Starting phenix.real_space_refine on Fri Feb 16 12:47:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5k_26353/02_2024/7u5k_26353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5k_26353/02_2024/7u5k_26353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5k_26353/02_2024/7u5k_26353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5k_26353/02_2024/7u5k_26353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5k_26353/02_2024/7u5k_26353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5k_26353/02_2024/7u5k_26353.pdb" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.087 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9552 2.51 5 N 2596 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15316 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 469} Chain: "B" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 469} Chain: "C" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 469} Chain: "D" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 469} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Time building chain proxies: 8.38, per 1000 atoms: 0.55 Number of scatterers: 15316 At special positions: 0 Unit cell: (129.47, 95.23, 95.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3096 8.00 N 2596 7.00 C 9552 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.21 Conformation dependent library (CDL) restraints added in 3.0 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 40.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 115 through 129 removed outlier: 3.851A pdb=" N SER A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.981A pdb=" N GLN A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.613A pdb=" N GLU A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 Processing helix chain 'A' and resid 228 through 247 removed outlier: 3.642A pdb=" N GLU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.249A pdb=" N HIS A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.628A pdb=" N PHE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.850A pdb=" N SER B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.982A pdb=" N GLN B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.613A pdb=" N GLU B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 226 Processing helix chain 'B' and resid 228 through 247 removed outlier: 3.642A pdb=" N GLU B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.249A pdb=" N HIS B 289 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.629A pdb=" N PHE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 323 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 385 through 392 Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 99 Processing helix chain 'C' and resid 115 through 129 removed outlier: 3.850A pdb=" N SER C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 3.981A pdb=" N GLN C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.612A pdb=" N GLU C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 226 Processing helix chain 'C' and resid 228 through 247 removed outlier: 3.641A pdb=" N GLU C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 286 through 292 removed outlier: 4.250A pdb=" N HIS C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.629A pdb=" N PHE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 323 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 385 through 392 Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.850A pdb=" N SER D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.982A pdb=" N GLN D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.613A pdb=" N GLU D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 Processing helix chain 'D' and resid 228 through 247 removed outlier: 3.642A pdb=" N GLU D 232 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 286 through 292 removed outlier: 4.249A pdb=" N HIS D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TRP D 291 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 301 removed outlier: 3.628A pdb=" N PHE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 323 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 385 through 392 Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.556A pdb=" N LYS D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 56 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 64 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL A 410 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 447 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP A 412 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL A 445 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 416 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 418 " --> pdb=" O CYS A 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A 437 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU A 444 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU A 455 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A 446 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.277A pdb=" N GLY A 69 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 105 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP A 71 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N HIS A 107 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N HIS A 73 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 102 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER A 136 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 104 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS A 138 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A 106 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP A 140 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL A 108 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER A 163 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR A 167 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA A 195 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 253 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 197 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 56 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU B 38 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET B 64 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL B 410 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE B 447 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP B 412 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 445 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER B 416 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 418 " --> pdb=" O CYS B 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET B 437 " --> pdb=" O ILE B 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU B 444 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 455 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL B 446 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.276A pdb=" N GLY B 69 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE B 105 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP B 71 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N HIS B 107 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N HIS B 73 " --> pdb=" O HIS B 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 102 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER B 136 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 104 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS B 138 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 106 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP B 140 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 108 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER B 163 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR B 167 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA B 195 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 253 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 197 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU C 38 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 56 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU C 38 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET C 64 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL C 410 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE C 447 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP C 412 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 