Starting phenix.real_space_refine on Tue Apr 9 03:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvh_17966/04_2024/8pvh_17966.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvh_17966/04_2024/8pvh_17966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvh_17966/04_2024/8pvh_17966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvh_17966/04_2024/8pvh_17966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvh_17966/04_2024/8pvh_17966.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvh_17966/04_2024/8pvh_17966.pdb" } resolution = 2.9 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= 0.005 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: 5 Type Number sf(0) Gaussians S 76 5.16 5 Cl 4 4.86 5 C 9684 2.51 5 N 2568 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15172 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} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.66, per 1000 atoms: 0.50 Number of scatterers: 15172 At special positions: 0 Unit cell: (105.187, 98.4555, 103.504, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 76 16.00 O 2840 8.00 N 2568 7.00 C 9684 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: 5.79 Conformation dependent library (CDL) restraints added in 3.3 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: 3568 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 45.8% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP A 136 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 171 through 186 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 199 through 213 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 137 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 171 through 186 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 171 through 186 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 199 through 213 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 137 " --> pdb=" O CYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 171 through 186 Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 199 through 213 Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 347 through 364 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= 2, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE A 38 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN A 51 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 40 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR A 153 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS A 163 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS A 193 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL A 386 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 309 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A 411 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL A 311 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE A 433 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 277 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA A 430 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE A 381 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 23 through 25 Processing sheet with id= 8, first strand: chain 'B' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE B 38 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN B 51 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR B 153 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS B 193 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN B 165 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL B 386 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 309 " --> pdb=" O MET B 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE B 411 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 311 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE B 433 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 277 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 430 " --> pdb=" O TRP B 453 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE B 381 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 23 through 25 Processing sheet with id= 14, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR C 153 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS C 163 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS C 193 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL C 386 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 309 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE C 411 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 311 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE C 433 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 277 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 430 " --> pdb=" O TRP C 453 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'C' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE C 381 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 23 through 25 Processing sheet with id= 20, first strand: chain 'D' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN D 51 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR D 153 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS D 163 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS D 193 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN D 165 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE D 309 " --> pdb=" O MET D 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE D 411 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL D 311 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE D 433 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE D 277 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 430 " --> pdb=" O TRP D 453 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE D 381 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2100 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: 4.96 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3300 1.34 - 1.46: 4508 1.46 - 1.58: 7580 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 15496 Sorted by residual: bond pdb=" CA PRO D 215 " pdb=" C PRO D 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA PRO A 215 " pdb=" C PRO A 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA PRO B 215 " pdb=" C PRO B 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA SER B 185 " pdb=" CB SER B 185 " ideal model delta sigma weight residual 1.528 1.473 0.056 1.56e-02 4.11e+03 1.27e+01 ... (remaining 15491 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.65: 584 106.65 - 113.78: 7452 113.78 - 120.91: 7860 120.91 - 128.03: 4984 128.03 - 135.16: 104 Bond angle restraints: 20984 Sorted by residual: angle pdb=" CA PHE D 469 " pdb=" CB PHE D 469 " pdb=" CG PHE D 469 " ideal model delta sigma weight residual 113.80 119.84 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" CA PHE C 469 " pdb=" CB PHE C 469 " pdb=" CG PHE C 469 " ideal model delta sigma weight residual 113.80 119.84 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" CA PHE B 469 " pdb=" CB PHE B 469 " pdb=" CG PHE B 469 " ideal model delta sigma weight residual 113.80 119.84 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" CA PHE A 469 " pdb=" CB PHE A 469 " pdb=" CG PHE A 469 " ideal model delta sigma weight residual 113.80 119.84 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" CB GLU B 47 " pdb=" CG GLU B 47 " pdb=" CD GLU B 47 " ideal model delta sigma weight residual 112.60 121.85 -9.25 1.70e+00 3.46e-01 2.96e+01 ... (remaining 20979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 8104 15.25 - 30.49: 800 30.49 - 45.73: 188 45.73 - 60.98: 104 60.98 - 76.22: 48 Dihedral angle restraints: 9244 sinusoidal: 3644 harmonic: 5600 Sorted by residual: dihedral pdb=" CA PRO B 275 " pdb=" C PRO B 275 " pdb=" N CYS B 276 " pdb=" CA CYS B 276 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PRO A 275 " pdb=" C PRO A 275 " pdb=" N CYS A 276 " pdb=" CA CYS A 276 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PRO D 275 " pdb=" C PRO D 275 " pdb=" N CYS D 276 " pdb=" CA CYS D 276 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 9241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1040 0.050 - 0.101: 692 0.101 - 0.151: 440 0.151 - 0.202: 124 0.202 - 0.252: 28 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA ASN A 455 " pdb=" N ASN A 455 " pdb=" C ASN A 455 " pdb=" CB ASN A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASN C 455 " pdb=" N ASN C 455 " pdb=" C ASN C 455 " pdb=" CB ASN C 455 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASN D 455 " pdb=" N ASN D 455 " pdb=" C ASN D 455 " pdb=" CB ASN D 455 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2321 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 265 " -0.233 9.50e-02 1.11e+02 1.07e-01 1.34e+01 pdb=" NE ARG D 265 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG D 265 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG D 265 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG D 265 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 265 " 0.233 9.50e-02 1.11e+02 1.07e-01 1.34e+01 pdb=" NE ARG C 265 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 265 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG C 265 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 265 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 265 " -0.233 9.50e-02 1.11e+02 1.07e-01 1.34e+01 pdb=" NE ARG B 265 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 265 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG B 265 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 265 " 0.006 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5636 2.93 - 3.42: 14702 3.42 - 3.91: 27148 3.91 - 4.41: 32116 4.41 - 4.90: 50954 Nonbonded interactions: 130556 Sorted by model distance: nonbonded pdb=" OD1 ASP C 438 " pdb=" N SER D 497 " model vdw 2.437 2.520 nonbonded pdb=" N SER C 497 " pdb=" OD1 ASP D 438 " model vdw 2.437 2.520 nonbonded pdb=" OD1 ASP A 438 " pdb=" N SER B 497 " model vdw 2.437 2.520 nonbonded pdb=" N SER A 497 " pdb=" OD1 ASP B 438 " model vdw 2.437 2.520 nonbonded