --> pdb=" O GLN N 111 " (cutoff:3.500A) removed outlier: 3.565A 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 30 through 35 removed outlier: 3.793A pdb=" N PHE O 34 " --> pdb=" O PRO O 30 " (cutoff:3.500A) removed outlier: 3.830A 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: 3.602A pdb=" N ALA P 13 " --> pdb=" O PRO P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 27 removed outlier: 3.590A pdb=" N CYS P 22 " --> pdb=" O PHE P 18 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE P 24 " --> pdb=" O LEU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 17 through 43 removed outlier: 3.523A pdb=" N ILE Q 21 " --> pdb=" O SER Q 17 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE Q 23 " --> pdb=" O ALA Q 19 " (cutoff:3.500A) 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 71 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: 3.755A pdb=" N VAL H 329 " --> pdb=" O ILE H 340 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE H 340 " --> pdb=" O VAL H 329 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY H 339 " --> pdb=" O ARG H 356 " (cutoff:3.500A) removed outlier: 3.701A 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: 5.790A pdb=" N ASP S 85 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP S 84 " --> pdb=" O GLY S 81 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY S 81 " --> pdb=" O TRP S 84 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE S 70 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA S 76 " --> pdb=" O GLN S 68 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU S 80 " --> pdb=" O GLN S 64 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLN S 64 " --> pdb=" O GLU S 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 81 through 84 removed outlier: 7.172A pdb=" N ASP I 81 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.661A 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 28 removed outlier: 3.628A pdb=" N GLU J 27 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE J 39 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE J 99 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS J 63 " --> pdb=" O HIS J 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE J 82 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 5.368A 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: 3.559A 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 13 through 14 Processing sheet with id=AB3, first strand: chain 'K' and resid 45 through 47 removed outlier: 6.695A pdb=" N LEU K 46 " --> pdb=" O ILE K 85 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER K 87 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL K 143 " --> pdb=" O VAL K 111 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA K 113 " --> pdb=" O VAL K 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 183 through 187 removed outlier: 3.537A pdb=" N ALA K 186 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE M 12 " --> pdb=" O SER M 5 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER M 5 " --> pdb=" O ILE M 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 189 through 191 removed outlier: 8.027A pdb=" N LYS K 189 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU M 63 " --> pdb=" O LYS K 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 46 through 47 removed outlier: 7.043A pdb=" N LEU N 98 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL N 129 " --> pdb=" O LEU N 98 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU N 100 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU N 131 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU N 102 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU N 19 " --> pdb=" O VAL N 130 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL N 132 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU N 21 " --> pdb=" O VAL N 132 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG N 139 " --> pdb=" O PHE N 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 63 through 65 Processing sheet with id=AB8, first strand: chain 'O' and resid 9 through 11 Processing sheet with id=AB9, first strand: chain 'O' and resid 39 through 43 removed outlier: 6.817A pdb=" N GLN O 49 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE O 43 " --> pdb=" O TYR O 47 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR O 47 " --> pdb=" O ILE O 43 " (cutoff:3.500A) 1625 hydrogen bonds defined for protein. 4824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 3.63 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: 13765 1.44 - 1.66: 19720 1.66 - 1.88: 294 1.88 - 2.11: 0 2.11 - 2.33: 36 Bond restraints: 33815 Sorted by residual: bond pdb=" C12 PQN B 601 " pdb=" C13 PQN B 601 " ideal model delta sigma weight residual 1.334 1.525 -0.191 2.00e-02 2.50e+03 9.09e+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 8.60e+01 bond pdb=" C VAL C 32 " pdb=" N PRO C 33 " ideal model delta sigma weight residual 1.336 1.404 -0.068 1.20e-02 6.94e+03 3.24e+01 bond pdb=" C ILE D 148 " pdb=" N PRO D 149 " ideal model delta sigma weight residual 1.336 1.402 -0.066 1.20e-02 6.94e+03 3.03e+01 ... (remaining 33810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 44489 3.02 - 6.04: 1299 6.04 - 9.07: 485 9.07 - 12.09: 143 12.09 - 15.11: 21 Bond angle restraints: 46437 Sorted by residual: angle pdb=" CBB DGD A 405 " pdb=" CCB DGD A 405 " pdb=" CDB DGD A 405 " ideal model delta sigma weight residual 115.38 100.27 15.11 3.00e+00 1.11e-01 2.54e+01 angle pdb=" CBB DGD A 404 " pdb=" CCB DGD A 404 " pdb=" CDB DGD A 404 " ideal model delta sigma weight residual 115.38 100.44 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" C11 PQN B 601 " pdb=" C12 PQN B 601 " pdb=" C13 PQN B 601 " ideal model delta sigma weight residual 126.56 112.66 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" C GLU D 75 " pdb=" N ILE D 76 " pdb=" CA ILE D 76 " ideal model delta sigma weight residual 121.97 130.31 -8.34 1.80e+00 3.09e-01 2.15e+01 angle pdb=" C GLU A 239 " pdb=" N GLU A 240 " pdb=" CA GLU A 240 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 ... (remaining 46432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 17836 27.12 - 54.23: 885 54.23 - 81.35: 100 81.35 - 108.47: 71 108.47 - 135.59: 79 Dihedral angle restraints: 18971 sinusoidal: 7751 harmonic: 11220 Sorted by residual: dihedral pdb=" CA THR H 129 " pdb=" C THR H 129 " pdb=" N PRO H 130 " pdb=" CA PRO H 130 " ideal model delta harmonic sigma weight residual 180.00 