445 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER C 416 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 418 " --> pdb=" O CYS C 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET C 437 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU C 444 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU C 455 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 446 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 69 through 74 removed outlier: 6.276A pdb=" N GLY C 69 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C 105 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP C 71 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N HIS C 107 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N HIS C 73 " --> pdb=" O HIS C 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 102 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER C 136 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 104 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS C 138 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP C 106 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP C 140 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 108 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N SER C 163 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR C 167 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 195 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 253 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 197 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 56 " --> pdb=" O ARG D 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 41 through 46 removed outlier: 5.080A pdb=" N ILE D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU D 38 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET D 64 " --> pdb=" O TRP D 412 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL D 410 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE D 447 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TRP D 412 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL D 445 " --> pdb=" O TRP D 412 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER D 416 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 418 " --> pdb=" O CYS D 439 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET D 437 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU D 444 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU D 455 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 446 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 69 through 74 removed outlier: 6.276A pdb=" N GLY D 69 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE D 105 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP D 71 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N HIS D 107 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N HIS D 73 " --> pdb=" O HIS D 107 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D 102 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N SER D 136 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 104 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS D 138 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP D 106 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP D 140 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 108 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER D 163 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR D 167 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 195 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR D 253 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 197 " --> pdb=" O THR D 253 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1884 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: 5.51 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5077 1.34 - 1.46: 2909 1.46 - 1.58: 7378 1.58 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 15480 Sorted by residual: bond pdb=" N LYS A 43 " pdb=" CA LYS A 43 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.28e-02 6.10e+03 6.32e+00 bond pdb=" N LYS D 43 " pdb=" CA LYS D 43 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.28e-02 6.10e+03 6.07e+00 bond pdb=" N LYS B 43 " pdb=" CA LYS B 43 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 6.02e+00 bond pdb=" N LYS A 146 " pdb=" CA LYS A 146 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.88e+00 bond pdb=" N LYS C 43 " pdb=" CA LYS C 43 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.28e-02 6.10e+03 5.78e+00 ... (remaining 15475 not shown) Histogram of bond angle deviations from ideal: 96.68 - 104.15: 297 104.15 - 111.61: 7194 111.61 - 119.08: 5487 119.08 - 126.54: 7783 126.54 - 134.01: 251 Bond angle restraints: 21012 Sorted by residual: angle pdb=" N PRO A 79 " pdb=" CD PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 103.20 97.72 5.48 1.50e+00 4.44e-01 1.33e+01 angle pdb=" N PRO C 79 " pdb=" CD PRO C 79 " pdb=" CG PRO C 79 " ideal model delta sigma weight residual 103.20 97.73 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" N PRO B 79 " pdb=" CD PRO B 79 " pdb=" CG PRO B 79 " ideal model delta sigma weight residual 103.20 97.73 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" N PRO D 79 " pdb=" CD PRO D 79 " pdb=" CG PRO D 79 " ideal model delta sigma weight residual 103.20 97.75 5.45 1.50e+00 4.44e-01 1.32e+01 angle pdb=" N LEU C 444 " pdb=" CA LEU C 444 " pdb=" C LEU C 444 " ideal model delta sigma weight residual 112.45 107.46 4.99 1.39e+00 5.18e-01 1.29e+01 ... (remaining 21007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 7836 16.21 - 32.42: 960 32.42 - 48.63: 336 48.63 - 64.84: 120 64.84 - 81.05: 28 Dihedral angle restraints: 9280 sinusoidal: 3644 harmonic: 5636 Sorted by residual: dihedral pdb=" CA LEU B 137 " pdb=" C LEU B 137 " pdb=" N HIS B 138 " pdb=" CA HIS B 138 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU A 137 " pdb=" C LEU A 137 " pdb=" N HIS A 138 " pdb=" CA HIS A 138 " ideal model delta harmonic sigma weight residual 180.00 158.26 21.74 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA LEU C 137 " pdb=" C LEU C 137 " pdb=" N HIS C 138 " pdb=" CA HIS C 138 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 9277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1688 0.038 - 0.075: 442 0.075 - 0.113: 182 0.113 - 0.151: 52 0.151 - 0.189: 8 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CA LEU D 444 " pdb=" N LEU D 444 " pdb=" C LEU D 444 " pdb=" CB LEU D 444 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 chirality pdb=" CA LEU C 444 " pdb=" N LEU C 444 " pdb=" C LEU C 444 " pdb=" CB LEU C 444 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA LEU A 444 " pdb=" N LEU A 444 " pdb=" C LEU A 444 " pdb=" CB LEU A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2369 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 219 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO C 220 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 219 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 220 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 219 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 220 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 220 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 220 " -0.031 5.00e-02 4.00e+02 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 16 2.15 - 2.84: 5003 2.84 - 3.53: 22799 3.53 - 4.21: 41895 4.21 - 4.90: 70505 Nonbonded interactions: 140218 Sorted by model distance: nonbonded pdb=" OD2 ASP A 178 " pdb=" O HOH A 601 " model vdw 1.465 2.440 nonbonded pdb=" OD2 ASP C 178 " pdb=" O HOH C 601 " model vdw 1.477 2.440 nonbonded pdb=" OD2 ASP D 178 " pdb=" O HOH D 601 " model vdw 1.478 2.440 nonbonded pdb=" OD2 ASP B 178 " pdb=" O HOH B 601 " model vdw 1.483 2.440 nonbonded pdb=" NH2 ARG D 487 " pdb=" O HOH D 602 " model vdw 1.953 2.520 ... (remaining 140213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.270 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 43.960 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.003 0.047 15480 Z= 0.190 Angle : 0.638 13.407 21012 Z= 0.359 Chirality : 0.044 0.189 2372 Planarity : 0.005 0.055 2740 Dihedral : 17.745 81.050 5664 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.48 % Allowed : 24.94 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 1964 helix: 0.89 (0.19), residues: 