pdb=" OE1 GLU C 312 " pdb=" OG SER C 314 " model vdw 2.528 2.440 ... (remaining 130551 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: 2.960 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: 7.420 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 41.410 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.010 0.056 15496 Z= 0.634 Angle : 1.695 9.248 20984 Z= 1.159 Chirality : 0.084 0.252 2324 Planarity : 0.010 0.107 2716 Dihedral : 15.363 76.218 5676 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.04 % Favored : 97.76 % Rotamer: Outliers : 1.49 % Allowed : 5.46 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.17), residues: 1964 helix: -0.92 (0.15), residues: 792 sheet: -0.01 (0.24), residues: 412 loop : -0.65 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP A 178 HIS 0.012 0.004 HIS B 204 PHE 0.038 0.008 PHE A 151 TYR 0.037 0.008 TYR B 481 ARG 0.045 0.007 ARG A 265 *********************** 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 496 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 472 time to evaluate : 1.636 Fit side-chains REVERT: A 22 LYS cc_start: 0.6530 (mttt) cc_final: 0.6284 (mtmt) REVERT: A 31 ASP cc_start: 0.7135 (m-30) cc_final: 0.6585 (p0) REVERT: A 51 GLN cc_start: 0.6239 (mm110) cc_final: 0.5951 (mm-40) REVERT: A 53 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7026 (mm-30) REVERT: A 57 LYS cc_start: 0.6739 (tttm) cc_final: 0.6534 (ttmt) REVERT: A 84 GLU cc_start: 0.6639 (tp30) cc_final: 0.5713 (mm-30) REVERT: A 97 GLU cc_start: 0.6025 (tt0) cc_final: 0.5621 (tt0) REVERT: A 109 MET cc_start: 0.7441 (ttm) cc_final: 0.7002 (mtm) REVERT: A 110 ASN cc_start: 0.7969 (t0) cc_final: 0.7716 (t0) REVERT: A 115 TYR cc_start: 0.7381 (t80) cc_final: 0.7158 (t80) REVERT: A 119 TYR cc_start: 0.7540 (t80) cc_final: 0.7118 (t80) REVERT: A 158 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6927 (tt0) REVERT: A 175 MET cc_start: 0.8095 (mmp) cc_final: 0.7870 (mmm) REVERT: A 238 ASP cc_start: 0.6962 (t70) cc_final: 0.6708 (t0) REVERT: A 240 ASP cc_start: 0.7231 (m-30) cc_final: 0.6758 (m-30) REVERT: A 245 THR cc_start: 0.7707 (m) cc_final: 0.7507 (p) REVERT: A 253 LEU cc_start: 0.7140 (mt) cc_final: 0.6899 (mm) REVERT: A 256 GLU cc_start: 0.6988 (tt0) cc_final: 0.6682 (tt0) REVERT: A 265 ARG cc_start: 0.7054 (mpt90) cc_final: 0.6752 (mmt-90) REVERT: A 293 HIS cc_start: 0.6754 (m-70) cc_final: 0.5122 (t-90) REVERT: A 315 ILE cc_start: 0.6977 (pt) cc_final: 0.6507 (pt) REVERT: A 321 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: A 329 LYS cc_start: 0.7457 (mttt) cc_final: 0.6991 (mtpm) REVERT: A 341 THR cc_start: 0.7461 (p) cc_final: 0.7228 (p) REVERT: A 356 ASP cc_start: 0.6114 (t70) cc_final: 0.5897 (t70) REVERT: A 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mtpt) REVERT: A 364 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6142 (mt-10) REVERT: A 380 TYR cc_start: 0.6750 (m-80) cc_final: 0.5946 (m-80) REVERT: A 394 MET cc_start: 0.7472 (mtt) cc_final: 0.7108 (mtt) REVERT: A 399 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 415 ASP cc_start: 0.6841 (m-30) cc_final: 0.6342 (p0) REVERT: A 416 ASP cc_start: 0.5713 (t70) cc_final: 0.5307 (t0) REVERT: A 423 ASN cc_start: 0.6753 (t0) cc_final: 0.6522 (t0) REVERT: A 425 PHE cc_start: 0.7674 (m-80) cc_final: 0.7382 (m-80) REVERT: A 436 ASP cc_start: 0.7105 (t70) cc_final: 0.6425 (t0) REVERT: A 477 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7079 (mm-30) REVERT: A 480 GLU cc_start: 0.7684 (tt0) cc_final: 0.7044 (tt0) REVERT: B 22 LYS cc_start: 0.6531 (mttt) cc_final: 0.6285 (mtmt) REVERT: B 31 ASP cc_start: 0.7131 (m-30) cc_final: 0.6582 (p0) REVERT: B 51 GLN cc_start: 0.6240 (mm110) cc_final: 0.5950 (mm-40) REVERT: B 53 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7032 (mm-30) REVERT: B 57 LYS cc_start: 0.6738 (tttm) cc_final: 0.6535 (ttmt) REVERT: B 84 GLU cc_start: 0.6638 (tp30) cc_final: 0.5713 (mm-30) REVERT: B 94 ASP cc_start: 0.7192 (m-30) cc_final: 0.6989 (m-30) REVERT: B 97 GLU cc_start: 0.6024 (tt0) cc_final: 0.5621 (tt0) REVERT: B 109 MET cc_start: 0.7440 (ttm) cc_final: 0.7002 (mtm) REVERT: B 110 ASN cc_start: 0.7966 (t0) cc_final: 0.7714 (t0) REVERT: B 115 TYR cc_start: 0.7382 (t80) cc_final: 0.7157 (t80) REVERT: B 119 TYR cc_start: 0.7540 (t80) cc_final: 0.7118 (t80) REVERT: B 158 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6925 (tt0) REVERT: B 175 MET cc_start: 0.8095 (mmp) cc_final: 0.7870 (mmm) REVERT: B 238 ASP cc_start: 0.6961 (t70) cc_final: 0.6707 (t0) REVERT: B 240 ASP cc_start: 0.7231 (m-30) cc_final: 0.6758 (m-30) REVERT: B 245 THR cc_start: 0.7707 (m) cc_final: 0.7507 (p) REVERT: B 253 LEU cc_start: 0.7141 (mt) cc_final: 0.6900 (mm) REVERT: B 256 GLU cc_start: 0.6987 (tt0) cc_final: 0.6682 (tt0) REVERT: B 265 ARG cc_start: 0.7055 (mpt90) cc_final: 0.6754 (mmt-90) REVERT: B 293 HIS cc_start: 0.6755 (m-70) cc_final: 0.5122 (t-90) REVERT: B 315 ILE cc_start: 0.6974 (pt) cc_final: 0.6505 (pt) REVERT: B 321 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7172 (ttp-110) REVERT: B 329 LYS cc_start: 0.7460 (mttt) cc_final: 0.6993 (mtpm) REVERT: B 341 THR cc_start: 0.7461 (p) cc_final: 0.7229 (p) REVERT: B 356 ASP cc_start: 0.6113 (t70) cc_final: 0.5896 (t70) REVERT: B 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mtpt) REVERT: B 364 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6145 (mt-10) REVERT: B 380 TYR cc_start: 0.6750 (m-80) cc_final: 0.5945 (m-80) REVERT: B 394 MET cc_start: 0.7473 (mtt) cc_final: 0.7109 (mtt) REVERT: B 399 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6900 (mt-10) REVERT: B 415 ASP cc_start: 0.6841 (m-30) cc_final: 0.6342 (p0) REVERT: B 416 ASP cc_start: 0.5713 (t70) cc_final: 0.5306 (t0) REVERT: B 423 ASN cc_start: 0.6752 (t0) cc_final: 0.6519 (t0) REVERT: B 425 PHE cc_start: 0.7673 (m-80) cc_final: 0.7382 (m-80) REVERT: B 436 ASP cc_start: 0.7105 (t70) cc_final: 0.6424 (t0) REVERT: B 477 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7080 (mm-30) REVERT: B 480 GLU cc_start: 0.7684 (tt0) cc_final: 0.7045 (tt0) REVERT: C 22 LYS cc_start: 0.6533 (mttt) cc_final: 0.6288 (mtmt) REVERT: C 31 ASP cc_start: 0.7136 (m-30) cc_final: 0.6584 (p0) REVERT: C 51 GLN cc_start: 0.6240 (mm110) cc_final: 0.5953 (mm-40) REVERT: C 53 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7028 (mm-30) REVERT: C 57 LYS cc_start: 0.6736 (tttm) cc_final: 0.6532 (ttmt) REVERT: C 84 GLU cc_start: 0.6640 (tp30) cc_final: 0.5715 (mm-30) REVERT: C 97 GLU cc_start: 0.6025 (tt0) cc_final: 0.5621 (tt0) REVERT: C 109 MET cc_start: 0.7442 (ttm) cc_final: 0.7004 (mtm) REVERT: C 110 ASN cc_start: 0.7968 (t0) cc_final: 0.7715 (t0) REVERT: C 115 TYR cc_start: 0.7381 (t80) cc_final: 0.7157 (t80) REVERT: C 119 TYR cc_start: 0.7542 (t80) cc_final: 0.7119 (t80) REVERT: C 158 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6924 (tt0) REVERT: C 175 MET cc_start: 0.8096 (mmp) cc_final: 0.7871 (mmm) REVERT: C 238 ASP cc_start: 0.6960 (t70) cc_final: 0.6702 (t0) REVERT: C 240 ASP cc_start: 0.7231 (m-30) cc_final: 0.6765 (m-30) REVERT: C 245 THR cc_start: 0.7708 (m) cc_final: 0.7507 (p) REVERT: C 253 LEU cc_start: 0.7142 (mt) cc_final: 0.6901 (mm) REVERT: C 256 GLU cc_start: 0.6987 (tt0) cc_final: 0.6682 (tt0) REVERT: C 265 ARG cc_start: 0.7054 (mpt90) cc_final: 0.6754 (mmt-90) REVERT: C 293 HIS cc_start: 0.6755 (m-70) cc_final: 0.5122 (t-90) REVERT: C 315 ILE cc_start: 0.6975 (pt) cc_final: 0.6506 (pt) REVERT: C 321 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: C 329 LYS cc_start: 0.7459 (mttt) cc_final: 0.6994 (mtpm) REVERT: C 341 THR cc_start: 0.7458 (p) cc_final: 0.7225 (p) REVERT: C 356 ASP cc_start: 0.6117 (t70) cc_final: 0.5898 (t70) REVERT: C 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mtpt) REVERT: C 364 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6145 (mt-10) REVERT: C 380 TYR cc_start: 0.6749 (m-80) cc_final: 0.5948 (m-80) REVERT: C 394 MET cc_start: 0.7476 (mtt) cc_final: 0.7111 (mtt) REVERT: C 399 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6900 (mt-10) REVERT: C 415 ASP cc_start: 0.6840 (m-30) cc_final: 0.6342 (p0) REVERT: C 416 ASP cc_start: 0.5713 (t70) cc_final: 0.5307 (t0) REVERT: C 423 ASN cc_start: 0.6751 (t0) cc_final: 0.6518 (t0) REVERT: C 425 PHE cc_start: 0.7673 (m-80) cc_final: 0.7409 (m-80) REVERT: C 436 ASP cc_start: 0.7104 (t70) cc_final: 0.6426 (t0) REVERT: C 477 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7078 (mm-30) REVERT: C 480 GLU cc_start: 0.7684 (tt0) cc_final: 0.7044 (tt0) REVERT: D 22 LYS cc_start: 0.6531 (mttt) cc_final: 0.6286 (mtmt) REVERT: D 31 ASP cc_start: 0.7137 (m-30) cc_final: 0.6585 (p0) REVERT: D 51 GLN cc_start: 0.6239 (mm110) cc_final: 0.5951 (mm-40) REVERT: D 53 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7031 (mm-30) REVERT: D 57 LYS cc_start: 0.6738 (tttm) cc_final: 0.6533 (ttmt) REVERT: D 84 GLU cc_start: 0.6639 (tp30) cc_final: 0.5715 (mm-30) REVERT: D 94 ASP cc_start: 0.7192 (m-30) cc_final: 0.6990 (m-30) REVERT: D 97 GLU cc_start: 0.6023 (tt0) cc_final: 0.5621 (tt0) REVERT: D 109 MET cc_start: 0.7440 (ttm) cc_final: 0.7002 (mtm) REVERT: D 110 ASN cc_start: 0.7966 (t0) cc_final: 0.7714 (t0) REVERT: D 115 TYR cc_start: 0.7381 (t80) cc_final: 0.7157 (t80) REVERT: D 119 TYR cc_start: 0.7540 (t80) cc_final: 0.7118 (t80) REVERT: D 158 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6924 (tt0) REVERT: D 175 MET cc_start: 0.8095 (mmp) cc_final: 0.7871 (mmm) REVERT: D 238 ASP cc_start: 0.6961 (t70) cc_final: 0.6704 (t0) REVERT: D 240 ASP cc_start: 0.7229 (m-30) cc_final: 0.6764 (m-30) REVERT: D 245 THR cc_start: 0.7708 (m) cc_final: 0.7508 (p) REVERT: D 253 LEU cc_start: 0.7140 (mt) cc_final: 0.6899 (mm) REVERT: D 256 GLU cc_start: 0.6986 (tt0) cc_final: 0.6681 (tt0) REVERT: D 265 ARG cc_start: 0.7055 (mpt90) cc_final: 0.6753 (mmt-90) REVERT: D 293 HIS cc_start: 0.6756 (m-70) cc_final: 0.5122 (t-90) REVERT: D 315 ILE cc_start: 0.6974 (pt) cc_final: 0.6505 (pt) REVERT: D 321 