137.02 42.98 0 5.00e+00 4.00e-02 7.39e+01 dihedral pdb=" CA LEU N 91 " pdb=" C LEU N 91 " pdb=" N PRO N 92 " pdb=" CA PRO N 92 " ideal model delta harmonic sigma weight residual -180.00 -141.63 -38.37 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA GLU A 240 " pdb=" C GLU A 240 " pdb=" N LEU A 241 " pdb=" CA LEU A 241 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 18968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.291: 5049 4.291 - 8.582: 528 8.582 - 12.873: 0 12.873 - 17.164: 0 17.164 - 21.455: 12 Chirality restraints: 5589 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 -21.46 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 -10.82 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 10.76 -21.31 2.00e-01 2.50e+01 1.14e+04 ... (remaining 5586 not shown) Planarity restraints: 5365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 PQN B 601 " 0.154 2.00e-02 2.50e+03 2.33e-01 6.76e+02 pdb=" C12 PQN B 601 " -0.341 2.00e-02 2.50e+03 pdb=" C13 PQN B 601 " 0.332 2.00e-02 2.50e+03 pdb=" C14 PQN B 601 " -0.145 2.00e-02 2.50e+03 pdb=" C15 PQN B 601 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR A 401 " 0.032 2.00e-02 2.50e+03 2.47e-01 6.09e+02 pdb=" C11 BCR A 401 " -0.245 2.00e-02 2.50e+03 pdb=" C12 BCR A 401 " 0.389 2.00e-02 2.50e+03 pdb=" C13 BCR A 401 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 BCR D 602 " -0.100 2.00e-02 2.50e+03 2.27e-01 5.15e+02 pdb=" C7 BCR D 602 " 0.298 2.00e-02 2.50e+03 pdb=" C8 BCR D 602 " -0.308 2.00e-02 2.50e+03 pdb=" C9 BCR D 602 " 0.110 2.00e-02 2.50e+03 ... (remaining 5362 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 240 2.62 - 3.19: 25414 3.19 - 3.76: 49889 3.76 - 4.33: 66297 4.33 - 4.90: 109939 Nonbonded interactions: 251779 Sorted by model distance: nonbonded pdb=" C03 AJP F 708 " pdb=" C13 AJP Q 102 " model vdw 2.044 3.840 nonbonded pdb=" O79 AJP B 612 " pdb=" C18 AJP D 614 " model vdw 2.143 3.440 nonbonded pdb=" OH TYR D 70 " pdb=" O25 AJP D 608 " model vdw 2.151 2.432 nonbonded pdb=" CB PRO F 39 " pdb=" C83 AJP F 712 " model vdw 2.228 3.860 nonbonded pdb=" O LEU D 479 " pdb=" C83 AJP D 616 " model vdw 2.270 3.460 ... (remaining 251774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 29.430 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 1.136 33850 Z= 1.138 Angle : 1.513 49.713 46476 Z= 0.570 Chirality : 1.894 21.455 5589 Planarity : 0.013 0.247 5365 Dihedral : 19.272 135.586 11795 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.36 % Rotamer: Outliers : 0.25 % Allowed : 6.23 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.10), residues: 3854 helix: -2.32 (0.08), residues: 2179 sheet: -1.46 (0.35), residues: 198 loop : -3.83 (0.12), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 138 TYR 0.024 0.001 TYR F 445 PHE 0.034 0.001 PHE F 352 TRP 0.012 0.001 TRP B 274 HIS 0.014 0.001 HIS G 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.41 (33815) covalent geometry : angle 1.39747 / 0.57 (46437) hydrogen bonds : bond 0.12065 / 7.75 ( 1625) hydrogen bonds : angle 5.59712 / 3.96 ( 4824) metal coordination : bond 0.56500 / 36.91 ( 13) metal coordination : angle 20.05273 / 11.86 ( 39) Misc. bond : bond 0.39608 / 25.88 ( 22) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 752 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 PHE cc_start: 0.6906 (m-10) cc_final: 0.6704 (m-80) REVERT: B 40 ASP cc_start: 0.7626 (t0) cc_final: 0.7206 (t0) REVERT: B 183 LEU cc_start: 0.7097 (tp) cc_final: 0.6896 (mt) REVERT: C 125 ARG cc_start: 0.7882 (tpt170) cc_final: 0.7516 (tpt90) REVERT: D 89 MET cc_start: 0.7588 (tpt) cc_final: 0.7344 (tpt) REVERT: D 347 PHE cc_start: 0.7530 (m-80) cc_final: 0.7316 (m-80) REVERT: E 44 ASN cc_start: 0.8409 (t0) cc_final: 0.8186 (m-40) REVERT: F 7 TYR cc_start: 0.7492 (m-80) cc_final: 0.7038 (m-80) REVERT: F 109 LEU cc_start: 0.7792 (tp) cc_final: 0.7568 (tp) REVERT: F 391 MET cc_start: 0.7628 (mpp) cc_final: 0.7159 (mtm) REVERT: F 452 MET cc_start: 0.7991 (ttm) cc_final: 0.7492 (ttp) REVERT: F 455 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7710 (mm-30) REVERT: F 607 ASN cc_start: 0.8603 (m-40) cc_final: 0.8358 (m-40) REVERT: G 113 LYS cc_start: 0.8695 (tttm) cc_final: 0.8330 (tttt) REVERT: I 94 LYS cc_start: 0.8736 (tptt) cc_final: 0.8500 (mmtt) REVERT: N 87 HIS cc_start: 0.7267 (m-70) cc_final: 0.7051 (m-70) REVERT: N 118 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6520 (mm-40) REVERT: S 49 MET cc_start: 0.7656 (ptm) cc_final: 0.7282 (ptt) outliers start: 8 outliers final: 1 residues processed: 759 average time/residue: 0.2045 time to fit residues: 251.9766 Evaluate side-chains 517 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 516 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 41 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 199 GLN A 212 GLN A 246 GLN A 355 ASN ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN B 367 GLN D 65 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 239 HIS D 339 HIS E 42 ASN E 56 GLN F 146 GLN F 265 HIS F 312 GLN H 78 ASN H 84 ASN H 156 ASN H 196 ASN I 76 ASN I 108 ASN J 120 GLN J 165 GLN K 104 GLN ** K 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 ASN O 27 HIS O 49 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161131 restraints weight = 42038.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.164103 restraints weight = 28648.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166143 restraints weight = 22099.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167484 restraints weight = 18469.