756 sheet: -1.39 (0.31), residues: 236 loop : 0.04 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 412 HIS 0.004 0.001 HIS B 425 PHE 0.008 0.001 PHE A 380 TYR 0.008 0.001 TYR B 182 ARG 0.008 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 298 time to evaluate : 1.840 Fit side-chains REVERT: A 43 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7756 (mmtp) REVERT: A 64 MET cc_start: 0.8164 (mtp) cc_final: 0.7736 (ptp) REVERT: A 87 ASP cc_start: 0.7906 (m-30) cc_final: 0.7308 (m-30) REVERT: A 130 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6470 (ptpp) REVERT: A 262 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6654 (mt-10) REVERT: A 266 GLN cc_start: 0.7563 (mt0) cc_final: 0.7045 (mp-120) REVERT: A 367 ASP cc_start: 0.7799 (t70) cc_final: 0.7350 (t0) REVERT: A 483 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7488 (mmtp) REVERT: B 43 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7772 (mmtp) REVERT: B 64 MET cc_start: 0.8177 (mtp) cc_final: 0.7647 (ptp) REVERT: B 87 ASP cc_start: 0.7874 (m-30) cc_final: 0.7278 (m-30) REVERT: B 122 GLN cc_start: 0.7560 (tt0) cc_final: 0.7151 (tp-100) REVERT: B 130 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6449 (ptpp) REVERT: B 153 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7076 (mt-10) REVERT: B 217 ILE cc_start: 0.7745 (mt) cc_final: 0.7544 (tp) REVERT: B 229 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: B 266 GLN cc_start: 0.7587 (mt0) cc_final: 0.7187 (mm110) REVERT: B 367 ASP cc_start: 0.7776 (t70) cc_final: 0.7317 (t0) REVERT: B 483 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7467 (mmtp) REVERT: C 43 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7729 (mmtp) REVERT: C 64 MET cc_start: 0.8168 (mtp) cc_final: 0.7623 (ptp) REVERT: C 87 ASP cc_start: 0.7904 (m-30) cc_final: 0.7311 (m-30) REVERT: C 122 GLN cc_start: 0.7545 (tt0) cc_final: 0.7147 (tp-100) REVERT: C 130 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6489 (ptpp) REVERT: C 229 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6301 (pm20) REVERT: C 266 GLN cc_start: 0.7584 (mt0) cc_final: 0.7241 (mm110) REVERT: C 367 ASP cc_start: 0.7800 (t70) cc_final: 0.7342 (t0) REVERT: C 460 HIS cc_start: 0.7111 (m-70) cc_final: 0.6692 (m-70) REVERT: C 483 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7490 (mmtp) REVERT: D 43 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7720 (mmtp) REVERT: D 64 MET cc_start: 0.8178 (mtp) cc_final: 0.7635 (ptp) REVERT: D 87 ASP cc_start: 0.7877 (m-30) cc_final: 0.7293 (m-30) REVERT: D 130 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6498 (ptpp) REVERT: D 153 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7049 (mt-10) REVERT: D 229 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: D 266 GLN cc_start: 0.7554 (mt0) cc_final: 0.7053 (mp-120) REVERT: D 367 ASP cc_start: 0.7806 (t70) cc_final: 0.7345 (t0) REVERT: D 419 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7605 (m) outliers start: 41 outliers final: 28 residues processed: 323 average time/residue: 1.2865 time to fit residues: 459.0602 Evaluate side-chains 318 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 282 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15480 Z= 0.228 Angle : 0.572 13.989 21012 Z= 0.286 Chirality : 0.044 0.146 2372 Planarity : 0.005 0.052 2740 Dihedral : 6.723 48.959 2166 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.17 % Allowed : 21.37 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 1964 helix: 1.08 (0.19), residues: 760 sheet: -1.42 (0.32), residues: 228 loop : 0.07 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 295 HIS 0.005 0.001 HIS B 145 PHE 0.009 0.002 PHE D 89 TYR 0.013 0.002 TYR B 479 ARG 0.004 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 289 time to evaluate : 1.781 Fit side-chains REVERT: A 43 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7787 (mmtp) REVERT: A 130 LYS cc_start: 0.7044 (pttt) cc_final: 0.6544 (ptpp) REVERT: A 207 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: A 229 GLU cc_start: 0.6903 (pt0) cc_final: 0.6298 (pm20) REVERT: A 244 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7347 (m-40) REVERT: A 245 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: A 262 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 266 GLN cc_start: 0.7510 (mt0) cc_final: 0.7163 (mp10) REVERT: A 275 TYR cc_start: 0.8455 (m-80) cc_final: 0.8220 (m-80) REVERT: A 315 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6876 (t70) REVERT: A 367 ASP cc_start: 0.7815 (t70) cc_final: 0.7407 (t0) REVERT: A 435 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: A 451 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7052 (mttt) REVERT: A 468 TYR cc_start: 0.7973 (t80) cc_final: 0.7227 (t80) REVERT: A 483 LYS cc_start: 0.7847 (mmtp) cc_final: 0.7597 (mmtp) REVERT: B 43 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7806 (mmtp) REVERT: B 59 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6465 (mp0) REVERT: B 83 MET cc_start: 0.6368 (mtm) cc_final: 0.5686 (mtp) REVERT: B 122 GLN cc_start: 0.7661 (tt0) cc_final: 0.7278 (tp-100) REVERT: B 130 LYS cc_start: 0.7027 (pttt) cc_final: 0.6372 (ptpp) REVERT: B 153 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 207 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: B 229 GLU cc_start: 0.7036 (pt0) cc_final: 0.6212 (pm20) REVERT: B 244 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7387 (m-40) REVERT: B 245 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7618 (tp40) REVERT: B 266 GLN cc_start: 0.7562 (mt0) cc_final: 0.7308 (mm110) REVERT: B 275 TYR cc_start: 0.8460 (m-80) cc_final: 0.8250 (m-80) REVERT: B 315 ASP cc_start: 0.7436 (m-30) cc_final: 0.6888 (t70) REVERT: B 367 ASP cc_start: 0.7798 (t70) cc_final: 0.7379 (t0) REVERT: B 435 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: B 451 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7200 (mtpt) REVERT: B 468 TYR cc_start: 0.7959 (t80) cc_final: 0.7140 (t80) REVERT: B 483 LYS cc_start: 0.7823 (mmtp) cc_final: 0.7570 (mmtp) REVERT: C 20 LYS cc_start: 0.7097 (mtmt) cc_final: 0.6654 (mtpp) REVERT: C 43 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7717 (mmtp) REVERT: C 94 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7733 (mttm) REVERT: C 122 GLN cc_start: 0.7655 (tt0) cc_final: 0.7270 (tp-100) REVERT: C 130 LYS cc_start: 0.7059 (pttt) cc_final: 0.6537 (ptpp) REVERT: C 207 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: C 229 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6205 (pm20) REVERT: C 244 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.7379 (m-40) REVERT: C 245 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7617 (tp40) REVERT: C 266 GLN cc_start: 0.7569 (mt0) cc_final: 0.7364 (mm110) REVERT: C 275 TYR cc_start: 0.8455 (m-80) cc_final: 0.8243 (m-80) REVERT: C 315 ASP cc_start: 0.7391 (m-30) cc_final: 0.6888 (t70) REVERT: C 367 ASP cc_start: 0.7816 (t70) cc_final: 0.7405 (t0) REVERT: C 451 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7208 (mtpt) REVERT: C 458 THR cc_start: 0.6221 (OUTLIER) cc_final: 0.6003 (t) REVERT: C 460 HIS cc_start: 0.7165 (m-70) cc_final: 0.6737 (m-70) REVERT: C 468 TYR cc_start: 0.7950 (t80) cc_final: 0.7133 (t80) REVERT: C 483 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7641 (mmtp) REVERT: D 43 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7751 (mmtp) REVERT: D 59 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: D 94 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7715 (mttm) REVERT: D 130 LYS cc_start: 0.7105 (pttt) cc_final: 0.6580 (ptpp) REVERT: D 207 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: D 229 GLU cc_start: 0.7069 (pt0) cc_final: 0.6232 (pm20) REVERT: D 244 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7366 (m-40) REVERT: D 245 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7612 (tp40) REVERT: D 266 GLN cc_start: 0.7509 (mt0) cc_final: 0.7160 (mp10) REVERT: D 275 TYR cc_start: 0.8445 (m-80) cc_final: 0.8226 (m-80) REVERT: D 315 ASP cc_start: 0.7376 (m-30) cc_final: 0.6878 (t70) REVERT: D 367 ASP cc_start: 0.7825 (t70) cc_final: 0.7409 (t0) REVERT: D 451 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7201 (mtpt) REVERT: D 468 TYR cc_start: 0.7965 (t80) cc_final: 0.7170 (t80) REVERT: D 