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: D 329 LYS cc_start: 0.7459 (mttt) cc_final: 0.6993 (mtpm) REVERT: D 341 THR cc_start: 0.7460 (p) cc_final: 0.7228 (p) REVERT: D 356 ASP cc_start: 0.6117 (t70) cc_final: 0.5899 (t70) REVERT: D 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mtpt) REVERT: D 364 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6143 (mt-10) REVERT: D 380 TYR cc_start: 0.6749 (m-80) cc_final: 0.5949 (m-80) REVERT: D 394 MET cc_start: 0.7475 (mtt) cc_final: 0.7110 (mtt) REVERT: D 399 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6900 (mt-10) REVERT: D 415 ASP cc_start: 0.6840 (m-30) cc_final: 0.6340 (p0) REVERT: D 416 ASP cc_start: 0.5715 (t70) cc_final: 0.5308 (t0) REVERT: D 423 ASN cc_start: 0.6753 (t0) cc_final: 0.6520 (t0) REVERT: D 425 PHE cc_start: 0.7674 (m-80) cc_final: 0.7409 (m-80) REVERT: D 436 ASP cc_start: 0.7103 (t70) cc_final: 0.6424 (t0) REVERT: D 477 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7079 (mm-30) REVERT: D 480 GLU cc_start: 0.7682 (tt0) cc_final: 0.7044 (tt0) outliers start: 24 outliers final: 0 residues processed: 488 average time/residue: 1.5294 time to fit residues: 810.5385 Evaluate side-chains 286 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain D residue 363 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 383 GLN A 463 GLN A 474 ASN B 334 ASN B 383 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN C 334 ASN C 383 GLN C 463 GLN C 474 ASN D 334 ASN D 383 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15496 Z= 0.176 Angle : 0.547 6.452 20984 Z= 0.299 Chirality : 0.045 0.232 2324 Planarity : 0.004 0.037 2716 Dihedral : 5.234 18.339 2120 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.92 % Allowed : 13.71 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.19), residues: 1964 helix: 1.12 (0.18), residues: 816 sheet: 0.57 (0.25), residues: 412 loop : 0.00 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 453 HIS 0.001 0.000 HIS A 236 PHE 0.008 0.002 PHE A 24 TYR 0.016 0.002 TYR C 20 ARG 0.003 0.001 ARG B 85 *********************** 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 371 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 324 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7167 (m-30) cc_final: 0.6627 (p0) REVERT: A 51 GLN cc_start: 0.6323 (mm110) cc_final: 0.5996 (mm-40) REVERT: A 53 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 57 LYS cc_start: 0.6773 (tttm) cc_final: 0.6330 (tttt) REVERT: A 84 GLU cc_start: 0.6404 (tp30) cc_final: 0.5527 (mm-30) REVERT: A 97 GLU cc_start: 0.6124 (tt0) cc_final: 0.5760 (tt0) REVERT: A 98 ARG cc_start: 0.6988 (ttp-170) cc_final: 0.6643 (ttp-170) REVERT: A 107 GLU cc_start: 0.5822 (OUTLIER) cc_final: 0.5223 (tp30) REVERT: A 110 ASN cc_start: 0.7794 (t0) cc_final: 0.7481 (t0) REVERT: A 117 ASN cc_start: 0.6863 (m-40) cc_final: 0.6487 (m-40) REVERT: A 119 TYR cc_start: 0.7364 (t80) cc_final: 0.6717 (t80) REVERT: A 158 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6813 (tt0) REVERT: A 238 ASP cc_start: 0.7139 (t70) cc_final: 0.6714 (t0) REVERT: A 240 ASP cc_start: 0.7187 (m-30) cc_final: 0.6714 (m-30) REVERT: A 253 LEU cc_start: 0.6931 (mt) cc_final: 0.6606 (mm) REVERT: A 256 GLU cc_start: 0.6641 (tt0) cc_final: 0.6413 (tt0) REVERT: A 285 ASP cc_start: 0.6488 (t0) cc_final: 0.6029 (p0) REVERT: A 286 ASN cc_start: 0.6645 (t0) cc_final: 0.6429 (t0) REVERT: A 293 HIS cc_start: 0.6252 (m-70) cc_final: 0.4819 (t-90) REVERT: A 295 VAL cc_start: 0.7124 (p) cc_final: 0.6724 (t) REVERT: A 321 ARG cc_start: 0.6958 (ttp80) cc_final: 0.6751 (ttp80) REVERT: A 325 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7173 (tp30) REVERT: A 329 LYS cc_start: 0.7513 (mttt) cc_final: 0.6820 (mtpm) REVERT: A 352 ASP cc_start: 0.6829 (m-30) cc_final: 0.6422 (m-30) REVERT: A 357 LEU cc_start: 0.5857 (mt) cc_final: 0.5237 (mt) REVERT: A 364 GLU cc_start: 0.6577 (mt-10) cc_final: 0.6370 (mt-10) REVERT: A 367 LYS cc_start: 0.6923 (tttt) cc_final: 0.6447 (tttm) REVERT: A 380 TYR cc_start: 0.6787 (m-80) cc_final: 0.6037 (m-80) REVERT: A 412 LYS cc_start: 0.7089 (mtmm) cc_final: 0.6703 (mtpt) REVERT: A 415 ASP cc_start: 0.6756 (m-30) cc_final: 0.6187 (p0) REVERT: A 416 ASP cc_start: 0.5763 (t70) cc_final: 0.5479 (t0) REVERT: A 425 PHE cc_start: 0.7605 (m-80) cc_final: 0.7380 (m-80) REVERT: A 435 LYS cc_start: 0.6574 (mttm) cc_final: 0.6343 (mttm) REVERT: A 436 ASP cc_start: 0.6783 (t70) cc_final: 0.6282 (t0) REVERT: A 442 THR cc_start: 0.7623 (m) cc_final: 0.7356 (m) REVERT: B 31 ASP cc_start: 0.7170 (m-30) cc_final: 0.6629 (p0) REVERT: B 51 GLN cc_start: 0.6322 (mm110) cc_final: 0.5996 (mm-40) REVERT: B 53 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7083 (mm-30) REVERT: B 57 LYS cc_start: 0.6773 (tttm) cc_final: 0.6330 (tttt) REVERT: B 84 GLU cc_start: 0.6402 (tp30) cc_final: 0.5525 (mm-30) REVERT: B 97 GLU cc_start: 0.6129 (tt0) cc_final: 0.5760 (tt0) REVERT: B 98 ARG cc_start: 0.6984 (ttp-170) cc_final: 0.6642 (ttp-170) REVERT: B 107 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.5224 (tp30) REVERT: B 110 ASN cc_start: 0.7797 (t0) cc_final: 0.7482 (t0) REVERT: B 117 ASN cc_start: 0.6862 (m-40) cc_final: 0.6493 (m-40) REVERT: B 119 TYR cc_start: 0.7364 (t80) cc_final: 0.6716 (t80) REVERT: B 158 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6813 (tt0) REVERT: B 238 ASP cc_start: 0.7137 (t70) cc_final: 0.6715 (t0) REVERT: B 240 ASP cc_start: 0.7187 (m-30) cc_final: 0.6714 (m-30) REVERT: B 253 LEU cc_start: 0.6931 (mt) cc_final: 0.6606 (mm) REVERT: B 256 GLU cc_start: 0.6643 (tt0) cc_final: 0.6415 (tt0) REVERT: B 285 ASP cc_start: 0.6486 (t0) cc_final: 0.6030 (p0) REVERT: B 286 ASN cc_start: 0.6640 (t0) cc_final: 0.6431 (t0) REVERT: B 293 HIS cc_start: 0.6253 (m-70) cc_final: 0.4820 (t-90) REVERT: B 295 VAL cc_start: 0.7124 (p) cc_final: 0.6725 (t) REVERT: B 321 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6750 (ttp80) REVERT: B 325 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7175 (tp30) REVERT: B 329 LYS cc_start: 0.7514 (mttt) cc_final: 0.6821 (mtpm) REVERT: B 352 ASP cc_start: 0.6829 (m-30) cc_final: 0.6423 (m-30) REVERT: B 357 LEU cc_start: 0.5856 (mt) cc_final: 0.5237 (mt) REVERT: B 364 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6370 (mt-10) REVERT: B 367 LYS cc_start: 0.6922 (tttt) cc_final: 0.6446 (tttm) REVERT: B 380 TYR cc_start: 0.6793 (m-80) cc_final: 0.6038 (m-80) REVERT: B 412 LYS cc_start: 0.7089 (mtmm) cc_final: 0.6702 (mtpt) REVERT: B 415 ASP cc_start: 0.6756 (m-30) cc_final: 0.6188 (p0) REVERT: B 416 ASP cc_start: 0.5763 (t70) cc_final: 0.5479 (t0) REVERT: B 425 PHE cc_start: 0.7605 (m-80) cc_final: 0.7378 (m-80) REVERT: B 435 LYS cc_start: 0.6574 (mttm) cc_final: 0.6342 (mttm) REVERT: B 436 ASP cc_start: 0.6783 (t70) cc_final: 0.6281 (t0) REVERT: B 442 THR cc_start: 0.7622 (m) cc_final: 0.7355 (m) REVERT: C 31 ASP cc_start: 0.7170 (m-30) cc_final: 0.6629 (p0) REVERT: C 51 GLN cc_start: 0.6323 (mm110) cc_final: 0.5997 (mm-40) REVERT: C 53 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7082 (mm-30) REVERT: C 57 LYS cc_start: 0.6774 (tttm) cc_final: 0.6325 (tttt) REVERT: C 84 GLU cc_start: 0.6405 (tp30) cc_final: 0.5528 (mm-30) REVERT: C 97 GLU cc_start: 0.6124 (tt0) cc_final: 0.5759 (tt0) REVERT: C 98 ARG cc_start: 0.6987 (ttp-170) cc_final: 0.6643 (ttp-170) REVERT: C 107 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5222 (tp30) REVERT: C 110 ASN cc_start: 0.7796 (t0) cc_final: 0.7481 (t0) REVERT: C 117 ASN cc_start: 0.6866 (m-40) cc_final: 0.6490 (m-40) REVERT: C 119 TYR cc_start: 0.7366 (t80) cc_final: 0.6717 (t80) REVERT: C 158 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6812 (tt0) REVERT: C 238 ASP cc_start: 0.7105 (t70) cc_final: 0.6675 (t0) REVERT: C 240 ASP cc_start: 0.7189 (m-30) cc_final: 0.6713 (m-30) REVERT: C 253 LEU cc_start: 0.6961 (mt) cc_final: 0.6640 (mm) REVERT: C 256 GLU cc_start: 0.6633 (tt0) cc_final: 0.6420 (tt0) REVERT: C 285 ASP cc_start: 0.6487 (t0) cc_final: 0.6027 (p0) REVERT: C 286 ASN cc_start: 0.6641 (t0) cc_final: 0.6428 (t0) REVERT: C 293 HIS cc_start: 0.6249 (m-70) cc_final: 0.4816 (t-90) REVERT: C 295 VAL cc_start: 0.7126 (p) cc_final: 0.6727 (t) REVERT: C 321 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6750 (ttp80) REVERT: C 325 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7175 (tp30) REVERT: C 329 LYS cc_start: 0.7514 (mttt) cc_final: 0.6820 (mtpm) REVERT: C 352 ASP cc_start: 0.6830 (m-30) cc_final: 0.6423 (m-30) REVERT: C 357 LEU cc_start: 0.5853 (mt) cc_final: 0.5235 (mt) REVERT: C 364 GLU cc_start: 0.6577 (mt-10) cc_final: 0.6371 (mt-10) REVERT: C 367 LYS cc_start: 0.6926 (tttt) cc_final: 0.6449 (tttm) REVERT: C 380 TYR cc_start: 0.6788 (m-80) cc_final: 0.6036 (m-80) REVERT: C 412 LYS cc_start: 0.7090 (mtmm) cc_final: 0.6702 (mtpt) REVERT: C 415 ASP cc_start: 0.6756 (m-30) cc_final: 0.6186 (p0) REVERT: C 416 ASP cc_start: 0.5763 (t70) cc_final: 0.5478 (t0) REVERT: C 435 LYS cc_start: 0.6571 (mttm) cc_final: 0.6341 (mttm) REVERT: C 436 ASP cc_start: 0.6774 (t70) cc_final: 0.6253 (t0) REVERT: C 442 THR cc_start: 0.7626 (m) cc_final: 0.7360 (m) REVERT: D 31 ASP cc_start: 0.7168 (m-30) cc_final: 0.6629 (p0) REVERT: D 51 GLN cc_start: 0.6326 (mm110) cc_final: 0.5997 (mm-40) REVERT: D 53 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7085 (mm-30) REVERT: D 57 LYS cc_start: 0.6774 (tttm) cc_final: 0.6325 (tttt) REVERT: D 84 GLU cc_start: 0.6402 (tp30) cc_final: 0.5527 (mm-30) REVERT: D 97 GLU cc_start: 0.6129 (tt0) cc_final: 0.5758 (tt0) REVERT: D 98 ARG cc_start: 0.6985 (ttp-170) cc_final: 0.6643 (ttp-170) REVERT: D 107 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.5225 (tp30) REVERT: D 110 ASN cc_start: 0.7796 (t0) cc_final: 0.7481 (t0) REVERT: D 117 ASN cc_start: 0.6864 (m-40) cc_final: 0.6493 (m-40) REVERT: D 119 TYR cc_start: 0.7366 (t80) cc_final: 0.6716 (t80) REVERT: D 158 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6814 (tt0) REVERT: D 238 ASP cc_start: 0.7109 (t70) cc_final: 0.6676 (t0) REVERT: D 240 ASP cc_start: 0.7189 (m-30) cc_final: 0.6712 (m-30) REVERT: D 253 LEU cc_start: 0.6960 (mt) cc_final: 0.6639 (mm) REVERT: D 256 GLU cc_start: 0.6633 (tt0) cc_final: 0.6419 (tt0) REVERT: D 285 ASP cc_start: 0.6490 (t0) cc_final: 0.6031 (p0) REVERT: D 286 ASN cc_start: 0.6639 (t0) cc_final: 0.6429 (t0) REVERT: D 293 HIS cc_start: 0.6251 (m-70) cc_final: 0.4820 (t-90) REVERT: D 295 VAL cc_start: 0.7124 (p) cc_final: 0.6727 (t) REVERT: D 321 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6751 (ttp80) REVERT: D 325 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7172 (tp30) REVERT: D 329 LYS cc_start: 0.7513 (mttt) cc_final: 0.6820 (mtpm) REVERT: D 352 ASP cc_start: 0.6829 (m-30) cc_final: 0.6423 (m-30) REVERT: D 357 LEU cc_start: 0.5851 (mt) cc_final: 0.5235 (mt) REVERT: D 364 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6370 (mt-10) REVERT: D 367 LYS cc_start: 0.6924 (tttt) cc_final: 0.6446 (tttm) REVERT: D 380 TYR cc_start: 0.6790 (m-80) cc_final: 0.6039 (m-80) REVERT: D 412 LYS cc_start: 0.7090 (mtmm) cc_final: 0.6703 (mtpt) REVERT: D 415 ASP cc_start: 0.6757 (m-30) cc_final: 0.6186 (p0) REVERT: D 416 ASP cc_start: 0.5763 (t70) cc_final: 0.5478 (t0) REVERT: D 435 LYS cc_start: 0.6573 (mttm) cc_final: 0.6341 (mttm) REVERT: D 436 ASP cc_start: 0.6772 (t70) cc_final: 0.6250 (t0) REVERT: D 442 THR cc_start: 0.7627 (m) cc_final: 0.7361 (m) outliers start: 47 outliers final: 8 residues processed: 365 average time/residue: 1.2540 time to fit residues: 506.0349 Evaluate side-chains 287 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 234 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 165 GLN A 500 ASN B 72 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN B 463 GLN B 500 ASN C 72 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN C 500 ASN D 72 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 463 GLN D 500 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 15496 Z= 0.395 Angle : 0.617 7.075 20984 Z= 0.329 Chirality : 0.049 0.164 2324 Planarity : 0.005 0.035 2716 Dihedral : 5.117 23.281 2104 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.16 % Allowed : 15.94 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.18), residues: 1964 helix: 1.06 (0.17), residues: 828 sheet: 0.51 (0.25), residues: 400 loop : 0.10 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 178 HIS 0.007 0.002 HIS C 236 PHE 0.015 0.003 PHE A 483 TYR 0.017 0.003 TYR C 154 ARG 0.004 0.001 ARG A 85 *********************** 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 359 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 308 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7236 (m-30) cc_final: 0.6593 (p0) REVERT: A 48 GLU cc_start: 0.6002 (tt0) cc_final: 0.5768 (tt0) REVERT: A 53 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 54 GLU cc_start: 0.6968 (tt0) cc_final: 0.6338 (tp30) REVERT: A 57 LYS cc_start: 0.6763 (tttm) cc_final: 0.6366 (tttp) REVERT: A 69 GLN cc_start: 0.6927 (tp-100) cc_final: 0.6638 (tm-30) REVERT: A 84 GLU cc_start: 0.6319 (tp30) cc_final: 0.5388 (mm-30) REVERT: A 97 GLU cc_start: 0.6359 (tt0) cc_final: 0.5969 (tt0) REVERT: A 98 ARG cc_start: 0.7038 (ttp-170) cc_final: 0.6725 (ttp-170) REVERT: A 107 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5363 (mm-30) REVERT: A 109 MET cc_start: 0.6591 (mtm) cc_final: 0.6380 (mtm) REVERT: A 110 ASN cc_start: 0.7627 (t0) cc_final: 0.7204 (t0) REVERT: A 117 ASN cc_start: 0.7059 (m-40) cc_final: 0.6712 (m-40) REVERT: A 119 TYR cc_start: 0.7374 (t80) cc_final: 0.6944 (t80) REVERT: A 238 ASP cc_start: 0.7250 (t70) cc_final: 0.6783 (t0) REVERT: A 240 ASP cc_start: 0.7227 (m-30) cc_final: 0.6825 (m-30) REVERT: A 256 GLU cc_start: 0.6577 (tt0) cc_final: 0.6168 (tt0) REVERT: A 285 ASP cc_start: 0.6374 (t0) cc_final: 0.5943 (p0) REVERT: A 293 HIS cc_start: 0.6365 (m-70) cc_final: 0.4854 (t-90) REVERT: A 295 VAL cc_start: 0.7126 (p) cc_final: 0.6854 (t) REVERT: A 313 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6056 (pm20) REVERT: A 321 ARG cc_start: 0.6769 (ttp80) cc_final: 0.6390 (ttp-110) REVERT: A 325 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6946 (tp30) REVERT: A 329 LYS cc_start: 0.7400 (mttt) cc_final: 0.6782 (mtpm) REVERT: A 352 ASP cc_start: 0.7015 (m-30) cc_final: 0.6601 (m-30) REVERT: A 353 LYS cc_start: 0.5660 (ttpp) cc_final: 0.5302 (tptp) REVERT: A 357 LEU cc_start: 0.5997 (mt) cc_final: 0.5571 (mt) REVERT: A 367 LYS cc_start: 0.6809 (tttt) cc_final: 0.6357 (tttm) REVERT: A 380 TYR cc_start: 0.6802 (m-80) cc_final: 0.6107 (m-80) REVERT: A 409 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6529 (mtt) REVERT: A 425 PHE cc_start: 0.7245 (m-80) cc_final: 0.7012 (m-80) REVERT: A 435 LYS cc_start: 0.6815 (mttm) cc_final: 0.6605 (mttm) REVERT: A 436 ASP cc_start: 0.6797 (t70) cc_final: 0.6238 (t0) REVERT: B 31 ASP cc_start: 0.7236 (m-30) cc_final: 0.6593 (p0) REVERT: B 48 GLU cc_start: 0.6001 (tt0) cc_final: 0.5768 (tt0) REVERT: B 53 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 54 GLU cc_start: 0.6970 (tt0) cc_final: 0.6339 (tp30) REVERT: B 57 LYS cc_start: 0.6764 (tttm) cc_final: 0.6366 (tttp) REVERT: B 69 GLN cc_start: 0.6926 (tp-100) cc_final: 0.6637 (tm-30) REVERT: B 84 GLU cc_start: 0.6315 (tp30) cc_final: 0.5383 (mm-30) REVERT: B 97 GLU cc_start: 0.6358 (tt0) cc_final: 0.5967 (tt0) REVERT: B 98 ARG cc_start: 0.7038 (ttp-170) cc_final: 0.6725 (ttp-170) REVERT: B 107 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5364 (mm-30) REVERT: B 109 MET cc_start: 0.6590 (mtm) cc_final: 0.6377 (mtm) REVERT: B 110 ASN cc_start: 0.7627 (t0) cc_final: 0.7206 (t0) REVERT: B 117 ASN cc_start: 0.7064 (m-40) cc_final: 0.6717 (m-40) REVERT: B 119 TYR cc_start: 0.7373 (t80) cc_final: 0.6944 (t80) REVERT: B 238 ASP cc_start: 0.7250 (t70) cc_final: 0.6785 (t0) REVERT: B 240 ASP cc_start: 0.7227 (m-30) cc_final: 0.6825 (m-30) REVERT: B 256 GLU cc_start: 0.6579 (tt0) cc_final: 0.6170 (tt0) REVERT: B 285 ASP cc_start: 0.6374 (t0) cc_final: 0.5942 (p0) REVERT: B 293 HIS cc_start: 0.6364 (m-70) cc_final: 0.4853 (t-90) REVERT: B 295 VAL cc_start: 0.7127 (p) cc_final: 0.6857 (t) REVERT: B 313 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6056 (pm20) REVERT: B 321 ARG cc_start: 0.6768 (ttp80) cc_final: 0.6390 (ttp-110) REVERT: B 325 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6945 (tp30) REVERT: B 329 LYS cc_start: 0.7401 (mttt) cc_final: 0.6783 (mtpm) REVERT: B 352 ASP cc_start: 0.7014 (m-30) cc_final: 0.6600 (m-30) REVERT: B 353 LYS cc_start: 0.5659 (ttpp) cc_final: 0.5300 (tptp) REVERT: B 357 LEU cc_start: 0.5998 (mt) cc_final: 0.5573 (mt) REVERT: B 367 LYS cc_start: 0.6806 (tttt) cc_final: 0.6356 (tttm) REVERT: B 380 TYR cc_start: 0.6803 (m-80) cc_final: 0.6108 (m-80) REVERT: B 409 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6529 (mtt) REVERT: B 425 PHE cc_start: 0.7245 (m-80) cc_final: 0.7012 (m-80) REVERT: B 435 LYS cc_start: 0.6816 (mttm) cc_final: 0.6606 (mttm) REVERT: B 436 ASP cc_start: 0.6797 (t70) cc_final: 0.6239 (t0) REVERT: C 31 ASP cc_start: 0.7236 (m-30) cc_final: 0.6593 (p0) REVERT: C 48 GLU cc_start: 0.6003 (tt0) cc_final: 0.5769 (tt0) REVERT: C 53 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7011 (mm-30) REVERT: C 54 GLU cc_start: 0.6967 (tt0) cc_final: 0.6338 (tp30) REVERT: C 57 LYS cc_start: 0.6758 (tttm) cc_final: 0.6362 (tttp) REVERT: C 69 GLN cc_start: 0.6928 (tp-100) cc_final: 0.6639 (tm-30) REVERT: C 84 GLU cc_start: 0.6319 (tp30) cc_final: 0.5388 (mm-30) REVERT: C 97 GLU cc_start: 0.6361 (tt0) cc_final: 0.5969 (tt0) REVERT: C 98 ARG cc_start: 0.7036 (ttp-170) cc_final: 0.6723 (ttp-170) REVERT: C 107 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5360 (mm-30) REVERT: C 109 MET cc_start: 0.6590 (mtm) cc_final: 0.6380 (mtm) REVERT: C 110 ASN cc_start: 0.7626 (t0) cc_final: 0.7205 (t0) REVERT: C 117 ASN cc_start: 0.7059 (m-40) cc_final: 0.6712 (m-40) REVERT: C 119 TYR cc_start: 0.7373 (t80) cc_final: 0.6944 (t80) REVERT: C 238 ASP cc_start: 0.7198 (t70) cc_final: 0.6701 (t0) REVERT: C 240 ASP cc_start: 0.7220 (m-30) cc_final: 0.6816 (m-30) REVERT: C 256 GLU cc_start: 0.6608 (tt0) cc_final: 0.6200 (tt0) REVERT: C 285 ASP cc_start: 0.6375 (t0) cc_final: 0.5942 (p0) REVERT: C 293 HIS cc_start: 0.6365 (m-70) cc_final: 0.4854 (t-90) REVERT: C 295 VAL cc_start: 0.7127 (p) cc_final: 0.6859 (t) REVERT: C 313 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6056 (pm20) REVERT: C 321 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6389 (ttp-110) REVERT: C 325 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6947 (tp30) REVERT: C 329 LYS cc_start: 0.7401 (mttt) cc_final: 0.6783 (mtpm) REVERT: C 353 LYS cc_start: 0.5659 (ttpp) cc_final: 0.5298 (tptp) REVERT: C 357 LEU cc_start: 0.5999 (mt) cc_final: 0.5573 (mt) REVERT: C 367 LYS cc_start: 0.6810 (tttt) cc_final: 0.6359 (tttm) REVERT: C 380 TYR cc_start: 0.6802 (m-80) cc_final: 0.6105 (m-80) REVERT: C 409 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6533 (mtt) REVERT: C 435 LYS cc_start: 0.6814 (mttm) cc_final: 0.6588 (mttm) REVERT: C 436 ASP cc_start: 0.6798 (t70) cc_final: 0.6241 (t0) REVERT: D 31 ASP cc_start: 0.7237 (m-30) cc_final: 0.6594 (p0) REVERT: D 48 GLU cc_start: 0.6003 (tt0) cc_final: 0.5769 (tt0) REVERT: D 53 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7009 (mm-30) REVERT: D 54 GLU cc_start: 0.6968 (tt0) cc_final: 0.6339 (tp30) REVERT: D 57 LYS cc_start: 0.6759 (tttm) cc_final: 0.6363 (tttp) REVERT: D 69 GLN cc_start: 0.6929 (tp-100) cc_final: 0.6640 (tm-30) REVERT: D 84 GLU cc_start: 0.6317 (tp30) cc_final: 0.5385 (mm-30) REVERT: D 97 GLU cc_start: 0.6358 (tt0) cc_final: 0.5968 (tt0) REVERT: D 98 ARG cc_start: 0.7037 (ttp-170) cc_final: 0.6723 (ttp-170) REVERT: D 107 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5361 (mm-30) REVERT: D 109 MET cc_start: 0.6589 (mtm) cc_final: 0.6378 (mtm) REVERT: D 110 ASN cc_start: 0.7626 (t0) cc_final: 0.7205 (t0) REVERT: D 117 ASN cc_start: 0.7066 (m-40) cc_final: 0.6718 (m-40) REVERT: D 