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.168476 restraints weight = 16277.241| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.270 33850 Z= 0.312 Angle : 3.221 55.390 46476 Z= 1.345 Chirality : 0.434 6.903 5589 Planarity : 0.005 0.077 5365 Dihedral : 12.675 123.185 4936 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.14 % Rotamer: Outliers : 2.03 % Allowed : 12.96 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: -2.19 (0.12), residues: 3854 helix: -0.24 (0.10), residues: 2213 sheet: -1.24 (0.34), residues: 214 loop : -3.51 (0.13), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 133 TYR 0.017 0.001 TYR B 236 PHE 0.027 0.001 PHE F 352 TRP 0.018 0.001 TRP C 124 HIS 0.007 0.001 HIS G 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00871 / 0.31 (33815) covalent geometry : angle 3.07881 / 1.34 (46437) hydrogen bonds : bond 0.03380 / 2.22 ( 1625) hydrogen bonds : angle 3.95681 / 2.79 ( 4824) metal coordination : bond 0.03207 / 1.77 ( 13) metal coordination : angle 32.78482 / 19.67 ( 39) Misc. bond : bond 0.00297 / 0.19 ( 22) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 546 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7440 (tt0) REVERT: A 271 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7226 (mp) REVERT: D 89 MET cc_start: 0.7519 (tpt) cc_final: 0.7275 (tpt) REVERT: D 127 GLN cc_start: 0.7479 (mt0) cc_final: 0.7260 (mt0) REVERT: D 136 MET cc_start: 0.8648 (tpt) cc_final: 0.8173 (tpt) REVERT: F 7 TYR cc_start: 0.7692 (m-80) cc_final: 0.7055 (m-80) REVERT: F 391 MET cc_start: 0.7693 (mpp) cc_final: 0.7439 (mtm) REVERT: F 452 MET cc_start: 0.8022 (ttm) cc_final: 0.7789 (ttp) REVERT: H 139 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6630 (tm-30) REVERT: H 204 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7625 (pp) REVERT: M 41 TRP cc_start: 0.8446 (m100) cc_final: 0.8179 (m100) REVERT: N 40 LYS cc_start: 0.8620 (tppt) cc_final: 0.7878 (tptm) REVERT: N 87 HIS cc_start: 0.7467 (m-70) cc_final: 0.7232 (m-70) REVERT: N 118 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6488 (mm-40) REVERT: Q 20 MET cc_start: 0.5063 (ttm) cc_final: 0.4848 (tpp) outliers start: 65 outliers final: 33 residues processed: 584 average time/residue: 0.1931 time to fit residues: 188.3349 Evaluate side-chains 530 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 495 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 114 TYR Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 326 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain P residue 19 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 299 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN B 130 GLN B 290 ASN C 99 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 HIS D 486 GLN E 42 ASN E 87 ASN F 54 HIS F 146 GLN F 578 HIS ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 361 ASN I 31 HIS I 108 ASN J 64 GLN J 165 GLN K 188 HIS O 27 HIS P 44 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.163815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135128 restraints weight = 41218.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137733 restraints weight = 30645.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138819 restraints weight = 23523.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139738 restraints weight = 20398.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139916 restraints weight = 19699.322| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.255 33850 Z= 0.317 Angle : 3.193 58.438 46476 Z= 1.343 Chirality : 0.432 6.736 5589 Planarity : 0.005 0.086 5365 Dihedral : 11.559 122.376 4936 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.49 % Rotamer: Outliers : 2.96 % Allowed : 14.65 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 3854 helix: 0.79 (0.11), residues: 2235 sheet: -0.84 (0.35), residues: 217 loop : -3.35 (0.13), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 125 TYR 0.019 0.002 TYR D 297 PHE 0.030 0.002 PHE H 153 TRP 0.017 0.001 TRP C 124 HIS 0.010 0.001 HIS D 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.32 (33815) covalent geometry : angle 3.04662 / 1.34 (46437) hydrogen bonds : bond 0.05057 / 3.34 ( 1625) hydrogen bonds : angle 3.75307 / 2.64 ( 4824) metal coordination : bond 0.03524 / 2.17 ( 13) metal coordination : angle 33.14435 / 19.84 ( 39) Misc. bond : bond 0.00453 / 0.28 ( 22) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 536 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7104 (tm-30) REVERT: A 198 GLN cc_start: 0.7925 (mp10) cc_final: 0.7670 (mp10) REVERT: B 315 MET cc_start: 0.8178 (mmm) cc_final: 0.7834 (mtt) REVERT: C 43 LEU cc_start: 0.7775 (tp) cc_final: 0.7429 (tp) REVERT: D 43 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8712 (mt) REVERT: D 136 MET cc_start: 0.8864 (tpt) cc_final: 0.8232 (tpt) REVERT: D 172 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.7625 (t80) REVERT: D 347 PHE cc_start: 0.8396 (m-80) cc_final: 0.8173 (m-80) REVERT: E 81 ILE cc_start: 0.8636 (mm) cc_final: 0.8383 (mt) REVERT: F 7 TYR cc_start: 0.7973 (m-80) cc_final: 0.7235 (m-80) REVERT: F 48 MET cc_start: 0.8077 (tpp) cc_final: 0.7866 (mmt) REVERT: F 141 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.7938 (t) REVERT: F 291 MET cc_start: 0.7004 (mmm) cc_final: 0.6691 (mmt) REVERT: F 304 MET cc_start: 0.7868 (tmm) cc_final: 0.7385 (ttp) REVERT: F 471 HIS cc_start: 0.4804 (t70) cc_final: 0.4599 (t-170) REVERT: H 116 LEU cc_start: 0.8407 (tp) cc_final: 0.8122 (tp) REVERT: I 34 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8177 (mtm-85) REVERT: J 93 GLU cc_start: 0.7791 (pm20) cc_final: 0.7480 (pm20) REVERT: J 143 MET cc_start: 0.8892 (mmm) cc_final: 0.8503 (mmt) REVERT: J 155 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7183 (p0) REVERT: K 190 MET cc_start: 0.8379 (mtt) cc_final: 0.8130 (mtt) REVERT: N 40 LYS cc_start: 0.8654 (tppt) cc_final: 0.8088 (tptm) REVERT: N 47 MET cc_start: 0.7993 (tpp) cc_final: 0.7784 (ttm) REVERT: N 118 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6808 (mm-40) REVERT: P 28 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7137 (tpp80) REVERT: S 49 MET cc_start: 0.7599 (ptm) cc_final: 0.7159 (ptt) outliers start: 95 outliers final: 44 residues processed: 593 average time/residue: 0.2029 time to fit residues: 197.5135 Evaluate side-chains 514 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 466 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 76 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 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 457 VAL 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 58 LEU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 559 THR 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 G residue 182 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 3 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 354 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 363 optimal weight: 0.6980 chunk 292 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 290 ASN B 367 GLN D 55 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 196 ASN ** I 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.159714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131070 restraints weight = 40985.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133667 restraints weight = 29175.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135341 restraints weight = 23411.