483 LYS cc_start: 0.7857 (mmtp) cc_final: 0.7596 (mmtp) outliers start: 102 outliers final: 34 residues processed: 340 average time/residue: 1.3232 time to fit residues: 495.1766 Evaluate side-chains 345 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 286 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 192 optimal weight: 0.0170 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 0.4980 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15480 Z= 0.262 Angle : 0.579 13.180 21012 Z= 0.293 Chirality : 0.044 0.135 2372 Planarity : 0.005 0.049 2740 Dihedral : 5.712 40.345 2123 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.05 % Allowed : 21.07 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 1964 helix: 0.96 (0.19), residues: 756 sheet: -1.26 (0.33), residues: 228 loop : -0.01 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.004 0.001 HIS D 145 PHE 0.012 0.002 PHE D 89 TYR 0.015 0.002 TYR C 479 ARG 0.003 0.001 ARG B 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 298 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6490 (mtm) cc_final: 0.5774 (mtp) REVERT: A 130 LYS cc_start: 0.7090 (pttt) cc_final: 0.6485 (ptpp) REVERT: A 229 GLU cc_start: 0.6957 (pt0) cc_final: 0.6508 (pm20) REVERT: A 244 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7401 (m-40) REVERT: A 245 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7498 (tp40) REVERT: A 262 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 266 GLN cc_start: 0.7559 (mt0) cc_final: 0.7131 (mp10) REVERT: A 315 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6867 (t70) REVERT: A 367 ASP cc_start: 0.7880 (t70) cc_final: 0.7479 (t0) REVERT: A 451 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7212 (mttt) REVERT: A 483 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7614 (mmtp) REVERT: B 83 MET cc_start: 0.6435 (mtm) cc_final: 0.5815 (mtp) REVERT: B 122 GLN cc_start: 0.7745 (tt0) cc_final: 0.7270 (tp-100) REVERT: B 130 LYS cc_start: 0.7062 (pttt) cc_final: 0.6455 (ptpp) REVERT: B 153 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7146 (mt-10) REVERT: B 207 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: B 229 GLU cc_start: 0.6953 (pt0) cc_final: 0.6180 (pm20) REVERT: B 244 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7446 (m-40) REVERT: B 245 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7503 (tp40) REVERT: B 266 GLN cc_start: 0.7517 (mt0) cc_final: 0.7248 (mm110) REVERT: B 315 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6894 (t70) REVERT: B 367 ASP cc_start: 0.7863 (t70) cc_final: 0.7448 (t0) REVERT: B 451 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7288 (mtpt) REVERT: B 460 HIS cc_start: 0.7071 (m90) cc_final: 0.6473 (m-70) REVERT: B 483 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7582 (mmtp) REVERT: C 20 LYS cc_start: 0.7152 (mtmt) cc_final: 0.6753 (mtpp) REVERT: C 122 GLN cc_start: 0.7740 (tt0) cc_final: 0.7264 (tp-100) REVERT: C 130 LYS cc_start: 0.7091 (pttt) cc_final: 0.6481 (ptpp) REVERT: C 207 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7472 (mm-30) REVERT: C 229 GLU cc_start: 0.7029 (pt0) cc_final: 0.6352 (pm20) REVERT: C 244 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7421 (m-40) REVERT: C 245 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7504 (tp40) REVERT: C 266 GLN cc_start: 0.7525 (mt0) cc_final: 0.7270 (mm110) REVERT: C 315 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6951 (t70) REVERT: C 367 ASP cc_start: 0.7875 (t70) cc_final: 0.7470 (t0) REVERT: C 451 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7271 (mtpt) REVERT: C 458 THR cc_start: 0.6283 (OUTLIER) cc_final: 0.6076 (t) REVERT: C 460 HIS cc_start: 0.7176 (m-70) cc_final: 0.6726 (m-70) REVERT: C 483 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7610 (mmtp) REVERT: D 20 LYS cc_start: 0.7318 (mtpp) cc_final: 0.7103 (mtmt) REVERT: D 43 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7813 (mmtp) REVERT: D 83 MET cc_start: 0.6469 (mtm) cc_final: 0.5743 (mtp) REVERT: D 130 LYS cc_start: 0.7121 (pttt) cc_final: 0.6497 (ptpp) REVERT: D 207 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: D 229 GLU cc_start: 0.7043 (pt0) cc_final: 0.6233 (pm20) REVERT: D 244 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7415 (m-40) REVERT: D 245 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7502 (tp40) REVERT: D 266 GLN cc_start: 0.7555 (mt0) cc_final: 0.7130 (mp10) REVERT: D 315 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6870 (t70) REVERT: D 367 ASP cc_start: 0.7885 (t70) cc_final: 0.7473 (t0) REVERT: D 451 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7281 (mtpt) REVERT: D 483 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7602 (mmtp) outliers start: 100 outliers final: 55 residues processed: 341 average time/residue: 1.4105 time to fit residues: 525.6038 Evaluate side-chains 365 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 290 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 505 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15480 Z= 0.488 Angle : 0.697 13.774 21012 Z= 0.366 Chirality : 0.049 0.157 2372 Planarity : 0.006 0.054 2740 Dihedral : 6.143 39.412 2120 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 6.30 % Allowed : 21.55 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 1964 helix: 0.48 (0.19), residues: 748 sheet: -0.85 (0.41), residues: 196 loop : -0.33 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 295 HIS 0.005 0.001 HIS D 198 PHE 0.021 0.003 PHE C 89 TYR 0.021 0.003 TYR C 479 ARG 0.005 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 296 time to evaluate : 1.817 Fit side-chains REVERT: A 43 LYS cc_start: 0.8409 (mmpt) cc_final: 0.7842 (mmtp) REVERT: A 83 MET cc_start: 0.6777 (mtm) cc_final: 0.6066 (mtp) REVERT: A 130 LYS cc_start: 0.7215 (pttt) cc_final: 0.6492 (ptpp) REVERT: A 162 ASN cc_start: 0.8684 (p0) cc_final: 0.8432 (p0) REVERT: A 207 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: A 229 GLU cc_start: 0.7070 (pt0) cc_final: 0.6543 (pm20) REVERT: A 245 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7415 (tp40) REVERT: A 262 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 266 GLN cc_start: 0.7560 (mt0) cc_final: 0.7130 (mp10) REVERT: A 315 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: A 367 ASP cc_start: 0.7898 (t70) cc_final: 0.7513 (t0) REVERT: A 440 ARG cc_start: 0.7445 (ttp80) cc_final: 0.7135 (ttp-170) REVERT: A 451 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7543 (mtpt) REVERT: A 483 LYS cc_start: 0.7919 (mttp) cc_final: 0.7680 (mmtp) REVERT: B 43 LYS cc_start: 0.8343 (mmpt) cc_final: 0.7791 (mmtp) REVERT: B 59 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: B 83 MET cc_start: 0.6762 (mtm) cc_final: 0.6155 (mtp) REVERT: B 94 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7740 (mttm) REVERT: B 122 GLN cc_start: 0.7729 (tt0) cc_final: 0.7249 (tp-100) REVERT: B 130 LYS cc_start: 0.7166 (pttt) cc_final: 0.6488 (ptpp) REVERT: B 153 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7184 (mt-10) REVERT: B 162 ASN cc_start: 0.8688 (p0) cc_final: 0.8441 (p0) REVERT: B 207 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: B 229 GLU cc_start: 0.7059 (pt0) cc_final: 0.6230 (pm20) REVERT: B 245 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7398 (tp40) REVERT: B 266 GLN cc_start: 0.7499 (mt0) cc_final: 0.7165 (mm110) REVERT: B 315 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: B 367 ASP cc_start: 0.7880 (t70) cc_final: 0.7489 (t0) REVERT: B 451 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7570 (mtpt) REVERT: B 460 HIS cc_start: 0.7112 (m90) cc_final: 0.6835 (m90) REVERT: B 483 LYS cc_start: 0.7896 (mttp) cc_final: 0.7658 (mmtp) REVERT: C 20 LYS cc_start: 0.7185 (mtmt) cc_final: 0.6774 (mtpp) REVERT: C 43 LYS cc_start: 0.8406 (mmpt) cc_final: 0.7821 (mmtp) REVERT: C 122 GLN cc_start: 0.7731 (tt0) cc_final: 0.7245 (tp-100) REVERT: C 130 LYS cc_start: 0.7173 (pttt) cc_final: 0.6945 (mttp) REVERT: C 162 ASN cc_start: 0.8685 (p0) cc_final: 0.8441 (p0) REVERT: C 207 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: C 229 GLU cc_start: 0.7236 (pt0) cc_final: 0.6353 (pm20) REVERT: C 245 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7413 (tp40) REVERT: C 266 GLN cc_start: 0.7491 (mt0) cc_final: 0.7165 (mm110) REVERT: C 345 LYS cc_start: 0.7587 (tptp) cc_final: 0.7330 (tppp) REVERT: C 367 ASP cc_start: 0.7891 (t70) cc_final: 0.7512 (t0) REVERT: C 451 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7556 (mtpt) REVERT: C 458 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.6085 (t) REVERT: C 460 HIS cc_start: 0.7227 (m-70) cc_final: 0.6689 (m-70) REVERT: C 483 LYS cc_start: 0.7856 (mttp) cc_final: 0.7619 (mmtp) REVERT: D 43 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7872 (mmtp) REVERT: D 59 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: D 130 LYS cc_start: 0.7235 (pttt) cc_final: 0.6968 (mttp) REVERT: D 162 ASN cc_start: 0.8685 (p0) cc_final: 0.8423 (p0) REVERT: D 207 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: D 229 GLU cc_start: 0.7089 (pt0) cc_final: 0.6247 (pm20) REVERT: D 245 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7400 (tp40) REVERT: D 266 GLN cc_start: 0.7541 (mt0) cc_final: 0.7125 (mp10) REVERT: D 315 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7188 (m-30) REVERT: D 345 LYS cc_start: 0.7543 (tptp) cc_final: 0.7272 (tppp) REVERT: D 367 ASP cc_start: 0.7898 (t70) cc_final: 0.7514 (t0) REVERT: D 451 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7572 (mtpt) outliers start: 104 outliers final: 64 residues processed: 338 average time/residue: 1.3745 time to fit residues: 510.3954 Evaluate side-chains 372 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 289 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 435 GLU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 435 GLU Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 141 optimal weight: 0.0170 chunk 78 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 96 optimal weight: 0.0370 chunk 170 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS C 107 HIS D 460 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15480 Z= 0.141 Angle : 0.512 12.091 21012 Z= 0.255 Chirality : 0.042 0.138 2372 Planarity : 0.004 0.048 2740 Dihedral : 4.766 26.130 2108 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.87 % Allowed : 23.73 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 1964 helix: 1.05 (0.19), residues: 760 sheet: -1.19 (0.34), residues: 228 loop : -0.05 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 295 HIS 0.004 0.001 HIS A 138 PHE 0.008 0.001 PHE D 380 TYR 0.008 0.001 TYR D 499 ARG 0.005 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 319 time to evaluate : 1.815 Fit side-chains REVERT: A 20 LYS cc_start: 0.7209 (mtpp) cc_final: 0.6974 (mtmt) REVERT: A 43 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7695 (mmtp) REVERT: A 64 MET cc_start: 0.8623 (mtp) cc_final: 0.7965 (ptp) REVERT: A 83 MET cc_start: 0.6379 (mtm) cc_final: 0.5765 (mtp) REVERT: A 130 LYS cc_start: 0.7047 (pttt) cc_final: 0.6364 (ptpp) REVERT: A 229 GLU cc_start: 0.6915 (pt0) cc_final: 0.6502 (pm20) REVERT: A 245 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7318 (tp40) REVERT: A 262 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 266 GLN cc_start: 0.7585 (mt0) cc_final: 0.7269 (mp10) REVERT: A 315 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6857 (t70) REVERT: A 367 ASP cc_start: 0.7823 (t70) cc_final: 0.7384 (t0) REVERT: A 468 TYR cc_start: 0.7895 (t80) cc_final: 0.7177 (t80) REVERT: A 483 LYS cc_start: 0.7774 (mttp) cc_final: 0.7560 (mmtp) REVERT: B 43 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7608 (mmtp) REVERT: B 64 MET cc_start: 0.8621 (mtp) cc_final: 0.7940 (ptp) REVERT: B 83 MET cc_start: 0.6366 (mtm) cc_final: 0.5853 (mtp) REVERT: B 122 GLN cc_start: 0.7734 (tt0) cc_final: 0.7251 (tp-100) REVERT: B 130 LYS cc_start: 0.7046 (pttt) cc_final: 0.6422 (ptpp) REVERT: B 153 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7080 (mt-10) REVERT: B 229 GLU cc_start: 0.7038 (pt0) cc_final: 0.6232 (pm20) REVERT: B 245 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7371 (tp40) REVERT: B 262 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6767 (mm-30) REVERT: B 266 GLN cc_start: 0.7593 (mt0) cc_final: 0.7386 (mm110) REVERT: B 315 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6912 (t70) REVERT: B 367 ASP cc_start: 0.7801 (t70) cc_final: 0.7359 (t0) REVERT: B 460 HIS cc_start: 0.7090 (m90) cc_final: 0.6508 (m-70) REVERT: B 483 LYS cc_start: 0.7742 (mttp) cc_final: 0.7477 (mmtp) REVERT: C 20 LYS cc_start: 0.7039 (mtmt) cc_final: 0.6678 (mtpp) REVERT: C 43 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7554 (mmtp) REVERT: C 64 MET cc_start: 0.8584 (mtp) cc_final: 0.7865 (ptp) REVERT: C 122 GLN cc_start: 0.7721 (tt0) cc_final: 0.7247 (tp-100) REVERT: C 130 LYS cc_start: 0.7037 (pttt) cc_final: 0.6373 (ptpp) REVERT: C 229 GLU cc_start: 0.7070 (pt0) cc_final: 0.6397 (pm20) REVERT: C 245 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7337 (tp40) REVERT: C 262 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6771 (mm-30) REVERT: C 315 ASP cc_start: 0.7382 (m-30) cc_final: 0.6939 (t70) REVERT: C 367 ASP cc_start: 0.7822 (t70) cc_final: 0.7375 (t0) REVERT: C 460 HIS cc_start: 0.7163 (m-70) cc_final: 0.6722 (m-70) REVERT: C 483 LYS cc_start: 0.7729 (mttp) cc_final: 0.7503 (mmtp) REVERT: D 20 LYS cc_start: 0.7253 (mtpp) cc_final: 0.7023 (mtmt) REVERT: D 43 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7762 (mmtp) REVERT: D 64 MET cc_start: 0.8572 (mtp) cc_final: 0.7851 (ptp) REVERT: D 83 MET cc_start: 0.6394 (mtm) cc_final: 0.5757 (mtp) REVERT: D 130 LYS cc_start: 0.7090 (pttt) cc_final: 0.6409 (ptpp) REVERT: D 162 ASN cc_start: 0.8588 (p0) cc_final: 0.8227 (p0) REVERT: D 210 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7108 (mm-40) REVERT: D 229 GLU cc_start: 0.7027 (pt0) cc_final: 0.6232 (pm20) REVERT: D 245 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7317 (tp40) REVERT: D 266 GLN cc_start: 0.7582 (mt0) cc_final: 0.7356 (mm110) REVERT: D 315 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6880 (t70) REVERT: D 367 ASP cc_start: 0.7817 (t70) cc_final: 0.7370 (t0) REVERT: D 460 HIS cc_start: 0.7086 (m90) cc_final: 0.6496 (m-70) REVERT: D 468 TYR cc_start: 0.7904 (t80) cc_final: 0.7185 (t80) REVERT: D 483 LYS cc_start: 0.7825 (mmtp) cc_final: 0.7546 (mmtp) outliers start: 64 outliers final: 29 residues processed: 346 average time/residue: 1.3607 time to fit residues: 516.6363 Evaluate side-chains 346 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 310 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN C 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15480 Z= 0.265 Angle : 0.579 13.089 21012 Z= 0.293 Chirality : 0.044 0.150 2372 Planarity : 0.004 0.047 2740 Dihedral : 5.110 27.547 2108 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.48 % Allowed : 23.91 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 1964 helix: 0.98 (0.19), residues: 756 sheet: -0.99 (0.38), residues: 188 loop : -0.18 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 295 HIS 0.003 0.001 HIS C 425 PHE 0.012 0.002 PHE B 89 TYR 0.015 0.002 TYR D 479 ARG 0.006 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 304 time to evaluate : 1.893 Fit side-chains REVERT: A 43 LYS cc_start: 0.8270 (mmpt) cc_final: 0.7718 (mmtp) REVERT: A 83 MET cc_start: 0.6534 (mtm) cc_final: 0.5937 (mtp) REVERT: A 94 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7532 (mttm) REVERT: A 130 LYS cc_start: 0.7081 (pttt) cc_final: 0.6410 (ptpp) REVERT: A 162 ASN cc_start: 0.8652 (p0) cc_final: 0.8315 (p0) REVERT: A 229 GLU cc_start: 0.6961 (pt0) cc_final: 0.6528 (pm20) REVERT: A 245 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7453 (tp40) REVERT: A 262 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6975 (mt-10) REVERT: A 266 GLN cc_start: 0.7569 (mt0) cc_final: 0.7214 (mp10) REVERT: A 367 ASP cc_start: 0.7883 (t70) cc_final: 0.7473 (t0) REVERT: A 483 LYS cc_start: 0.7857 (mttp) cc_final: 0.7641 (mmtp) REVERT: B 43 LYS cc_start: 0.8183 (mmpt) cc_final: 0.7636 (mmtp) REVERT: B 59 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: B 83 MET cc_start: 0.6530 (mtm) cc_final: 0.6048 (mtp) REVERT: B 122 GLN cc_start: 0.7708 (tt0) cc_final: 0.7198 (tp-100) REVERT: B 130 LYS cc_start: 0.7060 (pttt) cc_final: 0.6375 (ptpp) REVERT: B 153 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7139 (mt-10) REVERT: B 162 ASN cc_start: 0.8654 (p0) cc_final: 0.8347 (p0) REVERT: B 229 GLU