119 TYR cc_start: 0.7374 (t80) cc_final: 0.6945 (t80) REVERT: D 238 ASP cc_start: 0.7198 (t70) cc_final: 0.6701 (t0) REVERT: D 240 ASP cc_start: 0.7221 (m-30) cc_final: 0.6816 (m-30) REVERT: D 256 GLU cc_start: 0.6608 (tt0) cc_final: 0.6199 (tt0) REVERT: D 285 ASP cc_start: 0.6374 (t0) cc_final: 0.5941 (p0) REVERT: D 293 HIS cc_start: 0.6366 (m-70) cc_final: 0.4856 (t-90) REVERT: D 295 VAL cc_start: 0.7127 (p) cc_final: 0.6858 (t) REVERT: D 313 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6057 (pm20) REVERT: D 321 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6388 (ttp-110) REVERT: D 325 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6944 (tp30) REVERT: D 329 LYS cc_start: 0.7400 (mttt) cc_final: 0.6782 (mtpm) REVERT: D 352 ASP cc_start: 0.7016 (m-30) cc_final: 0.6602 (m-30) REVERT: D 353 LYS cc_start: 0.5661 (ttpp) cc_final: 0.5302 (tptp) REVERT: D 357 LEU cc_start: 0.5999 (mt) cc_final: 0.5572 (mt) REVERT: D 367 LYS cc_start: 0.6808 (tttt) cc_final: 0.6357 (tttm) REVERT: D 380 TYR cc_start: 0.6801 (m-80) cc_final: 0.6107 (m-80) REVERT: D 409 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6530 (mtt) REVERT: D 435 LYS cc_start: 0.6813 (mttm) cc_final: 0.6587 (mttm) REVERT: D 436 ASP cc_start: 0.6794 (t70) cc_final: 0.6239 (t0) outliers start: 51 outliers final: 16 residues processed: 342 average time/residue: 1.4281 time to fit residues: 538.3887 Evaluate side-chains 310 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 286 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 0.0770 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15496 Z= 0.229 Angle : 0.509 6.750 20984 Z= 0.272 Chirality : 0.044 0.142 2324 Planarity : 0.004 0.035 2716 Dihedral : 4.743 21.566 2104 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.73 % Allowed : 17.93 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.19), residues: 1964 helix: 1.73 (0.18), residues: 800 sheet: 0.54 (0.26), residues: 400 loop : 0.11 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.003 0.001 HIS B 30 PHE 0.009 0.002 PHE B 483 TYR 0.012 0.002 TYR D 154 ARG 0.002 0.000 ARG C 265 *********************** 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 324 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 280 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7155 (m-30) cc_final: 0.6540 (p0) REVERT: A 48 GLU cc_start: 0.5993 (tt0) cc_final: 0.5767 (tt0) REVERT: A 53 GLU cc_start: 0.7616 (mm-30) cc_final: 0.6904 (mm-30) REVERT: A 54 GLU cc_start: 0.6904 (tt0) cc_final: 0.6222 (tp30) REVERT: A 57 LYS cc_start: 0.6691 (tttm) cc_final: 0.6309 (tttp) REVERT: A 69 GLN cc_start: 0.6878 (tp-100) cc_final: 0.6606 (tm-30) REVERT: A 84 GLU cc_start: 0.6367 (tp30) cc_final: 0.5419 (mm-30) REVERT: A 97 GLU cc_start: 0.6327 (tt0) cc_final: 0.5960 (tt0) REVERT: A 98 ARG cc_start: 0.7009 (ttp-170) cc_final: 0.6643 (ttm170) REVERT: A 107 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5431 (tp30) REVERT: A 109 MET cc_start: 0.6522 (mtm) cc_final: 0.6306 (mtp) REVERT: A 110 ASN cc_start: 0.7522 (t0) cc_final: 0.7038 (t0) REVERT: A 128 LYS cc_start: 0.7225 (mttp) cc_final: 0.6656 (mttm) REVERT: A 238 ASP cc_start: 0.7256 (t70) cc_final: 0.6786 (t0) REVERT: A 240 ASP cc_start: 0.7385 (m-30) cc_final: 0.7024 (m-30) REVERT: A 256 GLU cc_start: 0.6589 (tt0) cc_final: 0.6182 (tt0) REVERT: A 285 ASP cc_start: 0.6357 (t0) cc_final: 0.5937 (p0) REVERT: A 293 HIS cc_start: 0.6276 (m-70) cc_final: 0.4834 (t-90) REVERT: A 313 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: A 325 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6953 (tp30) REVERT: A 329 LYS cc_start: 0.7263 (mttt) cc_final: 0.6628 (mtpm) REVERT: A 352 ASP cc_start: 0.6998 (m-30) cc_final: 0.6600 (m-30) REVERT: A 353 LYS cc_start: 0.5629 (ttpp) cc_final: 0.5253 (tptp) REVERT: A 357 LEU cc_start: 0.6017 (mt) cc_final: 0.5597 (mt) REVERT: A 367 LYS cc_start: 0.6818 (tttt) cc_final: 0.6384 (tttm) REVERT: A 380 TYR cc_start: 0.6750 (m-80) cc_final: 0.6009 (m-80) REVERT: A 409 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6415 (mtt) REVERT: A 435 LYS cc_start: 0.6717 (mttm) cc_final: 0.6445 (mttm) REVERT: A 436 ASP cc_start: 0.6846 (t70) cc_final: 0.6303 (t0) REVERT: B 31 ASP cc_start: 0.7157 (m-30) cc_final: 0.6539 (p0) REVERT: B 48 GLU cc_start: 0.5994 (tt0) cc_final: 0.5768 (tt0) REVERT: B 53 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6906 (mm-30) REVERT: B 54 GLU cc_start: 0.6906 (tt0) cc_final: 0.6224 (tp30) REVERT: B 57 LYS cc_start: 0.6691 (tttm) cc_final: 0.6308 (tttp) REVERT: B 69 GLN cc_start: 0.6878 (tp-100) cc_final: 0.6607 (tm-30) REVERT: B 84 GLU cc_start: 0.6360 (tp30) cc_final: 0.5414 (mm-30) REVERT: B 97 GLU cc_start: 0.6328 (tt0) cc_final: 0.5981 (tt0) REVERT: B 98 ARG cc_start: 0.7008 (ttp-170) cc_final: 0.6638 (ttm170) REVERT: B 107 GLU cc_start: 0.6075 (OUTLIER) cc_final: 0.5432 (tp30) REVERT: B 109 MET cc_start: 0.6521 (mtm) cc_final: 0.6306 (mtp) REVERT: B 110 ASN cc_start: 0.7523 (t0) cc_final: 0.7041 (t0) REVERT: B 128 LYS cc_start: 0.7226 (mttp) cc_final: 0.6657 (mttm) REVERT: B 238 ASP cc_start: 0.7257 (t70) cc_final: 0.6787 (t0) REVERT: B 240 ASP cc_start: 0.7384 (m-30) cc_final: 0.7024 (m-30) REVERT: B 256 GLU cc_start: 0.6590 (tt0) cc_final: 0.6184 (tt0) REVERT: B 285 ASP cc_start: 0.6359 (t0) cc_final: 0.5942 (p0) REVERT: B 293 HIS cc_start: 0.6278 (m-70) cc_final: 0.4835 (t-90) REVERT: B 313 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6120 (pm20) REVERT: B 325 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6955 (tp30) REVERT: B 329 LYS cc_start: 0.7263 (mttt) cc_final: 0.6628 (mtpm) REVERT: B 352 ASP cc_start: 0.7000 (m-30) cc_final: 0.6603 (m-30) REVERT: B 353 LYS cc_start: 0.5631 (ttpp) cc_final: 0.5256 (tptp) REVERT: B 357 LEU cc_start: 0.6018 (mt) cc_final: 0.5599 (mt) REVERT: B 367 LYS cc_start: 0.6817 (tttt) cc_final: 0.6383 (tttm) REVERT: B 380 TYR cc_start: 0.6747 (m-80) cc_final: 0.6006 (m-80) REVERT: B 409 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6431 (mtt) REVERT: B 416 ASP cc_start: 0.6644 (m-30) cc_final: 0.6058 (t0) REVERT: B 435 LYS cc_start: 0.6715 (mttm) cc_final: 0.6442 (mttm) REVERT: B 436 ASP cc_start: 0.6845 (t70) cc_final: 0.6303 (t0) REVERT: C 31 ASP cc_start: 0.7157 (m-30) cc_final: 0.6541 (p0) REVERT: C 48 GLU cc_start: 0.5995 (tt0) cc_final: 0.5769 (tt0) REVERT: C 53 GLU cc_start: 0.7619 (mm-30) cc_final: 0.6906 (mm-30) REVERT: C 54 GLU cc_start: 0.6905 (tt0) cc_final: 0.6224 (tp30) REVERT: C 57 LYS cc_start: 0.6683 (tttm) cc_final: 0.6288 (tttp) REVERT: C 69 GLN cc_start: 0.6878 (tp-100) cc_final: 0.6609 (tm-30) REVERT: C 84 GLU cc_start: 0.6367 (tp30) cc_final: 0.5420 (mm-30) REVERT: C 97 GLU cc_start: 0.6330 (tt0) cc_final: 0.5962 (tt0) REVERT: C 98 ARG cc_start: 0.7008 (ttp-170) cc_final: 0.6643 (ttm170) REVERT: C 107 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5429 (tp30) REVERT: C 109 MET cc_start: 0.6522 (mtm) cc_final: 0.6306 (mtp) REVERT: C 110 ASN cc_start: 0.7522 (t0) cc_final: 0.7039 (t0) REVERT: C 128 LYS cc_start: 0.7226 (mttp) cc_final: 0.6657 (mttm) REVERT: C 238 ASP cc_start: 0.7262 (t70) cc_final: 0.6751 (t0) REVERT: C 240 ASP cc_start: 0.7388 (m-30) cc_final: 0.7023 (m-30) REVERT: C 256 GLU cc_start: 0.6590 (tt0) cc_final: 0.6204 (tt0) REVERT: C 285 ASP cc_start: 0.6357 (t0) cc_final: 0.5940 (p0) REVERT: C 293 HIS cc_start: 0.6280 (m-70) cc_final: 0.4837 (t-90) REVERT: C 313 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: C 325 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6955 (tp30) REVERT: C 329 LYS cc_start: 0.7263 (mttt) cc_final: 0.6629 (mtpm) REVERT: C 353 LYS cc_start: 0.5630 (ttpp) cc_final: 0.5252 (tptp) REVERT: C 357 LEU cc_start: 0.6019 (mt) cc_final: 0.5601 (mt) REVERT: C 367 LYS cc_start: 0.6819 (tttt) cc_final: 0.6386 (tttm) REVERT: C 380 TYR cc_start: 0.6746 (m-80) cc_final: 0.6007 (m-80) REVERT: C 409 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6416 (mtt) REVERT: C 435 LYS cc_start: 0.6714 (mttm) cc_final: 0.6443 (mttm) REVERT: C 436 ASP cc_start: 0.6844 (t70) cc_final: 0.6304 (t0) REVERT: D 31 ASP cc_start: 0.7157 (m-30) cc_final: 0.6541 (p0) REVERT: D 48 GLU cc_start: 0.5994 (tt0) cc_final: 0.5768 (tt0) REVERT: D 53 GLU cc_start: 0.7619 (mm-30) cc_final: 0.6905 (mm-30) REVERT: D 54 GLU cc_start: 0.6903 (tt0) cc_final: 0.6224 (tp30) REVERT: D 57 LYS cc_start: 0.6683 (tttm) cc_final: 0.6288 (tttp) REVERT: D 69 GLN cc_start: 0.6879 (tp-100) cc_final: 0.6610 (tm-30) REVERT: D 84 GLU cc_start: 0.6363 (tp30) cc_final: 0.5416 (mm-30) REVERT: D 97 GLU cc_start: 0.6329 (tt0) cc_final: 0.5981 (tt0) REVERT: D 98 ARG cc_start: 0.7008 (ttp-170) cc_final: 0.6639 (ttm170) REVERT: D 107 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5430 (tp30) REVERT: D 109 MET cc_start: 0.6520 (mtm) cc_final: 0.6305 (mtp) REVERT: D 110 ASN cc_start: 0.7522 (t0) cc_final: 0.7039 (t0) REVERT: D 128 LYS cc_start: 0.7227 (mttp) cc_final: 0.6659 (mttm) REVERT: D 238 ASP cc_start: 0.7261 (t70) cc_final: 0.6749 (t0) REVERT: D 240 ASP cc_start: 0.7389 (m-30) cc_final: 0.7024 (m-30) REVERT: D 256 GLU cc_start: 0.6586 (tt0) cc_final: 0.6200 (tt0) REVERT: D 285 ASP cc_start: 0.6360 (t0) cc_final: 0.5941 (p0) REVERT: D 293 HIS cc_start: 0.6277 (m-70) cc_final: 0.4836 (t-90) REVERT: D 313 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6121 (pm20) REVERT: D 325 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6953 (tp30) REVERT: D 329 LYS cc_start: 0.7262 (mttt) cc_final: 0.6628 (mtpm) REVERT: D 353 LYS cc_start: 0.5644 (ttpp) cc_final: 0.5268 (tptp) REVERT: D 357 LEU cc_start: 0.6019 (mt) cc_final: 0.5600 (mt) REVERT: D 367 LYS cc_start: 0.6818 (tttt) cc_final: 0.6385 (tttm) REVERT: D 380 TYR cc_start: 0.6745 (m-80) cc_final: 0.6006 (m-80) REVERT: D 409 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6418 (mtt) REVERT: D 435 LYS cc_start: 0.6712 (mttm) cc_final: 0.6441 (mttm) REVERT: D 436 ASP cc_start: 0.6843 (t70) cc_final: 0.6302 (t0) outliers start: 44 outliers final: 16 residues processed: 