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136587 restraints weight = 20271.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137297 restraints weight = 18426.995| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.255 33850 Z= 0.307 Angle : 3.186 56.664 46476 Z= 1.338 Chirality : 0.427 6.393 5589 Planarity : 0.005 0.081 5365 Dihedral : 11.237 113.627 4936 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 3.05 % Allowed : 16.89 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.14), residues: 3854 helix: 1.24 (0.11), residues: 2245 sheet: -0.81 (0.35), residues: 228 loop : -3.22 (0.13), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.016 0.001 TYR D 124 PHE 0.040 0.001 PHE F 29 TRP 0.022 0.001 TRP C 124 HIS 0.020 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.31 (33815) covalent geometry : angle 3.03832 / 1.34 (46437) hydrogen bonds : bond 0.04444 / 2.96 ( 1625) hydrogen bonds : angle 3.65817 / 2.58 ( 4824) metal coordination : bond 0.02276 / 1.44 ( 13) metal coordination : angle 33.22432 / 19.98 ( 39) Misc. bond : bond 0.00345 / 0.23 ( 22) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 483 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.7717 (ttm) cc_final: 0.7387 (mtt) REVERT: B 315 MET cc_start: 0.8156 (mmm) cc_final: 0.7874 (mtt) REVERT: B 447 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: B 483 ASN cc_start: 0.7867 (m-40) cc_final: 0.7506 (t0) REVERT: C 43 LEU cc_start: 0.7756 (tp) cc_final: 0.7504 (tp) REVERT: D 43 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8696 (mt) REVERT: D 172 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7553 (t80) REVERT: D 347 PHE cc_start: 0.8336 (m-80) cc_final: 0.8111 (m-80) REVERT: F 7 TYR cc_start: 0.7944 (m-80) cc_final: 0.7281 (m-80) REVERT: F 141 SER cc_start: 0.8898 (t) cc_final: 0.8445 (t) REVERT: F 291 MET cc_start: 0.7105 (mmm) cc_final: 0.6900 (mmt) REVERT: F 304 MET cc_start: 0.7996 (tmm) cc_final: 0.7421 (ttp) REVERT: F 358 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8193 (mt) REVERT: F 449 MET cc_start: 0.8671 (ttm) cc_final: 0.8062 (mtp) REVERT: F 580 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.6940 (t60) REVERT: F 585 LEU cc_start: 0.8383 (tt) cc_final: 0.7947 (tp) REVERT: G 79 MET cc_start: 0.8216 (mmm) cc_final: 0.7670 (mmt) REVERT: G 142 ASP cc_start: 0.8203 (m-30) cc_final: 0.8000 (m-30) REVERT: H 116 LEU cc_start: 0.8489 (tp) cc_final: 0.8286 (tp) REVERT: H 204 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7650 (pp) REVERT: I 34 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8252 (mtm-85) REVERT: I 153 MET cc_start: 0.7575 (tpp) cc_final: 0.7123 (tpt) REVERT: I 168 MET cc_start: 0.6241 (mmt) cc_final: 0.5966 (mmt) REVERT: J 45 ARG cc_start: 0.6567 (mpp80) cc_final: 0.6211 (mtm180) REVERT: J 93 GLU cc_start: 0.7732 (pm20) cc_final: 0.7439 (pm20) REVERT: J 155 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7303 (p0) REVERT: N 107 ARG cc_start: 0.8262 (mpp80) cc_final: 0.7753 (mtt-85) REVERT: N 118 GLN cc_start: 0.7532 (mm-40) cc_final: 0.6855 (mm-40) REVERT: O 10 LYS cc_start: 0.8218 (tttt) cc_final: 0.7969 (tttp) REVERT: P 28 ARG cc_start: 0.7600 (tpp80) cc_final: 0.7131 (tpp80) REVERT: Q 6 ASN cc_start: 0.8136 (p0) cc_final: 0.7726 (p0) REVERT: S 49 MET cc_start: 0.7535 (ptm) cc_final: 0.7145 (ptt) outliers start: 98 outliers final: 45 residues processed: 550 average time/residue: 0.1914 time to fit residues: 173.2949 Evaluate side-chains 492 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 440 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 447 TYR Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 172 TYR Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE 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 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 559 THR Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain P residue 4 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 379 optimal weight: 7.9990 chunk 371 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 227 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN B 290 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS E 87 ASN F 312 GLN F 471 HIS H 156 ASN H 196 ASN J 80 HIS ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129255 restraints weight = 40680.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130158 restraints weight = 31677.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130391 restraints weight = 27219.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131159 restraints weight = 25583.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131538 restraints weight = 22208.995| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 33850 Z= 0.302 Angle : 3.175 56.825 46476 Z= 1.335 Chirality : 0.426 6.388 5589 Planarity : 0.004 0.080 5365 Dihedral : 10.856 111.271 4936 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 3.02 % Allowed : 17.76 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3854 helix: 1.53 (0.11), residues: 2247 sheet: -0.67 (0.35), residues: 228 loop : -3.08 (0.14), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 122 TYR 0.013 0.001 TYR B 336 PHE 0.027 0.001 PHE F 187 TRP 0.023 0.001 TRP C 124 HIS 0.012 0.001 HIS F 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.30 (33815) covalent geometry : angle 3.02834 / 1.33 (46437) hydrogen bonds : bond 0.04284 / 2.85 ( 1625) hydrogen bonds : angle 3.61873 / 2.55 ( 4824) metal coordination : bond 0.02468 / 1.53 ( 13) metal coordination : angle 33.06308 / 19.80 ( 39) Misc. bond : bond 0.00376 / 0.23 ( 22) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 475 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7758 (ttm) cc_final: 0.7374 (mtp) REVERT: A 194 GLU cc_start: 0.6603 (mp0) cc_final: 0.5712 (mp0) REVERT: A 198 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: B 161 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6119 (tt0) REVERT: B 315 MET cc_start: 0.8167 (mmm) cc_final: 0.7955 (mtt) REVERT: B 483 ASN cc_start: 0.7903 (m-40) cc_final: 0.7545 (t0) REVERT: C 43 LEU cc_start: 0.7786 (tp) cc_final: 0.7486 (tp) REVERT: D 43 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8745 (mt) REVERT: D 136 MET cc_start: 0.8898 (tpp) cc_final: 0.8459 (tpt) REVERT: D 172 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7505 (t80) REVERT: D 365 MET cc_start: 0.7466 (mtt) cc_final: 0.7105 (mtt) REVERT: F 7 TYR cc_start: 0.7969 (m-80) cc_final: 0.7310 (m-80) REVERT: F 141 SER cc_start: 0.8878 (t) cc_final: 0.8436 (t) REVERT: F 291 MET cc_start: 0.7235 (mmm) cc_final: 0.7031 (mmt) REVERT: F 304 MET cc_start: 0.8012 (tmm) cc_final: 0.7543 (ttp) REVERT: F 352 PHE cc_start: 0.7693 (p90) cc_final: 0.7482 (p90) REVERT: F 358 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8246 (mt) REVERT: F 411 PHE cc_start: 0.5001 (OUTLIER) cc_final: 0.3143 (t80) REVERT: F 580 TRP cc_start: 0.7584 (OUTLIER) cc_final: 0.7110 (t60) REVERT: F 585 LEU cc_start: 0.8425 (tt) cc_final: 0.8065 (tp) REVERT: G 79 MET cc_start: 0.8332 (mmm) cc_final: 0.7754 (mmt) REVERT: H 22 MET cc_start: 0.6777 (tpp) cc_final: 0.6562 (tpt) REVERT: H 204 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7656 (pp) REVERT: H 389 MET cc_start: 0.7538 (mmp) cc_final: 0.7142 (mmp) REVERT: I 168 MET cc_start: 0.6561 (mmt) cc_final: 0.6163 (mmm) REVERT: J 93 GLU cc_start: 0.7768 (pm20) cc_final: 0.7469 (pm20) REVERT: J 155 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7460 (p0) REVERT: K 89 THR cc_start: 0.9092 (m) cc_final: 0.8794 (t) REVERT: N 40 LYS cc_start: 0.8731 (tppt) cc_final: 0.8141 (tptm) REVERT: N 118 GLN cc_start: 0.7497 (mm-40) cc_final: 0.6936 (mm-40) REVERT: P 28 ARG cc_start: 0.7655 (tpp80) cc_final: 0.7256 (tpp80) REVERT: S 49 MET cc_start: 0.7539 (ptm) cc_final: 0.7201 (ptt) outliers start: 97 outliers final: 56 residues processed: 542 average time/residue: 0.1882 time to fit residues: 170.9746 Evaluate side-chains 512 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 447 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 157 TRP 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 425 VAL 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 E residue 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 156 ASN Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 371 LYS Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 138 LEU Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 3 LEU Chi-restraints excluded: chain P residue 4 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 185 optimal weight: 0.0970 chunk 310 optimal weight: 0.0020 chunk 242 optimal weight: 0.3980 chunk 373 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 375 optimal weight: 8.9990 chunk 356 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN F 6 GLN F 460 ASN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133618 restraints weight = 40851.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134466 restraints weight = 32330.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135145 restraints weight = 27524.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135949 restraints weight = 24604.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136176 restraints weight = 22375.191| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 33850 Z= 0.295 Angle : 3.166 53.527 46476 Z= 1.330 Chirality : 0.425 6.442 5589 Planarity : 0.004 0.079 5365 Dihedral : 10.585 110.366 4936 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.84 % Favored : 94.14 % Rotamer: Outliers : 2.56 % Allowed : 18.76 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: 0.08 (0.14), residues: 3854 helix: 1.78 (0.11), residues: 2236 sheet: -0.50 (0.35), residues: 229 loop : -2.95 (0.14), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 353 TYR 0.015 0.001 TYR F 445 PHE 0.027 0.001 PHE F 352 TRP 0.024 0.001 TRP C 124 HIS 0.010 0.000 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.29 (33815) covalent geometry : angle 3.01746 / 1.33 (46437) hydrogen bonds : bond 0.03619 / 2.41 ( 1625) hydrogen bonds : angle 3.51905 / 2.49 ( 4824) metal coordination : bond 0.02246 / 1.42 ( 13) metal coordination : angle 33.17856 / 20.20 ( 39) Misc. bond : bond 0.00343 / 0.21 ( 22) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 462 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.7748 (ttm) cc_final: 0.7389 (mtp) REVERT: A 194 GLU cc_start: 0.6527 (mp0) cc_final: 0.5525 (mp0) REVERT: A 198 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: B 30 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 161 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6070 (tt0) REVERT: B 315 MET cc_start: 0.8205 (mmm) cc_final: 0.7919 (mtt) REVERT: B 483 ASN cc_start: 0.7848 (m-40) cc_final: 0.7522 (t0) REVERT: C 43 LEU cc_start: 0.7785 (tp) cc_final: 0.7480 (tp) REVERT: D 43 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8734 (mt) REVERT: D 134 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8425 (mt0) REVERT: D 172 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7744 (t80) REVERT: D 365 MET cc_start: 0.7357 (mtt) cc_final: 0.7090 (mtt) REVERT: F 7 TYR cc_start: 0.8024 (m-80) cc_final: 0.7368 (m-80) REVERT: F 141 SER cc_start: 0.8834 (t) cc_final: 0.8377 (t) REVERT: F 304 MET cc_start: 0.7996 (tmm) cc_final: 0.7708 (ttp) REVERT: F 334 MET cc_start: 0.8511 (tpp) cc_final: 0.8179 (tpp) REVERT: F 352 PHE cc_start: 0.7609 (p90) cc_final: 0.7373 (p90) REVERT: F 358 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8197 (mt) REVERT: F 411 PHE cc_start: 0.4794 (OUTLIER) cc_final: 0.2875 (t80) REVERT: G 79 MET cc_start: 0.8240 (mmm) cc_final: 0.7670 (mmt) REVERT: H 22 MET cc_start: 0.6896 (tpp) cc_final: 0.6691 (tpt) REVERT: H 389 MET cc_start: 0.7432 (mmp) cc_final: 0.7094 (mmp) REVERT: I 168 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6319 (mmm) REVERT: J 45 ARG cc_start: 0.6842 (mtm-85) cc_final: 0.6495 (mtm180) REVERT: J 93 GLU cc_start: 0.7719 (pm20) cc_final: 0.7493 (pm20) REVERT: J 155 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7558 (p0) REVERT: N 40 LYS cc_start: 0.8742 (tppt) cc_final: 0.8113 (tptm) REVERT: N 47 MET cc_start: 0.7999 (mtp) cc_final: 0.7797 (mtt) REVERT: N 118 GLN cc_start: 0.7485 (mm-40) cc_final: 0.6896 (mm-40) REVERT: O 62 ARG cc_start: 0.8332 (mtp85) cc_final: 0.7762 (ttt-90) REVERT: P 28 ARG cc_start: 0.7643 (tpp80) cc_final: 0.7167 (tpp80) outliers start: 82 outliers final: 51 residues processed: 517 average time/residue: 0.1875 time to fit residues: 163.5465 Evaluate side-chains 501 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 441 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 157 TRP 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 425 VAL Chi-restraints excluded: chain D residue 430 THR 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 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain S residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 94 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 374 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 263 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 372 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN C 99 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN F 6 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN K 168 ASN O 27 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128886 restraints weight = 41049.