cc_start: 0.7080 (pt0) cc_final: 0.6232 (pm20) REVERT: B 245 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7395 (tp40) REVERT: B 266 GLN cc_start: 0.7586 (mt0) cc_final: 0.7231 (mm110) REVERT: B 315 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6880 (t70) REVERT: B 367 ASP cc_start: 0.7858 (t70) cc_final: 0.7438 (t0) REVERT: B 460 HIS cc_start: 0.7122 (m90) cc_final: 0.6544 (m-70) REVERT: B 483 LYS cc_start: 0.7792 (mttp) cc_final: 0.7559 (mmtp) REVERT: C 20 LYS cc_start: 0.7086 (mtmt) cc_final: 0.6674 (mtpp) REVERT: C 43 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7596 (mmtp) REVERT: C 83 MET cc_start: 0.6479 (mtm) cc_final: 0.5736 (mtp) REVERT: C 122 GLN cc_start: 0.7705 (tt0) cc_final: 0.7204 (tp-100) REVERT: C 130 LYS cc_start: 0.7120 (pttt) cc_final: 0.6811 (mttp) REVERT: C 162 ASN cc_start: 0.8656 (p0) cc_final: 0.8318 (p0) REVERT: C 207 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: C 229 GLU cc_start: 0.7092 (pt0) cc_final: 0.6387 (pm20) REVERT: C 245 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7409 (tp40) REVERT: C 367 ASP cc_start: 0.7875 (t70) cc_final: 0.7462 (t0) REVERT: C 460 HIS cc_start: 0.7238 (m-70) cc_final: 0.6737 (m-70) REVERT: C 483 LYS cc_start: 0.7792 (mttp) cc_final: 0.7564 (mmtp) REVERT: D 20 LYS cc_start: 0.7255 (mtpp) cc_final: 0.7004 (mtmt) REVERT: D 43 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7864 (mmtp) REVERT: D 59 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6428 (mp0) REVERT: D 83 MET cc_start: 0.6557 (mtm) cc_final: 0.5932 (mtp) REVERT: D 94 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7502 (mttm) REVERT: D 130 LYS cc_start: 0.7105 (pttt) cc_final: 0.6766 (mttp) REVERT: D 162 ASN cc_start: 0.8657 (p0) cc_final: 0.8297 (p0) REVERT: D 207 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: D 210 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7143 (mm-40) REVERT: D 229 GLU cc_start: 0.7088 (pt0) cc_final: 0.6255 (pm20) REVERT: D 245 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7475 (tp40) REVERT: D 266 GLN cc_start: 0.7574 (mt0) cc_final: 0.7206 (mp10) REVERT: D 315 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6850 (t70) REVERT: D 345 LYS cc_start: 0.6937 (tppp) cc_final: 0.6429 (tptm) REVERT: D 367 ASP cc_start: 0.7891 (t70) cc_final: 0.7470 (t0) REVERT: D 459 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7629 (mt) REVERT: D 460 HIS cc_start: 0.7158 (m90) cc_final: 0.6561 (m-70) REVERT: D 483 LYS cc_start: 0.7903 (mmtp) cc_final: 0.7624 (mmtp) outliers start: 74 outliers final: 44 residues processed: 336 average time/residue: 1.3770 time to fit residues: 506.8843 Evaluate side-chains 353 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 296 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 188 optimal weight: 0.0970 chunk 118 optimal weight: 5.9990 chunk 115 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 210 GLN B 209 GLN C 209 GLN D 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15480 Z= 0.166 Angle : 0.529 12.447 21012 Z= 0.263 Chirality : 0.042 0.135 2372 Planarity : 0.004 0.046 2740 Dihedral : 4.777 26.694 2108 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.09 % Allowed : 25.67 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 1964 helix: 1.17 (0.19), residues: 760 sheet: -1.06 (0.41), residues: 168 loop : -0.16 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 295 HIS 0.004 0.001 HIS C 145 PHE 0.009 0.001 PHE D 90 TYR 0.008 0.001 TYR D 251 ARG 0.007 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 311 time to evaluate : 1.815 Fit side-chains REVERT: A 20 LYS cc_start: 0.7058 (mtmt) cc_final: 0.6674 (mtpp) REVERT: A 43 LYS cc_start: 0.8032 (mmpt) cc_final: 0.7533 (mmtp) REVERT: A 64 MET cc_start: 0.8550 (mtp) cc_final: 0.7887 (ptp) REVERT: A 83 MET cc_start: 0.6391 (mtm) cc_final: 0.5870 (mtp) REVERT: A 94 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7622 (mttm) REVERT: A 130 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6331 (ptpp) REVERT: A 229 GLU cc_start: 0.7021 (pt0) cc_final: 0.6605 (pm20) REVERT: A 245 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7541 (tp40) REVERT: A 262 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6960 (mt-10) REVERT: A 266 GLN cc_start: 0.7578 (mt0) cc_final: 0.7338 (mm110) REVERT: A 315 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6861 (t70) REVERT: A 367 ASP cc_start: 0.7837 (t70) cc_final: 0.7401 (t0) REVERT: A 468 TYR cc_start: 0.7894 (t80) cc_final: 0.7148 (t80) REVERT: A 483 LYS cc_start: 0.7775 (mttp) cc_final: 0.7532 (mmtp) REVERT: B 43 LYS cc_start: 0.8053 (mmpt) cc_final: 0.7552 (mmtp) REVERT: B 59 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: B 83 MET cc_start: 0.6364 (mtm) cc_final: 0.5940 (mtp) REVERT: B 122 GLN cc_start: 0.7733 (tt0) cc_final: 0.7213 (tp-100) REVERT: B 130 LYS cc_start: 0.6994 (pttt) cc_final: 0.6341 (ptpp) REVERT: B 153 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 209 GLN cc_start: 0.8285 (mt0) cc_final: 0.8009 (pt0) REVERT: B 229 GLU cc_start: 0.7016 (pt0) cc_final: 0.6221 (pm20) REVERT: B 245 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7391 (tp40) REVERT: B 266 GLN cc_start: 0.7624 (mt0) cc_final: 0.7335 (mm110) REVERT: B 315 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6901 (t70) REVERT: B 367 ASP cc_start: 0.7810 (t70) cc_final: 0.7373 (t0) REVERT: B 460 HIS cc_start: 0.7059 (m90) cc_final: 0.6495 (m-70) REVERT: B 483 LYS cc_start: 0.7724 (mttp) cc_final: 0.7471 (mmtp) REVERT: C 20 LYS cc_start: 0.7103 (mtmt) cc_final: 0.6719 (mtpp) REVERT: C 43 LYS cc_start: 0.8113 (mmpt) cc_final: 0.7555 (mmtp) REVERT: C 83 MET cc_start: 0.6388 (mtm) cc_final: 0.5769 (mtp) REVERT: C 122 GLN cc_start: 0.7723 (tt0) cc_final: 0.7251 (tp-100) REVERT: C 130 LYS cc_start: 0.7026 (pttt) cc_final: 0.6704 (mttp) REVERT: C 150 GLU cc_start: 0.7064 (pp20) cc_final: 0.6821 (pp20) REVERT: C 207 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: C 209 GLN cc_start: 0.8253 (mt0) cc_final: 0.8009 (pt0) REVERT: C 229 GLU cc_start: 0.7086 (pt0) cc_final: 0.6342 (pm20) REVERT: C 262 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6909 (mm-30) REVERT: C 315 ASP cc_start: 0.7361 (m-30) cc_final: 0.6914 (t70) REVERT: C 367 ASP cc_start: 0.7830 (t70) cc_final: 0.7396 (t0) REVERT: C 458 THR cc_start: 0.6434 (OUTLIER) cc_final: 0.6219 (t) REVERT: C 460 HIS cc_start: 0.7214 (m-70) cc_final: 0.6723 (m-70) REVERT: C 483 LYS cc_start: 0.7738 (mttp) cc_final: 0.7520 (mmtp) REVERT: D 16 ARG cc_start: 0.7567 (mtt90) cc_final: 0.6983 (mtp-110) REVERT: D 20 LYS cc_start: 0.7212 (mtpp) cc_final: 0.7006 (mtmt) REVERT: D 43 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7807 (mmtp) REVERT: D 59 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: D 63 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7942 (mtt180) REVERT: D 64 MET cc_start: 0.8632 (mtp) cc_final: 0.7932 (ptp) REVERT: D 83 MET cc_start: 0.6417 (mtm) cc_final: 0.5846 (mtp) REVERT: D 94 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7566 (mttm) REVERT: D 130 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6283 (ptpp) REVERT: D 150 GLU cc_start: 0.7017 (pp20) cc_final: 0.6792 (pp20) REVERT: D 162 ASN cc_start: 0.8631 (p0) cc_final: 0.8276 (p0) REVERT: D 207 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: D 209 GLN cc_start: 0.8221 (mt0) cc_final: 0.7993 (pt0) REVERT: D 229 GLU cc_start: 0.7031 (pt0) cc_final: 0.6252 (pm20) REVERT: D 245 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7413 (tp40) REVERT: D 266 GLN cc_start: 0.7583 (mt0) cc_final: 0.7349 (mm110) REVERT: D 315 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6859 (t70) REVERT: D 367 ASP cc_start: 0.7834 (t70) cc_final: 0.7392 (t0) REVERT: D 460 HIS cc_start: 0.7144 (m90) cc_final: 0.6565 (m-70) REVERT: D 468 TYR cc_start: 0.7896 (t80) cc_final: 0.7158 (t80) REVERT: D 483 LYS cc_start: 0.7732 (mmtp) cc_final: 0.7456 (mmtp) outliers start: 51 outliers final: 32 residues processed: 334 average time/residue: 1.3788 time to fit residues: 506.3417 Evaluate side-chains 346 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 299 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15480 Z= 0.186 Angle : 0.544 12.823 21012 Z= 0.270 Chirality : 0.043 0.144 2372 Planarity : 0.004 0.047 2740 Dihedral : 4.797 27.150 2108 