312 average time/residue: 1.3734 time to fit residues: 470.8529 Evaluate side-chains 290 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15496 Z= 0.423 Angle : 0.607 7.517 20984 Z= 0.323 Chirality : 0.048 0.145 2324 Planarity : 0.005 0.036 2716 Dihedral : 5.037 23.052 2104 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.22 % Allowed : 16.56 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.19), residues: 1964 helix: 1.21 (0.18), residues: 828 sheet: 0.48 (0.26), residues: 400 loop : -0.05 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 178 HIS 0.004 0.002 HIS C 236 PHE 0.015 0.003 PHE C 483 TYR 0.018 0.003 TYR A 351 ARG 0.007 0.001 ARG A 321 *********************** 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 334 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 266 time to evaluate : 1.751 Fit side-chains REVERT: A 31 ASP cc_start: 0.7215 (m-30) cc_final: 0.6651 (p0) REVERT: A 48 GLU cc_start: 0.5843 (tt0) cc_final: 0.5613 (tt0) REVERT: A 53 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 54 GLU cc_start: 0.6914 (tt0) cc_final: 0.6311 (tp30) REVERT: A 57 LYS cc_start: 0.6645 (tttm) cc_final: 0.6328 (tttp) REVERT: A 69 GLN cc_start: 0.6852 (tp-100) cc_final: 0.6546 (tm-30) REVERT: A 84 GLU cc_start: 0.6468 (tp30) cc_final: 0.5607 (mp0) REVERT: A 97 GLU cc_start: 0.6410 (tt0) cc_final: 0.6037 (tt0) REVERT: A 107 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.4797 (mm-30) REVERT: A 109 MET cc_start: 0.6537 (mtm) cc_final: 0.6308 (mtp) REVERT: A 110 ASN cc_start: 0.7562 (t0) cc_final: 0.7133 (t0) REVERT: A 238 ASP cc_start: 0.7270 (t70) cc_final: 0.6798 (t0) REVERT: A 240 ASP cc_start: 0.7403 (m-30) cc_final: 0.7065 (m-30) REVERT: A 285 ASP cc_start: 0.6372 (t0) cc_final: 0.5981 (p0) REVERT: A 293 HIS cc_start: 0.6334 (m-70) cc_final: 0.4820 (t-90) REVERT: A 313 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6172 (pm20) REVERT: A 325 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6976 (tp30) REVERT: A 329 LYS cc_start: 0.7084 (mttt) cc_final: 0.6489 (mtpm) REVERT: A 352 ASP cc_start: 0.7025 (m-30) cc_final: 0.6646 (m-30) REVERT: A 353 LYS cc_start: 0.5737 (ttpp) cc_final: 0.5290 (tptp) REVERT: A 357 LEU cc_start: 0.6031 (mt) cc_final: 0.5603 (mt) REVERT: A 367 LYS cc_start: 0.6898 (tttt) cc_final: 0.6463 (tttm) REVERT: A 380 TYR cc_start: 0.6821 (m-80) cc_final: 0.6240 (m-80) REVERT: A 409 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.6481 (mtt) REVERT: A 435 LYS cc_start: 0.6833 (mttm) cc_final: 0.6629 (mtpt) REVERT: A 436 ASP cc_start: 0.6862 (t70) cc_final: 0.6322 (t0) REVERT: A 477 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 31 ASP cc_start: 0.7215 (m-30) cc_final: 0.6650 (p0) REVERT: B 48 GLU cc_start: 0.5844 (tt0) cc_final: 0.5615 (tt0) REVERT: B 53 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 54 GLU cc_start: 0.6915 (tt0) cc_final: 0.6311 (tp30) REVERT: B 57 LYS cc_start: 0.6645 (tttm) cc_final: 0.6328 (tttp) REVERT: B 69 GLN cc_start: 0.6854 (tp-100) cc_final: 0.6547 (tm-30) REVERT: B 84 GLU cc_start: 0.6465 (tp30) cc_final: 0.5602 (mp0) REVERT: B 97 GLU cc_start: 0.6410 (tt0) cc_final: 0.6038 (tt0) REVERT: B 107 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.4796 (mm-30) REVERT: B 109 MET cc_start: 0.6537 (mtm) cc_final: 0.6308 (mtp) REVERT: B 110 ASN cc_start: 0.7564 (t0) cc_final: 0.7135 (t0) REVERT: B 238 ASP cc_start: 0.7270 (t70) cc_final: 0.6799 (t0) REVERT: B 240 ASP cc_start: 0.7404 (m-30) cc_final: 0.7066 (m-30) REVERT: B 285 ASP cc_start: 0.6375 (t0) cc_final: 0.5983 (p0) REVERT: B 293 HIS cc_start: 0.6336 (m-70) cc_final: 0.4821 (t-90) REVERT: B 313 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6169 (pm20) REVERT: B 325 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6974 (tp30) REVERT: B 329 LYS cc_start: 0.7083 (mttt) cc_final: 0.6488 (mtpm) REVERT: B 352 ASP cc_start: 0.7027 (m-30) cc_final: 0.6647 (m-30) REVERT: B 353 LYS cc_start: 0.5739 (ttpp) cc_final: 0.5292 (tptp) REVERT: B 357 LEU cc_start: 0.6032 (mt) cc_final: 0.5604 (mt) REVERT: B 367 LYS cc_start: 0.6900 (tttt) cc_final: 0.6464 (tttm) REVERT: B 380 TYR cc_start: 0.6821 (m-80) cc_final: 0.6242 (m-80) REVERT: B 409 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6503 (mtt) REVERT: B 435 LYS cc_start: 0.6833 (mttm) cc_final: 0.6629 (mtpt) REVERT: B 436 ASP cc_start: 0.6863 (t70) cc_final: 0.6323 (t0) REVERT: B 477 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7715 (mt-10) REVERT: C 31 ASP cc_start: 0.7217 (m-30) cc_final: 0.6651 (p0) REVERT: C 48 GLU cc_start: 0.5844 (tt0) cc_final: 0.5614 (tt0) REVERT: C 53 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7080 (mm-30) REVERT: C 54 GLU cc_start: 0.6914 (tt0) cc_final: 0.6310 (tp30) REVERT: C 57 LYS cc_start: 0.6638 (tttm) cc_final: 0.6322 (tttp) REVERT: C 69 GLN cc_start: 0.6853 (tp-100) cc_final: 0.6547 (tm-30) REVERT: C 84 GLU cc_start: 0.6469 (tp30) cc_final: 0.5607 (mp0) REVERT: C 97 GLU cc_start: 0.6413 (tt0) cc_final: 0.6039 (tt0) REVERT: C 107 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.4795 (mm-30) REVERT: C 109 MET cc_start: 0.6538 (mtm) cc_final: 0.6311 (mtp) REVERT: C 110 ASN cc_start: 0.7564 (t0) cc_final: 0.7134 (t0) REVERT: C 238 ASP cc_start: 0.7269 (t70) cc_final: 0.6762 (t0) REVERT: C 240 ASP cc_start: 0.7406 (m-30) cc_final: 0.7066 (m-30) REVERT: C 285 ASP cc_start: 0.6374 (t0) cc_final: 0.5985 (p0) REVERT: C 293 HIS cc_start: 0.6336 (m-70) cc_final: 0.4822 (t-90) REVERT: C 313 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6170 (pm20) REVERT: C 325 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6976 (tp30) REVERT: C 329 LYS cc_start: 0.7085 (mttt) cc_final: 0.6490 (mtpm) REVERT: C 353 LYS cc_start: 0.5738 (ttpp) cc_final: 0.5288 (tptp) REVERT: C 357 LEU cc_start: 0.6034 (mt) cc_final: 0.5606 (mt) REVERT: C 367 LYS cc_start: 0.6899 (tttt) cc_final: 0.6463 (tttm) REVERT: C 380 TYR cc_start: 0.6821 (m-80) cc_final: 0.6241 (m-80) REVERT: C 409 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6486 (mtt) REVERT: C 436 ASP cc_start: 0.6859 (t70) cc_final: 0.6318 (t0) REVERT: C 477 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 31 ASP cc_start: 0.7215 (m-30) cc_final: 0.6650 (p0) REVERT: D 48 GLU cc_start: 0.5844 (tt0) cc_final: 0.5613 (tt0) REVERT: D 53 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7082 (mm-30) REVERT: D 54 GLU cc_start: 0.6914 (tt0) cc_final: 0.6311 (tp30) REVERT: D 57 LYS cc_start: 0.6635 (tttm) cc_final: 0.6320 (tttp) REVERT: D 69 GLN cc_start: 0.6853 (tp-100) cc_final: 0.6548 (tm-30) REVERT: D 84 GLU cc_start: 0.6465 (tp30) cc_final: 0.5603 (mp0) REVERT: D 97 GLU cc_start: 0.6412 (tt0) cc_final: 0.6039 (tt0) REVERT: D 107 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.4796 (mm-30) REVERT: D 109 MET cc_start: 0.6539 (mtm) cc_final: 0.6310 (mtp) REVERT: D 110 ASN cc_start: 0.7562 (t0) cc_final: 0.7133 (t0) REVERT: D 238 ASP cc_start: 0.7268 (t70) cc_final: 0.6760 (t0) REVERT: D 240 ASP cc_start: 0.7404 (m-30) cc_final: 0.7064 (m-30) REVERT: D 285 ASP cc_start: 0.6374 (t0) cc_final: 0.5984 (p0) REVERT: D 293 HIS cc_start: 0.6331 (m-70) cc_final: 0.4819 (t-90) REVERT: D 313 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6170 (pm20) REVERT: D 325 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6972 (tp30) REVERT: D 329 LYS cc_start: 0.7084 (mttt) cc_final: 0.6489 (mtpm) REVERT: D 353 LYS cc_start: 0.5737 (ttpp) cc_final: 0.5287 (tptp) REVERT: D 357 LEU cc_start: 0.6032 (mt) cc_final: 0.5604 (mt) REVERT: D 367 LYS cc_start: 0.6898 (tttt) cc_final: 0.6462 (tttm) REVERT: D 380 TYR cc_start: 0.6819 (m-80) cc_final: 0.6239 (m-80) REVERT: D 409 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6482 (mtt) REVERT: D 436 ASP cc_start: 0.6859 (t70) cc_final: 0.6317 (t0) REVERT: D 477 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7725 (mt-10) outliers start: 68 outliers final: 20 residues processed: 313 average time/residue: 1.3683 time to fit residues: 470.3146 Evaluate side-chains 282 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 250 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 121 ASN A 220 ASN B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 121 ASN B 220 ASN C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN C 121 ASN C 220 ASN D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 121 ASN D 220 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15496 Z= 0.183 Angle : 0.485 6.552 20984 Z= 0.258 Chirality : 0.043 0.179 2324 Planarity : 0.004 0.035 2716 Dihedral : 4.585 20.514 2104 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.71 % Allowed : 16.56 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.19), residues: 1964 helix: 1.92 (0.19), residues: 800 sheet: 0.34 (0.26), residues: 396 loop : 0.10 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 453 HIS 0.003 0.001 HIS C 30 PHE 0.007 0.001 PHE D 483 TYR 0.016 0.002 TYR C 351 ARG 0.007 0.001 ARG D 321 *********************** 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 348 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 272 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7296 (m-30) cc_final: 0.6721 (p0) REVERT: A 48 GLU cc_start: 0.5905 (tt0) cc_final: 0.5635 (tt0) REVERT: A 53 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 54 GLU cc_start: 0.6978 (tt0) cc_final: 0.6334 (tm-30) REVERT: A 57 LYS cc_start: 0.6633 (tttm) cc_final: 0.6208 (tttt) REVERT: A 69 GLN cc_start: 0.6857 (tp-100) cc_final: 0.6557 (tm-30) REVERT: A 84 GLU cc_start: 0.6355 (tp30) cc_final: 0.5513 (mm-30) REVERT: A 97 GLU cc_start: 0.6406 (tt0) cc_final: 0.6034 (tt0) REVERT: A 107 GLU cc_start: 0.6035 (OUTLIER) cc_final: 0.5451 (tp30) REVERT: A 110 ASN cc_start: 0.7546 (t0) cc_final: 0.6997 (t0) REVERT: A 238 ASP cc_start: 0.7233 (t70) cc_final: 0.6766 (t0) REVERT: A 240 ASP cc_start: 0.7412 (m-30) cc_final: 0.7049 (m-30) REVERT: A 285 ASP cc_start: 0.6495 (t0) cc_final: 0.6240 (p0) REVERT: A 293 HIS cc_start: 0.6226 (m-70) cc_final: 0.4817 (t-90) REVERT: A 313 