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131470 restraints weight = 28681.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133262 restraints weight = 22951.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134453 restraints weight = 19849.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.135116 restraints weight = 17995.547| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 33850 Z= 0.296 Angle : 3.174 65.734 46476 Z= 1.332 Chirality : 0.425 6.456 5589 Planarity : 0.004 0.078 5365 Dihedral : 10.544 110.276 4936 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.36 % Favored : 93.62 % Rotamer: Outliers : 2.84 % Allowed : 19.07 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: 0.21 (0.14), residues: 3854 helix: 1.85 (0.11), residues: 2245 sheet: -0.36 (0.36), residues: 224 loop : -2.85 (0.14), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 45 TYR 0.017 0.001 TYR F 445 PHE 0.025 0.001 PHE F 352 TRP 0.035 0.001 TRP C 124 HIS 0.033 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.30 (33815) covalent geometry : angle 3.02030 / 1.33 (46437) hydrogen bonds : bond 0.03962 / 2.64 ( 1625) hydrogen bonds : angle 3.54764 / 2.50 ( 4824) metal coordination : bond 0.02614 / 1.52 ( 13) metal coordination : angle 33.80429 / 20.23 ( 39) Misc. bond : bond 0.00388 / 0.24 ( 22) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 446 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7830 (ttm) cc_final: 0.7523 (mtp) REVERT: A 194 GLU cc_start: 0.6524 (mp0) cc_final: 0.5628 (mp0) REVERT: A 198 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: B 30 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 161 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6003 (tt0) REVERT: B 422 ILE cc_start: 0.8983 (tp) cc_final: 0.8733 (tt) REVERT: C 43 LEU cc_start: 0.7819 (tp) cc_final: 0.7552 (tp) REVERT: D 172 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7694 (t80) REVERT: F 1 MET cc_start: 0.6953 (tmm) cc_final: 0.6636 (tmm) REVERT: F 7 TYR cc_start: 0.7968 (m-80) cc_final: 0.7361 (m-80) REVERT: F 141 SER cc_start: 0.8901 (t) cc_final: 0.8454 (t) REVERT: F 304 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7580 (ttp) REVERT: F 334 MET cc_start: 0.8512 (tpp) cc_final: 0.8173 (tpp) REVERT: F 352 PHE cc_start: 0.7604 (p90) cc_final: 0.7404 (p90) REVERT: F 358 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8212 (mt) REVERT: F 411 PHE cc_start: 0.5178 (OUTLIER) cc_final: 0.3072 (t80) REVERT: F 580 TRP cc_start: 0.7687 (OUTLIER) cc_final: 0.7122 (t60) REVERT: G 79 MET cc_start: 0.8323 (mmm) cc_final: 0.7693 (mmt) REVERT: H 109 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8126 (m110) REVERT: H 269 MET cc_start: 0.8396 (mtp) cc_final: 0.8187 (mtp) REVERT: H 389 MET cc_start: 0.7585 (mmp) cc_final: 0.7256 (mmp) REVERT: I 168 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6558 (mmt) REVERT: J 45 ARG cc_start: 0.6842 (mtm-85) cc_final: 0.6521 (mtm180) REVERT: J 89 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: J 93 GLU cc_start: 0.7743 (pm20) cc_final: 0.7413 (pm20) REVERT: J 127 MET cc_start: 0.8199 (mmp) cc_final: 0.7923 (mmp) REVERT: K 89 THR cc_start: 0.9070 (m) cc_final: 0.8811 (t) REVERT: N 40 LYS cc_start: 0.8710 (tppt) cc_final: 0.8073 (tptm) REVERT: N 118 GLN cc_start: 0.7535 (mm-40) cc_final: 0.6964 (mm-40) REVERT: P 28 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7243 (tpp80) outliers start: 91 outliers final: 60 residues processed: 514 average time/residue: 0.1901 time to fit residues: 163.9617 Evaluate side-chains 508 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 437 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 157 TRP 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 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR 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 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 371 LYS Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain S residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 199 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 311 optimal weight: 0.0670 chunk 347 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN C 99 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN F 6 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.157549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130994 restraints weight = 40934.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131334 restraints weight = 34226.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132550 restraints weight = 28338.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133218 restraints weight = 25093.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133574 restraints weight = 23159.947| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.259 33850 Z= 0.295 Angle : 3.171 59.028 46476 Z= 1.331 Chirality : 0.425 6.394 5589 Planarity : 0.004 0.078 5365 Dihedral : 10.506 108.626 4936 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 2.59 % Allowed : 19.63 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: 0.32 (0.14), residues: 3854 helix: 1.92 (0.11), residues: 2246 sheet: -0.28 (0.36), residues: 224 loop : -2.78 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 353 TYR 0.017 0.001 TYR F 445 PHE 0.026 0.001 PHE F 352 TRP 0.023 0.001 TRP C 124 HIS 0.021 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00832 / 0.29 (33815) covalent geometry : angle 3.01896 / 1.33 (46437) hydrogen bonds : bond 0.03852 / 2.57 ( 1625) hydrogen bonds : angle 3.53611 / 2.49 ( 4824) metal coordination : bond 0.02081 / 1.22 ( 13) metal coordination : angle 33.57170 / 20.32 ( 39) Misc. bond : bond 0.00342 / 0.21 ( 22) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 446 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7825 (ttm) cc_final: 0.7540 (mtp) REVERT: A 194 GLU cc_start: 0.6547 (mp0) cc_final: 0.5640 (mp0) REVERT: A 198 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7096 (mp10) REVERT: B 161 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6031 (tt0) REVERT: B 422 ILE cc_start: 0.8876 (tp) cc_final: 0.8583 (tt) REVERT: C 43 LEU cc_start: 0.7833 (tp) cc_final: 0.7603 (tp) REVERT: D 172 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.7785 (t80) REVERT: D 435 LEU cc_start: 0.8582 (mt) cc_final: 0.8340 (mt) REVERT: F 1 MET cc_start: 0.6965 (tmm) cc_final: 0.6697 (tmm) REVERT: F 7 TYR cc_start: 0.8023 (m-80) cc_final: 0.7413 (m-80) REVERT: F 141 SER cc_start: 0.8881 (t) cc_final: 0.8457 (t) REVERT: F 304 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7583 (ttp) REVERT: F 358 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8225 (mt) REVERT: F 411 PHE cc_start: 0.5303 (OUTLIER) cc_final: 0.3220 (t80) REVERT: F 580 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.7136 (t60) REVERT: G 79 MET cc_start: 0.8299 (mmm) cc_final: 0.7705 (mmt) REVERT: H 3 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7433 (pptt) REVERT: H 109 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8497 (m-40) REVERT: H 389 MET cc_start: 0.7476 (mmp) cc_final: 0.7207 (mmp) REVERT: I 168 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6611 (mmt) REVERT: J 45 ARG cc_start: 0.6933 (mtm-85) cc_final: 0.6582 (mtm180) REVERT: J 89 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: J 93 GLU cc_start: 0.7744 (pm20) cc_final: 0.7422 (pm20) REVERT: K 89 THR cc_start: 0.9049 (m) cc_final: 0.8822 (t) REVERT: N 40 LYS cc_start: 0.8655 (tppt) cc_final: 0.8063 (tptm) REVERT: N 118 GLN cc_start: 0.7508 (mm-40) cc_final: 0.6936 (mm-40) REVERT: P 28 ARG cc_start: 0.7745 (tpp80) cc_final: 0.7248 (tpp80) outliers start: 83 outliers final: 59 residues processed: 502 average time/residue: 0.1934 time to fit residues: 163.8772 Evaluate side-chains 505 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 435 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 157 TRP 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 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR 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 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 3 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 371 LYS Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 69 CYS Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 168 MET Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain S residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 76 optimal weight: 4.9990 chunk 326 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 309 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 160 optimal weight: 0.0670 chunk 210 optimal weight: 0.9990 chunk 289 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN C 99 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN F 6 GLN F 471 HIS ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129939 restraints weight = 40254.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130859 restraints weight = 30848.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131289 restraints weight = 26082.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131958 restraints weight = 24905.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132236 restraints weight = 21777.337| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 33850 Z= 0.293 Angle : 3.175 68.919 46476 Z= 1.332 Chirality : 0.424 6.417 5589 Planarity : 0.004 0.076 5365 Dihedral : 10.412 103.757 4936 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 2.84 % Allowed : 19.66 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: 0.41 (0.14), residues: 3854 helix: 1.99 (0.11), residues: 2248 sheet: -0.22 (0.37), residues: 217 loop : -2.74 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 353 TYR 0.013 0.001 TYR F 445 PHE 0.026 0.001 PHE F 352 TRP 0.036 0.001 TRP C 124 HIS 0.033 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00829 / 0.29 (33815) covalent geometry : angle 3.01868 / 1.33 (46437) hydrogen bonds : bond 0.03757 / 2.50 ( 1625) hydrogen bonds : angle 3.51788 / 2.48 ( 4824) metal coordination : bond 0.02258 / 1.38 ( 13) metal coordination : angle 34.09599 / 20.30 ( 39) Misc. bond : bond 0.00297 / 0.19 ( 22) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 446 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.7760 (ttm) cc_final: 0.7470 (mtp) REVERT: A 194 GLU cc_start: 0.6550 (mp0) cc_final: 0.5649 (mp0) REVERT: A 198 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: B 161 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6033 (tt0) REVERT: B 422 ILE cc_start: 0.8858 (tp) cc_final: 0.8569 (tt) REVERT: C 43 LEU cc_start: 0.7925 (tp) cc_final: 0.7703 (tp) REVERT: D 172 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7789 (t80) REVERT: D 435 LEU cc_start: 0.8594 (mt) cc_final: 0.8362 (mt) REVERT: F 1 MET cc_start: 0.7024 (tmm) cc_final: 0.6806 (tmm) REVERT: F 7 TYR cc_start: 0.8029 (m-80) cc_final: 0.7435 (m-80) REVERT: F 141 SER cc_start: 0.8868 (t) cc_final: 0.8461 (t) REVERT: F 304 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7581 (ttp) REVERT: F 358 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8232 (mt) REVERT: F 411 PHE cc_start: 0.5364 (OUTLIER) cc_final: 0.3240 (t80) REVERT: F 580 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.7129 (t60) REVERT: G 78 ILE cc_start: 0.8904 (mm) cc_final: 0.8492 (mt) REVERT: G 79 MET cc_start: 0.8307 (mmm) cc_final: 0.7684 (mmt) REVERT: H 389 MET cc_start: 0.7448 (mmp) cc_final: 0.7200 (mmp) REVERT: J 89 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7670 (t0) REVERT: J 93 GLU cc_start: 0.7776 (pm20) cc_final: 0.7445 (pm20) REVERT: J 127 MET cc_start: 0.8206 (mmp) cc_final: 0.7987 (mmp) REVERT: K 89 THR cc_start: 0.9025 (m) cc_final: 0.8812 (t) REVERT: N 40 LYS cc_start: 0.8665 (tppt) cc_final: 0.8056 (tptm) REVERT: N 118 GLN cc_start: 0.7516 (mm-40) cc_final: 0.6871 (mm-40) REVERT: P 28 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7242 (tpp80) outliers start: 91 outliers final: 62 residues processed: 505 average time/residue: 0.1915 time to fit residues: 162.7854 Evaluate side-chains 508 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 438 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 157 TRP 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 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 THR 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 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 371 LYS Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 216 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 339 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 302 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 372 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 HIS D 134 GLN E 87 ASN F 6 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.157066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130710 restraints weight = 40863.