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.30 % Allowed : 24.64 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 1964 helix: 1.17 (0.19), residues: 760 sheet: -0.98 (0.41), residues: 168 loop : -0.13 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 295 HIS 0.004 0.001 HIS D 425 PHE 0.008 0.001 PHE D 90 TYR 0.010 0.001 TYR D 479 ARG 0.007 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 293 time to evaluate : 1.860 Fit side-chains REVERT: A 20 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6659 (mtpp) REVERT: A 43 LYS cc_start: 0.8029 (mmpt) cc_final: 0.7540 (mmtp) REVERT: A 83 MET cc_start: 0.6461 (mtm) cc_final: 0.5967 (mtp) REVERT: A 94 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7550 (mttm) REVERT: A 130 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6327 (ptpp) REVERT: A 229 GLU cc_start: 0.7030 (pt0) cc_final: 0.6606 (pm20) REVERT: A 245 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7555 (tp40) REVERT: A 262 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6973 (mt-10) REVERT: A 266 GLN cc_start: 0.7583 (mt0) cc_final: 0.7339 (mm110) REVERT: A 315 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6853 (t70) REVERT: A 367 ASP cc_start: 0.7837 (t70) cc_final: 0.7413 (t0) REVERT: A 435 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: A 483 LYS cc_start: 0.7819 (mttp) cc_final: 0.7567 (mmtp) REVERT: B 43 LYS cc_start: 0.8067 (mmpt) cc_final: 0.7577 (mmtp) REVERT: B 59 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: B 63 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7954 (mtt180) REVERT: B 83 MET cc_start: 0.6425 (mtm) cc_final: 0.6005 (mtp) REVERT: B 122 GLN cc_start: 0.7717 (tt0) cc_final: 0.7222 (tp-100) REVERT: B 130 LYS cc_start: 0.6925 (pttt) cc_final: 0.6250 (ptpp) REVERT: B 153 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 229 GLU cc_start: 0.6962 (pt0) cc_final: 0.6211 (pm20) REVERT: B 245 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7549 (tp40) REVERT: B 266 GLN cc_start: 0.7594 (mt0) cc_final: 0.7319 (mm110) REVERT: B 315 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6892 (t70) REVERT: B 362 MET cc_start: 0.8478 (mtm) cc_final: 0.8123 (mtm) REVERT: B 367 ASP cc_start: 0.7864 (t70) cc_final: 0.7422 (t0) REVERT: B 451 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7315 (mtpt) REVERT: B 460 HIS cc_start: 0.7063 (m90) cc_final: 0.6516 (m-70) REVERT: B 483 LYS cc_start: 0.7735 (mttp) cc_final: 0.7473 (mmtp) REVERT: C 20 LYS cc_start: 0.7103 (mtmt) cc_final: 0.6726 (mtpp) REVERT: C 43 LYS cc_start: 0.8086 (mmpt) cc_final: 0.7514 (mmtp) REVERT: C 83 MET cc_start: 0.6446 (mtm) cc_final: 0.5845 (mtp) REVERT: C 122 GLN cc_start: 0.7681 (tt0) cc_final: 0.7221 (tp-100) REVERT: C 130 LYS cc_start: 0.6983 (pttt) cc_final: 0.6660 (mttp) REVERT: C 150 GLU cc_start: 0.6969 (pp20) cc_final: 0.6728 (pp20) REVERT: C 207 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: C 209 GLN cc_start: 0.8248 (mt0) cc_final: 0.7806 (pt0) REVERT: C 229 GLU cc_start: 0.7042 (pt0) cc_final: 0.6315 (pm20) REVERT: C 262 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6916 (mm-30) REVERT: C 315 ASP cc_start: 0.7359 (m-30) cc_final: 0.6909 (t70) REVERT: C 367 ASP cc_start: 0.7880 (t70) cc_final: 0.7440 (t0) REVERT: C 451 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7304 (mtpt) REVERT: C 458 THR cc_start: 0.6443 (OUTLIER) cc_final: 0.6233 (t) REVERT: C 460 HIS cc_start: 0.7226 (m-70) cc_final: 0.6736 (m-70) REVERT: C 483 LYS cc_start: 0.7757 (mttp) cc_final: 0.7515 (mmtp) REVERT: D 16 ARG cc_start: 0.7580 (mtt90) cc_final: 0.7008 (mtp-110) REVERT: D 43 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7790 (mmtp) REVERT: D 59 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: D 63 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7951 (mtt180) REVERT: D 83 MET cc_start: 0.6488 (mtm) cc_final: 0.5917 (mtp) REVERT: D 94 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7570 (mttm) REVERT: D 130 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6659 (mttp) REVERT: D 150 GLU cc_start: 0.7005 (pp20) cc_final: 0.6782 (pp20) REVERT: D 210 GLN cc_start: 0.7541 (tp40) cc_final: 0.7189 (mm110) REVERT: D 229 GLU cc_start: 0.6998 (pt0) cc_final: 0.6224 (pm20) REVERT: D 245 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7615 (tp40) REVERT: D 315 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6866 (t70) REVERT: D 367 ASP cc_start: 0.7880 (t70) cc_final: 0.7438 (t0) REVERT: D 451 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7294 (mtpt) REVERT: D 460 HIS cc_start: 0.7150 (m90) cc_final: 0.6808 (m90) REVERT: D 483 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7495 (mmtp) outliers start: 71 outliers final: 43 residues processed: 328 average time/residue: 1.3755 time to fit residues: 494.4146 Evaluate side-chains 345 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 284 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 5.9990 chunk 180 optimal weight: 0.0870 chunk 165 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15480 Z= 0.239 Angle : 0.581 13.991 21012 Z= 0.290 Chirality : 0.044 0.155 2372 Planarity : 0.004 0.046 2740 Dihedral : 5.013 27.521 2108 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.06 % Allowed : 25.12 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 1964 helix: 1.04 (0.19), residues: 760 sheet: -1.02 (0.42), residues: 168 loop : -0.17 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.005 0.001 HIS D 425 PHE 0.012 0.002 PHE D 90 TYR 0.013 0.002 TYR D 479 ARG 0.007 0.000 ARG D 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 286 time to evaluate : 1.839 Fit side-chains REVERT: A 20 LYS cc_start: 0.7121 (mtmt) cc_final: 0.6728 (mtpp) REVERT: A 43 LYS cc_start: 0.8059 (mmpt) cc_final: 0.7579 (mmtp) REVERT: A 83 MET cc_start: 0.6508 (mtm) cc_final: 0.6005 (mtp) REVERT: A 94 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7587 (mttm) REVERT: A 130 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6284 (ptpp) REVERT: A 162 ASN cc_start: 0.8648 (p0) cc_final: 0.8292 (p0) REVERT: A 229 GLU cc_start: 0.6958 (pt0) cc_final: 0.6511 (pm20) REVERT: A 245 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7533 (tp40) REVERT: A 262 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6865 (mt-10) REVERT: A 266 GLN cc_start: 0.7571 (mt0) cc_final: 0.7227 (mp10) REVERT: A 362 MET cc_start: 0.8478 (mtm) cc_final: 0.8050 (mtm) REVERT: A 367 ASP cc_start: 0.7888 (t70) cc_final: 0.7472 (t0) REVERT: A 483 LYS cc_start: 0.7804 (mttp) cc_final: 0.7586 (mmtp) REVERT: B 43 LYS cc_start: 0.8095 (mmpt) cc_final: 0.7624 (mmtp) REVERT: B 59 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6459 (mp0) REVERT: B 83 MET cc_start: 0.6466 (mtm) cc_final: 0.6076 (mtp) REVERT: B 122 GLN cc_start: 0.7724 (tt0) cc_final: 0.7222 (tp-100) REVERT: B 130 LYS cc_start: 0.6950 (pttt) cc_final: 0.6271 (ptpp) REVERT: B 153 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 162 ASN cc_start: 0.8658 (p0) cc_final: 0.8315 (p0) REVERT: B 229 GLU cc_start: 0.7013 (pt0) cc_final: 0.6247 (pm20) REVERT: B 245 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7578 (tp40) REVERT: B 266 GLN cc_start: 0.7590 (mt0) cc_final: 0.7336 (mm110) REVERT: B 315 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6888 (t70) REVERT: B 362 MET cc_start: 0.8478 (mtm) cc_final: 0.8008 (mtm) REVERT: B 367 ASP cc_start: 0.7865 (t70) cc_final: 0.7438 (t0) REVERT: B 451 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7478 (mtpt) REVERT: B 460 HIS cc_start: 0.7089 (m90) cc_final: 0.6524 (m-70) REVERT: B 483 LYS cc_start: 0.7757 (mttp) cc_final: 0.7532 (mmtp) REVERT: C 20 LYS cc_start: 0.7049 (mtmt) cc_final: 0.6636 (mtpp) REVERT: C 43 LYS cc_start: 0.8145 (mmpt) cc_final: 0.7559 (mmtp) REVERT: C 83 MET cc_start: 0.6406 (mtm) cc_final: 0.5822 (mtp) REVERT: C 122 GLN cc_start: 0.7690 (tt0) cc_final: 0.7221 (tp-100) REVERT: C 130 LYS cc_start: 0.7120 (pttt) cc_final: 0.6821 (mttp) REVERT: C 162 ASN cc_start: 0.8649 (p0) cc_final: 0.8295 (p0) REVERT: C 207 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: C 229 GLU cc_start: 0.7063 (pt0) cc_final: 0.6334 (pm20) REVERT: C 367 ASP cc_start: 0.7877 (t70) cc_final: 0.7451 (t0) REVERT: C 451 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7404 (mtpt) REVERT: C 460 HIS cc_start: 0.7233 (m-70) cc_final: 0.6697 (m-70) REVERT: C 483 LYS cc_start: 0.7751 (mttp) cc_final: 0.7498 (mmtp) REVERT: C 487 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6950 (mtt180) REVERT: D 16 ARG cc_start: 0.7581 (mtt90) cc_final: 0.7006 (mtp-110) REVERT: D 20 LYS cc_start: 0.7061 (mtmt) cc_final: 0.6619 (mtpp) REVERT: D 43 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7861 (mmtp) REVERT: D 59 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: D 63 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7959 (mtt180) REVERT: D 83 MET cc_start: 0.6515 (mtm) cc_final: 0.5970 (mtp) REVERT: D 94 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7521 (mttm) REVERT: D 130 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6665 (mttp) REVERT: D 162 ASN cc_start: 0.8631 (p0) cc_final: 0.8319 (p0) REVERT: D 210 GLN cc_start: 0.7505 (tp40) cc_final: 0.7130 (mm110) REVERT: D 229 GLU cc_start: 0.7047 (pt0) cc_final: 0.6260 (pm20) REVERT: D 245 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7651 (tp40) REVERT: D 315 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6866 (t70) REVERT: D 362 MET cc_start: 0.8481 (mtm) cc_final: 0.8050 (mtm) REVERT: D 367 ASP cc_start: 0.7895 (t70) cc_final: 0.7463 (t0) REVERT: D 451 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7404 (mtpt) REVERT: D 459 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7556 (mt) REVERT: D 460 HIS cc_start: 0.7127 (m90) cc_final: 0.6759 (m90) REVERT: D 483 LYS cc_start: 0.7796 (mmtp) cc_final: 0.7547 (mmtp) outliers start: 67 outliers final: 48 residues processed: 319 average time/residue: 1.3556 time to fit residues: 474.6470 Evaluate side-chains 350 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 286 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 94 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 323 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 451 LYS Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 0.0870 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 460 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15480 Z= 0.166 Angle : 0.542 13.014 21012 Z= 0.266 Chirality : 0.042 0.143 2372 Planarity : 0.004 0.046 2740 Dihedral : 4.680 26.776 2108 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.75 % Allowed : 25.42 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 1964 helix: 1.23 (0.19), residues: 760 sheet: -0.89 (0.43), residues: 168 loop : -0.13 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.006 0.001 HIS B 425 PHE 0.008 0.001 PHE D 90 TYR 0.009 0.001 TYR A 251 ARG 0.007 0.000 ARG A 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 283 time to evaluate : 1.770 Fit side-chains REVERT: A 20 LYS cc_start: 0.7059 (mtmt) cc_final: 0.6658 (mtpp) REVERT: A 43 LYS cc_start: 0.8031 (mmpt) cc_final: 0.7535 (mmtp) REVERT: A 64 MET cc_start: 0.8568 (mtp) cc_final: 0.7883 (ptp) REVERT: A 83 MET cc_start: 0.6362 (mtm) cc_final: 0.5905 (mtp) REVERT: A 130 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6296 (ptpp) REVERT: A 229 GLU cc_start: 0.7021 (pt0) cc_final: 0.6593 (pm20) REVERT: A 262 GLU cc_start: 0.7253 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 266 GLN cc_start: 0.7575 (mt0) cc_final: 0.7347 (mm110) REVERT: A 362 MET cc_start: 0.8451 (mtm) cc_final: 0.8071 (mtm) REVERT: A 367 ASP cc_start: 0.7885 (t70) cc_final: 0.7449 (t0) REVERT: A 468 TYR cc_start: 0.7896 (t80) cc_final: 0.7189 (t80) REVERT: A 483 LYS cc_start: 0.7746 (mttp) cc_final: 0.7531 (mmtp) REVERT: B 43 LYS cc_start: 0.8022 (mmpt) cc_final: 0.7572 (mmtp) REVERT: B 59 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: B 63 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7973 (mtt180) REVERT: B 64 MET cc_start: 0.8570 (mtp) cc_final: 0.7883 (ptp) REVERT: B 83 MET cc_start: 0.6314 (mtm) cc_final: 0.5944 (mtp) REVERT: B 122 GLN cc_start: 0.7714 (tt0) cc_final: 0.7186 (tp-100) REVERT: B 130 LYS cc_start: 0.6950 (pttt) cc_final: 0.6298 (ptpp) REVERT: B 153 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7092 (mt-10) REVERT: B 229 GLU cc_start: 0.6930 (pt0) cc_final: 0.6143 (pm20) REVERT: B 245 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: B 266 GLN cc_start: 0.7562 (mt0) cc_final: 0.7329 (mm110) REVERT: B 315 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6878 (t70) REVERT: B 362 MET cc_start: 0.8443 (mtm) cc_final: 0.8113 (mtm) REVERT: B 367 ASP cc_start: 0.7859 (t70) cc_final: 0.7421 (t0) REVERT: B 451 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7318 (mtpt) REVERT: B 460 HIS cc_start: 0.7031 (m90) cc_final: 0.6478 (m-70) REVERT: B 483 LYS cc_start: 0.7697 (mttp) cc_final: 0.7489 (mmtp) REVERT: C 20 LYS cc_start: 0.7056 (mtmt) cc_final: 0.6663 (mtpp) REVERT: C 43 LYS cc_start: 0.8081 (mmpt) cc_final: 0.7499 (mmtp) REVERT: C 64 MET cc_start: 0.8551 (mtp) cc_final: 0.7870 (ptp) REVERT: C 83 MET cc_start: 0.6364 (mtm) cc_final: 0.5799 (mtp) REVERT: C 122 GLN cc_start: 0.7704 (tt0) cc_final: 0.7221 (tp-100) REVERT: C 130 LYS cc_start: 0.6934 (pttt) cc_final: 0.6577 (mttp) REVERT: C 150 GLU cc_start: 0.7018 (pp20) cc_final: 0.6717 (pp20) REVERT: C 209 GLN cc_start: 0.8483 (mt0) cc_final: 0.8143 (pt0) REVERT: C 229 GLU cc_start: 0.7036 (pt0) cc_final: 0.6317 (pm20) REVERT: C 245 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7533 (tp40) REVERT: C 315 ASP cc_start: 0.7338 (m-30) cc_final: 0.6944 (t70) REVERT: C 367 ASP cc_start: 0.7838 (t70) cc_final: 0.7391 (t0) REVERT: C 451 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7316 (mtpt) REVERT: C 460 HIS cc_start: 0.7152 (m90) cc_final: 0.6701 (m-70) REVERT: C 483 LYS cc_start: 0.7722 (mttp) cc_final: 0.7488 (mmtp) REVERT: C 487 ARG cc_start: 0.7265 (mtt180) cc_final: 0.6936 (mtt180) REVERT: D 16 ARG cc_start: 0.7566 (mtt90) cc_final: 0.7024 (mtp-110) REVERT: D 20 LYS cc_start: 0.7060 (mtmt) cc_final: 0.6620 (mtpp) REVERT: D 43 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7834 (mmtp) REVERT: D 58 ILE cc_start: 0.8129 (mp) cc_final: 0.7922 (pt) REVERT: D 59 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: D 64 MET cc_start: 0.8557 (mtp) cc_final: 0.7859 (ptp) REVERT: D 83 MET cc_start: 0.6378 (mtm) cc_final: 0.5877 (mtp) REVERT: D 130 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6239 (ptpp) REVERT: D 150 GLU cc_start: 0.7085 (pp20) cc_final: 0.6798 (pp20) REVERT: D 153 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7130 (mt-10) REVERT: D 229 GLU cc_start: 0.7009 (pt0) cc_final: 0.6240 (pm20) REVERT: D 245 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7627 (tp40) REVERT: D 315 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6849 (t70) REVERT: D 362 MET cc_start: 0.8453 (mtm) cc_final: 0.8081 (mtm) REVERT: D 367 ASP cc_start: 0.7886 (t70) cc_final: 0.7446 (t0) REVERT: D 460 HIS cc_start: 0.7114 (m90) cc_final: 0.6768 (m90) REVERT: D 468 TYR cc_start: 0.7873 (t80) cc_final: 0.7124 (t80) REVERT: D 483 LYS cc_start: 0.7755 (mmtp) cc_final: 0.7457 (mmtp) outliers start: 62 outliers final: 41 residues processed: 312 average time/residue: 1.4285 time to fit residues: 490.4199 Evaluate side-chains 332 residues out of total 1652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 280 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 439 CYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 439 CYS Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 323 CYS Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain D residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.149790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.126783 restraints weight = 15617.280| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.14 r_work: 0.3132 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15480 Z= 0.231 Angle : 0.582 14.269 21012 Z= 0.287 Chirality : 0.044 0.159 2372 Planarity : 0.004 0.046 2740 Dihedral : 4.908 27.330 2108 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.69 % Allowed : 25.42 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.18), residues: 1964 helix: 1.07 (0.19), residues: 760 sheet: -0.94 (0.42), residues: 168 loop : -0.15 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.006 0.001 HIS B 425 PHE 0.011 0.002 PHE B 90 TYR 0.012 0.002 TYR C 479 ARG 0.007 0.000 ARG A 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7206.30 seconds wall clock time: 128 minutes 29.71 seconds (7709.71 seconds total)