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131684 restraints weight = 31154.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133219 restraints weight = 27377.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133853 restraints weight = 23326.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133887 restraints weight = 20173.192| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 33850 Z= 0.294 Angle : 3.175 66.525 46476 Z= 1.332 Chirality : 0.424 6.427 5589 Planarity : 0.004 0.077 5365 Dihedral : 10.438 103.794 4936 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 2.31 % Allowed : 20.19 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: 0.48 (0.14), residues: 3854 helix: 2.05 (0.11), residues: 2237 sheet: -0.16 (0.37), residues: 217 loop : -2.69 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 45 TYR 0.018 0.001 TYR F 445 PHE 0.026 0.001 PHE F 352 TRP 0.056 0.001 TRP C 124 HIS 0.028 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.29 (33815) covalent geometry : angle 3.01969 / 1.33 (46437) hydrogen bonds : bond 0.03857 / 2.57 ( 1625) hydrogen bonds : angle 3.52695 / 2.49 ( 4824) metal coordination : bond 0.02325 / 1.36 ( 13) metal coordination : angle 33.96947 / 20.36 ( 39) Misc. bond : bond 0.00331 / 0.22 ( 22) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 438 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7764 (ttm) cc_final: 0.7482 (mtp) REVERT: A 52 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7861 (tt0) REVERT: A 194 GLU cc_start: 0.6584 (mp0) cc_final: 0.5671 (mp0) REVERT: A 198 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: B 161 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6051 (tt0) REVERT: B 422 ILE cc_start: 0.8828 (tp) cc_final: 0.8533 (tt) REVERT: C 30 SER cc_start: 0.8408 (t) cc_final: 0.8041 (t) REVERT: D 172 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7762 (t80) REVERT: F 7 TYR cc_start: 0.8048 (m-80) cc_final: 0.7459 (m-80) REVERT: F 141 SER cc_start: 0.8894 (t) cc_final: 0.8498 (t) REVERT: F 304 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7644 (ttp) REVERT: F 358 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8224 (mt) REVERT: F 411 PHE cc_start: 0.5456 (OUTLIER) cc_final: 0.3469 (t80) REVERT: F 491 VAL cc_start: 0.8970 (m) cc_final: 0.8691 (t) REVERT: F 580 TRP cc_start: 0.7646 (OUTLIER) cc_final: 0.7068 (t60) REVERT: G 78 ILE cc_start: 0.8889 (mm) cc_final: 0.8498 (mt) REVERT: G 79 MET cc_start: 0.8263 (mmm) cc_final: 0.7626 (mmt) REVERT: H 76 MET cc_start: 0.7455 (mtp) cc_final: 0.7189 (mtm) REVERT: H 373 MET cc_start: 0.7343 (mmt) cc_final: 0.7116 (mtt) REVERT: H 389 MET cc_start: 0.7536 (mmp) cc_final: 0.7297 (mmp) REVERT: J 89 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7633 (t0) REVERT: J 93 GLU cc_start: 0.7753 (pm20) cc_final: 0.7412 (pm20) REVERT: K 89 THR cc_start: 0.9061 (m) cc_final: 0.8804 (t) REVERT: N 40 LYS cc_start: 0.8658 (tppt) cc_final: 0.8038 (tptm) REVERT: N 80 GLN cc_start: 0.8050 (tt0) cc_final: 0.7850 (tt0) REVERT: N 118 GLN cc_start: 0.7505 (mm-40) cc_final: 0.6889 (mm-40) REVERT: P 28 ARG cc_start: 0.7817 (tpp80) cc_final: 0.7247 (tpp80) outliers start: 74 outliers final: 60 residues processed: 488 average time/residue: 0.1966 time to fit residues: 162.2144 Evaluate side-chains 493 residues out of total 3210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 425 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 330 TRP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 157 TRP 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 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 430 THR 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 78 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 304 MET Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 411 PHE Chi-restraints excluded: chain F residue 580 TRP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 169 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain I residue 93 LEU Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 117 CYS Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 SER Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain S residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 77 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 185 optimal weight: 0.3980 chunk 296 optimal weight: 6.9990 chunk 331 optimal weight: 0.9990 chunk 322 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 GLN C 99 HIS D 199 GLN E 87 ASN F 6 GLN ** G 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** N 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128780 restraints weight = 40864.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129034 restraints weight = 33852.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.130047 restraints weight = 28425.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130573 restraints weight = 26839.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130902 restraints weight = 23191.336| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.262 33850 Z= 0.295 Angle : 3.175 66.730 46476 Z= 1.333 Chirality : 0.424 6.426 5589 Planarity : 0.004 0.076 5365 Dihedral : 10.355 103.791 4936 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.43 % Favored : 93.54 % Rotamer: Outliers : 2.46 % Allowed : 20.26 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.03 % 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: 0.49 (0.14), residues: 3854 helix: 2.04 (0.11), residues: 2241 sheet: -0.11 (0.37), residues: 217 loop : -2.67 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 45 TYR 0.013 0.001 TYR B 336 PHE 0.026 0.001 PHE F 352 TRP 0.052 0.001 TRP C 124 HIS 0.029 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00833 / 0.30 (33815) covalent geometry : angle 3.01996 / 1.33 (46437) hydrogen bonds : bond 0.03984 / 2.65 ( 1625) hydrogen bonds : angle 3.54466 / 2.50 ( 4824) metal coordination : bond 0.02265 / 1.32 ( 13) metal coordination : angle 33.95886 / 20.34 ( 39) Misc. bond : bond 0.00316 / 0.21 ( 22) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5530.11 seconds wall clock time: 96 minutes 10.48 seconds (5770.48 seconds total)