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6104 (pm20) REVERT: A 325 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6956 (tp30) REVERT: A 329 LYS cc_start: 0.7087 (mttt) cc_final: 0.6414 (mtpm) REVERT: A 353 LYS cc_start: 0.5678 (ttpp) cc_final: 0.5223 (tptt) REVERT: A 357 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5530 (mt) REVERT: A 367 LYS cc_start: 0.6867 (tttt) cc_final: 0.6449 (tttm) REVERT: A 380 TYR cc_start: 0.6520 (m-80) cc_final: 0.5800 (m-80) REVERT: A 436 ASP cc_start: 0.6858 (t70) cc_final: 0.6284 (t0) REVERT: A 481 TYR cc_start: 0.6708 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: B 31 ASP cc_start: 0.7297 (m-30) cc_final: 0.6720 (p0) REVERT: B 48 GLU cc_start: 0.5906 (tt0) cc_final: 0.5636 (tt0) REVERT: B 53 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7069 (mm-30) REVERT: B 54 GLU cc_start: 0.6978 (tt0) cc_final: 0.6334 (tm-30) REVERT: B 57 LYS cc_start: 0.6634 (tttm) cc_final: 0.6243 (tttt) REVERT: B 69 GLN cc_start: 0.6858 (tp-100) cc_final: 0.6558 (tm-30) REVERT: B 84 GLU cc_start: 0.6351 (tp30) cc_final: 0.5521 (mm-30) REVERT: B 97 GLU cc_start: 0.6389 (tt0) cc_final: 0.6011 (tt0) REVERT: B 107 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5452 (tp30) REVERT: B 110 ASN cc_start: 0.7547 (t0) cc_final: 0.6997 (t0) REVERT: B 238 ASP cc_start: 0.7233 (t70) cc_final: 0.6769 (t0) REVERT: B 240 ASP cc_start: 0.7413 (m-30) cc_final: 0.7051 (m-30) REVERT: B 285 ASP cc_start: 0.6494 (t0) cc_final: 0.6233 (p0) REVERT: B 293 HIS cc_start: 0.6226 (m-70) cc_final: 0.4817 (t-90) REVERT: B 313 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6103 (pm20) REVERT: B 325 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6957 (tp30) REVERT: B 329 LYS cc_start: 0.7086 (mttt) cc_final: 0.6414 (mtpm) REVERT: B 352 ASP cc_start: 0.6948 (m-30) cc_final: 0.6595 (m-30) REVERT: B 353 LYS cc_start: 0.5679 (ttpp) cc_final: 0.5225 (tptt) REVERT: B 357 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5533 (mt) REVERT: B 367 LYS cc_start: 0.6867 (tttt) cc_final: 0.6448 (tttm) REVERT: B 380 TYR cc_start: 0.6519 (m-80) cc_final: 0.5802 (m-80) REVERT: B 436 ASP cc_start: 0.6857 (t70) cc_final: 0.6284 (t0) REVERT: B 481 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.5474 (m-80) REVERT: C 31 ASP cc_start: 0.7297 (m-30) cc_final: 0.6720 (p0) REVERT: C 48 GLU cc_start: 0.5905 (tt0) cc_final: 0.5635 (tt0) REVERT: C 53 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7068 (mm-30) REVERT: C 54 GLU cc_start: 0.6977 (tt0) cc_final: 0.6332 (tm-30) REVERT: C 57 LYS cc_start: 0.6623 (tttm) cc_final: 0.6234 (tttt) REVERT: C 69 GLN cc_start: 0.6857 (tp-100) cc_final: 0.6558 (tm-30) REVERT: C 84 GLU cc_start: 0.6356 (tp30) cc_final: 0.5513 (mm-30) REVERT: C 97 GLU cc_start: 0.6407 (tt0) cc_final: 0.6035 (tt0) REVERT: C 107 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5451 (tp30) REVERT: C 110 ASN cc_start: 0.7544 (t0) cc_final: 0.6998 (t0) REVERT: C 238 ASP cc_start: 0.7249 (t70) cc_final: 0.6746 (t0) REVERT: C 240 ASP cc_start: 0.7412 (m-30) cc_final: 0.7047 (m-30) REVERT: C 285 ASP cc_start: 0.6499 (t0) cc_final: 0.6235 (p0) REVERT: C 293 HIS cc_start: 0.6229 (m-70) cc_final: 0.4818 (t-90) REVERT: C 313 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6104 (pm20) REVERT: C 325 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6957 (tp30) REVERT: C 329 LYS cc_start: 0.7088 (mttt) cc_final: 0.6415 (mtpm) REVERT: C 353 LYS cc_start: 0.5678 (ttpp) cc_final: 0.5223 (tptt) REVERT: C 357 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5536 (mt) REVERT: C 367 LYS cc_start: 0.6866 (tttt) cc_final: 0.6449 (tttm) REVERT: C 380 TYR cc_start: 0.6517 (m-80) cc_final: 0.5798 (m-80) REVERT: C 436 ASP cc_start: 0.6853 (t70) cc_final: 0.6301 (t0) REVERT: C 481 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5476 (m-80) REVERT: D 31 ASP cc_start: 0.7297 (m-30) cc_final: 0.6721 (p0) REVERT: D 48 GLU cc_start: 0.5904 (tt0) cc_final: 0.5635 (tt0) REVERT: D 53 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7068 (mm-30) REVERT: D 54 GLU cc_start: 0.6976 (tt0) cc_final: 0.6333 (tm-30) REVERT: D 57 LYS cc_start: 0.6623 (tttm) cc_final: 0.6234 (tttt) REVERT: D 69 GLN cc_start: 0.6859 (tp-100) cc_final: 0.6559 (tm-30) REVERT: D 84 GLU cc_start: 0.6350 (tp30) cc_final: 0.5521 (mm-30) REVERT: D 97 GLU cc_start: 0.6388 (tt0) cc_final: 0.6010 (tt0) REVERT: D 107 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5452 (tp30) REVERT: D 110 ASN cc_start: 0.7545 (t0) cc_final: 0.6998 (t0) REVERT: D 238 ASP cc_start: 0.7246 (t70) cc_final: 0.6744 (t0) REVERT: D 240 ASP cc_start: 0.7411 (m-30) cc_final: 0.7048 (m-30) REVERT: D 285 ASP cc_start: 0.6499 (t0) cc_final: 0.6234 (p0) REVERT: D 293 HIS cc_start: 0.6226 (m-70) cc_final: 0.4817 (t-90) REVERT: D 313 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: D 325 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6956 (tp30) REVERT: D 329 LYS cc_start: 0.7087 (mttt) cc_final: 0.6414 (mtpm) REVERT: D 353 LYS cc_start: 0.5676 (ttpp) cc_final: 0.5221 (tptt) REVERT: D 357 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5533 (mt) REVERT: D 367 LYS cc_start: 0.6868 (tttt) cc_final: 0.6449 (tttm) REVERT: D 380 TYR cc_start: 0.6519 (m-80) cc_final: 0.5798 (m-80) REVERT: D 436 ASP cc_start: 0.6852 (t70) cc_final: 0.6299 (t0) REVERT: D 481 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.5478 (m-80) outliers start: 76 outliers final: 23 residues processed: 324 average time/residue: 1.2335 time to fit residues: 444.3844 Evaluate side-chains 293 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 254 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15496 Z= 0.330 Angle : 0.565 7.333 20984 Z= 0.299 Chirality : 0.046 0.204 2324 Planarity : 0.004 0.034 2716 Dihedral : 4.795 21.697 2104 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.72 % Allowed : 18.24 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.19), residues: 1964 helix: 1.67 (0.18), residues: 800 sheet: 0.31 (0.26), residues: 408 loop : -0.02 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 178 HIS 0.003 0.001 HIS C 30 PHE 0.011 0.002 PHE D 483 TYR 0.020 0.003 TYR C 351 ARG 0.008 0.001 ARG B 321 *********************** 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 325 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 265 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7186 (m-30) cc_final: 0.6632 (p0) REVERT: A 48 GLU cc_start: 0.5862 (tt0) cc_final: 0.5610 (tt0) REVERT: A 53 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7158 (mm-30) REVERT: A 54 GLU cc_start: 0.7015 (tt0) cc_final: 0.6304 (tp30) REVERT: A 57 LYS cc_start: 0.6629 (tttm) cc_final: 0.6237 (tttt) REVERT: A 69 GLN cc_start: 0.6881 (tp-100) cc_final: 0.6570 (tm-30) REVERT: A 84 GLU cc_start: 0.6475 (tp30) cc_final: 0.5628 (mp0) REVERT: A 97 GLU cc_start: 0.6533 (tt0) cc_final: 0.6152 (tt0) REVERT: A 107 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.4807 (mm-30) REVERT: A 110 ASN cc_start: 0.7569 (t0) cc_final: 0.7038 (t0) REVERT: A 238 ASP cc_start: 0.7286 (t70) cc_final: 0.6801 (t0) REVERT: A 240 ASP cc_start: 0.7430 (m-30) cc_final: 0.7056 (m-30) REVERT: A 285 ASP cc_start: 0.6512 (t0) cc_final: 0.6248 (p0) REVERT: A 293 HIS cc_start: 0.6275 (m-70) cc_final: 0.4882 (t-90) REVERT: A 313 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6146 (pm20) REVERT: A 325 GLU cc_start: 0.7211 (mm-30) cc_final: 0.7001 (tp30) REVERT: A 329 LYS cc_start: 0.6973 (mttt) cc_final: 0.6379 (mtpm) REVERT: A 352 ASP cc_start: 0.6960 (m-30) cc_final: 0.6612 (m-30) REVERT: A 353 LYS cc_start: 0.5657 (ttpp) cc_final: 0.5037 (mttp) REVERT: A 357 LEU cc_start: 0.5956 (mt) cc_final: 0.5508 (mt) REVERT: A 367 LYS cc_start: 0.6939 (tttt) cc_final: 0.6510 (tttm) REVERT: A 380 TYR cc_start: 0.6522 (m-80) cc_final: 0.5883 (m-80) REVERT: A 409 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6406 (mtm) REVERT: A 436 ASP cc_start: 0.6812 (t70) cc_final: 0.6225 (t0) REVERT: A 481 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5578 (m-80) REVERT: B 31 ASP cc_start: 0.7185 (m-30) cc_final: 0.6631 (p0) REVERT: B 48 GLU cc_start: 0.5863 (tt0) cc_final: 0.5611 (tt0) REVERT: B 53 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 54 GLU cc_start: 0.7016 (tt0) cc_final: 0.6305 (tp30) REVERT: B 57 LYS cc_start: 0.6654 (tttm) cc_final: 0.6258 (tttt) REVERT: B 69 GLN cc_start: 0.6880 (tp-100) cc_final: 0.6569 (tm-30) REVERT: B 84 GLU cc_start: 0.6470 (tp30) cc_final: 0.5623 (mp0) REVERT: B 97 GLU cc_start: 0.6532 (tt0) cc_final: 0.6149 (tt0) REVERT: B 107 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.4809 (mm-30) REVERT: B 110 ASN cc_start: 0.7570 (t0) cc_final: 0.7039 (t0) REVERT: B 238 ASP cc_start: 0.7286 (t70) cc_final: 0.6801 (t0) REVERT: B 240 ASP cc_start: 0.7430 (m-30) cc_final: 0.7057 (m-30) REVERT: B 285 ASP cc_start: 0.6511 (t0) cc_final: 0.6259 (p0) REVERT: B 293 HIS cc_start: 0.6275 (m-70) cc_final: 0.4882 (t-90) REVERT: B 313 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6144 (pm20) REVERT: B 325 GLU cc_start: 0.7210 (mm-30) cc_final: 0.7003 (tp30) REVERT: B 329 LYS cc_start: 0.6972 (mttt) cc_final: 0.6379 (mtpm) REVERT: B 352 ASP cc_start: 0.6962 (m-30) cc_final: 0.6615 (m-30) REVERT: B 353 LYS cc_start: 0.5658 (ttpp) cc_final: 0.5038 (mttp) REVERT: B 357 LEU cc_start: 0.5958 (mt) cc_final: 0.5510 (mt) REVERT: B 367 LYS cc_start: 0.6942 (tttt) cc_final: 0.6512 (tttm) REVERT: B 380 TYR cc_start: 0.6522 (m-80) cc_final: 0.5885 (m-80) REVERT: B 409 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6418 (mtm) REVERT: B 436 ASP cc_start: 0.6813 (t70) cc_final: 0.6224 (t0) REVERT: B 481 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.5579 (m-80) REVERT: C 31 ASP cc_start: 0.7186 (m-30) cc_final: 0.6633 (p0) REVERT: C 48 GLU cc_start: 0.5864 (tt0) cc_final: 0.5612 (tt0) REVERT: C 53 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7158 (mm-30) REVERT: C 54 GLU cc_start: 0.7013 (tt0) cc_final: 0.6302 (tp30) REVERT: C 57 LYS cc_start: 0.6646 (tttm) cc_final: 0.6250 (tttt) REVERT: C 69 GLN cc_start: 0.6881 (tp-100) cc_final: 0.6570 (tm-30) REVERT: C 84 GLU cc_start: 0.6474 (tp30) cc_final: 0.5626 (mp0) REVERT: C 97 GLU cc_start: 0.6534 (tt0) cc_final: 0.6152 (tt0) REVERT: C 107 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.4806 (mm-30) REVERT: C 110 ASN cc_start: 0.7569 (t0) cc_final: 0.7039 (t0) REVERT: C 238 ASP cc_start: 0.7260 (t70) cc_final: 0.6778 (t0) REVERT: C 240 ASP cc_start: 0.7418 (m-30) cc_final: 0.7040 (m-30) REVERT: C 285 ASP cc_start: 0.6512 (t0) cc_final: 0.6248 (p0) REVERT: C 293 HIS cc_start: 0.6271 (m-70) cc_final: 0.4866 (t-90) REVERT: C 313 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: C 325 GLU cc_start: 0.7211 (mm-30) cc_final: 0.7001 (tp30) REVERT: C 329 LYS cc_start: 0.6972 (mttt) cc_final: 0.6379 (mtpm) REVERT: C 353 LYS cc_start: 0.5658 (ttpp) cc_final: 0.5035 (mttp) REVERT: C 357 LEU cc_start: 0.5959 (mt) cc_final: 0.5510 (mt) REVERT: C 367 LYS cc_start: 0.6940 (tttt) cc_final: 0.6511 (tttm) REVERT: C 380 TYR cc_start: 0.6522 (m-80) cc_final: 0.5885 (m-80) REVERT: C 409 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6406 (mtm) REVERT: C 436 ASP cc_start: 0.6815 (t70) cc_final: 0.6250 (t0) REVERT: C 481 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.5580 (m-80) REVERT: D 31 ASP cc_start: 0.7186 (m-30) cc_final: 0.6633 (p0) REVERT: D 48 GLU cc_start: 0.5865 (tt0) cc_final: 0.5611 (tt0) REVERT: D 53 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7158 (mm-30) REVERT: D 54 GLU cc_start: 0.7015 (tt0) cc_final: 0.6302 (tp30) REVERT: D 57 LYS cc_start: 0.6646 (tttm) cc_final: 0.6250 (tttt) REVERT: D 69 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6571 (tm-30) REVERT: D 84 GLU cc_start: 0.6469 (tp30) cc_final: 0.5624 (mp0) REVERT: D 97 GLU cc_start: 0.6532 (tt0) cc_final: 0.6149 (tt0) REVERT: D 107 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.4807 (mm-30) REVERT: D 110 ASN cc_start: 0.7569 (t0) cc_final: 0.7040 (t0) REVERT: D 238 ASP cc_start: 0.7259 (t70) cc_final: 0.6779 (t0) REVERT: D 240 ASP cc_start: 0.7416 (m-30) cc_final: 0.7039 (m-30) REVERT: D 285 ASP cc_start: 0.6514 (t0) cc_final: 0.6248 (p0) REVERT: D 293 HIS cc_start: 0.6276 (m-70) cc_final: 0.4879 (t-90) REVERT: D 313 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6145 (pm20) REVERT: D 325 GLU cc_start: 0.7209 (mm-30) cc_final: 0.7000 (tp30) REVERT: D 329 LYS cc_start: 0.6972 (mttt) cc_final: 0.6379 (mtpm) REVERT: D 353 LYS cc_start: 0.5655 (ttpp) cc_final: 0.5032 (mttp) REVERT: D 357 LEU cc_start: 0.5956 (mt) cc_final: 0.5508 (mt) REVERT: D 367 LYS cc_start: 0.6939 (tttt) cc_final: 0.6510 (tttm) REVERT: D 380 TYR cc_start: 0.6520 (m-80) cc_final: 0.5883 (m-80) REVERT: D 409 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6404 (mtm) REVERT: D 436 ASP cc_start: 0.6804 (t70) cc_final: 0.6243 (t0) REVERT: D 481 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5580 (m-80) outliers start: 60 outliers final: 28 residues processed: 309 average time/residue: 1.2734 time to fit residues: 435.3213 Evaluate side-chains 304 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 260 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15496 Z= 0.233 Angle : 0.512 6.862 20984 Z= 0.271 Chirality : 0.044 0.179 2324 Planarity : 0.004 0.033 2716 Dihedral : 4.596 20.354 2104 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.98 % Allowed : 19.54 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.19), residues: 1964 helix: 1.85 (0.19), residues: 800 sheet: 0.22 (0.26), residues: 396 loop : 0.03 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 178 HIS 0.003 0.001 HIS D 30 PHE 0.008 0.001 PHE A 483 TYR 0.017 0.002 TYR C 351 ARG 0.007 0.001 ARG B 321 *********************** 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 303 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 255 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7231 (m-30) cc_final: 0.6609 (p0) REVERT: A 48 GLU cc_start: 0.5877 (tt0) cc_final: 0.5625 (tt0) REVERT: A 53 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 54 GLU cc_start: 0.6966 (tt0) cc_final: 0.6250 (tp30) REVERT: A 57 LYS cc_start: 0.6606 (tttm) cc_final: 0.6204 (tttt) REVERT: A 69 GLN cc_start: 0.6860 (tp-100) cc_final: 0.6541 (tm-30) REVERT: A 84 GLU cc_start: 0.6360 (tp30) cc_final: 0.5507 (mm-30) REVERT: A 97 GLU cc_start: 0.6539 (tt0) cc_final: 0.6162 (tt0) REVERT: A 107 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5443 (tp30) REVERT: A 110 ASN cc_start: 0.7553 (t0) cc_final: 0.7024 (t0) REVERT: A 238 ASP cc_start: 0.7209 (t70) cc_final: 0.6791 (t0) REVERT: A 240 ASP cc_start: 0.7405 (m-30) cc_final: 0.7045 (m-30) REVERT: A 285 ASP cc_start: 0.6497 (t0) cc_final: 0.6215 (p0) REVERT: A 293 HIS cc_start: 0.6178 (m-70) cc_final: 0.4781 (t-90) REVERT: A 313 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6097 (pm20) REVERT: A 325 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6841 (tp30) REVERT: A 329 LYS cc_start: 0.6929 (mttt) cc_final: 0.6316 (mtpm) REVERT: A 352 ASP cc_start: 0.6948 (m-30) cc_final: 0.6598 (m-30) REVERT: A 353 LYS cc_start: 0.5681 (ttpp) cc_final: 0.5235 (tptt) REVERT: A 357 LEU cc_start: 0.5909 (mt) cc_final: 0.5437 (mt) REVERT: A 367 LYS cc_start: 0.6869 (tttt) cc_final: 0.6449 (tttm) REVERT: A 409 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6335 (mtm) REVERT: A 436 ASP cc_start: 0.6811 (t70) cc_final: 0.6240 (t0) REVERT: A 481 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: B 31 ASP cc_start: 0.7232 (m-30) cc_final: 0.6610 (p0) REVERT: B 48 GLU cc_start: 0.5875 (tt0) cc_final: 0.5624 (tt0) REVERT: B 53 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7154 (mm-30) REVERT: B 54 GLU cc_start: 0.6969 (tt0) cc_final: 0.6251 (tp30) REVERT: B 57 LYS cc_start: 0.6642 (tttm) cc_final: 0.6202 (tttt) REVERT: B 69 GLN cc_start: 0.6880 (tp-100) cc_final: 0.6561 (tm-30) REVERT: B 84 GLU cc_start: 0.6356 (tp30) cc_final: 0.5503 (mm-30) REVERT: B 97 GLU cc_start: 0.6537 (tt0) cc_final: 0.6161 (tt0) REVERT: B 107 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5443 (tp30) REVERT: B 110 ASN cc_start: 0.7550 (t0) cc_final: 0.7002 (t0) REVERT: B 238 ASP cc_start: 0.7210 (t70) cc_final: 0.6790 (t0) REVERT: B 240 ASP cc_start: 0.7405 (m-30) cc_final: 0.7045 (m-30) REVERT: B 285 ASP cc_start: 0.6498 (t0) cc_final: 0.6216 (p0) REVERT: B 293 HIS cc_start: 0.6176 (m-70) cc_final: 0.4779 (t-90) REVERT: B 313 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6118 (pm20) REVERT: B 325 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6856 (tp30) REVERT: B 329 LYS cc_start: 0.6929 (mttt) cc_final: 0.6318 (mtpm) REVERT: B 352 ASP cc_start: 0.6950 (m-30) cc_final: 0.6599 (m-30) REVERT: B 353 LYS cc_start: 0.5683 (ttpp) cc_final: 0.5236 (tptt) REVERT: B 357 LEU cc_start: 0.5909 (mt) cc_final: 0.5437 (mt) REVERT: B 367 LYS cc_start: 0.6870 (tttt) cc_final: 0.6450 (tttm) REVERT: B 409 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6294 (mtm) REVERT: B 436 ASP cc_start: 0.6812 (t70) cc_final: 0.6240 (t0) REVERT: B 481 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.5599 (m-80) REVERT: C 31 ASP cc_start: 0.7230 (m-30) cc_final: 0.6611 (p0) REVERT: C 48 GLU cc_start: 0.5877 (tt0) cc_final: 0.5627 (tt0) REVERT: C 53 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7081 (mm-30) REVERT: C 54 GLU cc_start: 0.6965 (tt0) cc_final: 0.6247 (tp30) REVERT: C 57 LYS cc_start: 0.6632 (tttm) cc_final: 0.6201 (tttt) REVERT: C 69 GLN cc_start: 0.6879 (tp-100) cc_final: 0.6562 (tm-30) REVERT: C 84 GLU cc_start: 0.6358 (tp30) cc_final: 0.5507 (mm-30) REVERT: C 97 GLU cc_start: 0.6539 (tt0) cc_final: 0.6161 (tt0) REVERT: C 107 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5442 (tp30) REVERT: C 110 ASN cc_start: 0.7550 (t0) cc_final: 0.7023 (t0) REVERT: C 240 ASP cc_start: 0.7423 (m-30) cc_final: 0.7063 (m-30) REVERT: C 285 ASP cc_start: 0.6500 (t0) cc_final: 0.6200 (p0) REVERT: C 293 HIS cc_start: 0.6179 (m-70) cc_final: 0.4783 (t-90) REVERT: C 313 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6064 (pm20) REVERT: C 325 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6842 (tp30) REVERT: C 329 LYS cc_start: 0.6929 (mttt) cc_final: 0.6318 (mtpm) REVERT: C 353 LYS cc_start: 0.5683 (ttpp) cc_final: 0.5235 (tptt) REVERT: C 357 LEU cc_start: 0.5911 (mt) cc_final: 0.5440 (mt) REVERT: C 367 LYS cc_start: 0.6871 (tttt) cc_final: 0.6451 (tttm) REVERT: C 409 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6333 (mtm) REVERT: C 436 ASP cc_start: 0.6816 (t70) cc_final: 0.6251 (t0) REVERT: C 481 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5603 (m-80) REVERT: D 31 ASP cc_start: 0.7230 (m-30) cc_final: 0.6612 (p0) REVERT: D 48 GLU cc_start: 0.5877 (tt0) cc_final: 0.5624 (tt0) REVERT: D 53 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7154 (mm-30) REVERT: D 54 GLU cc_start: 0.6966 (tt0) cc_final: 0.6247 (tp30) REVERT: D 57 LYS cc_start: 0.6632 (tttm) cc_final: 0.6201 (tttt) REVERT: D 69 GLN cc_start: 0.6881 (tp-100) cc_final: 0.6562 (tm-30) REVERT: D 84 GLU cc_start: 0.6356 (tp30) cc_final: 0.5504 (mm-30) REVERT: D 97 GLU cc_start: 0.6539 (tt0) cc_final: 0.6161 (tt0) REVERT: D 107 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5443 (tp30) REVERT: D 110 ASN cc_start: 0.7551 (t0) cc_final: 0.7004 (t0) REVERT: D 240 ASP cc_start: 0.7423 (m-30) cc_final: 0.7064 (m-30) REVERT: D 285 ASP cc_start: 0.6499 (t0) cc_final: 0.6198 (p0) REVERT: D 293 HIS cc_start: 0.6176 (m-70) cc_final: 0.4781 (t-90) REVERT: D 313 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6066 (pm20) REVERT: D 325 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6855 (tp30) REVERT: D 329 LYS cc_start: 0.6928 (mttt) cc_final: 0.6315 (mtpm) REVERT: D 353 LYS cc_start: 0.5680 (ttpp) cc_final: 0.5232 (tptt) REVERT: D 357 LEU cc_start: 0.5910 (mt) cc_final: 0.5438 (mt) REVERT: D 367 LYS cc_start: 0.6870 (tttt) cc_final: 0.6449 (tttm) REVERT: D 409 MET cc_start: 0.7573 (OUTLIER) cc_final: 0.6331 (mtm) REVERT: D 436 ASP cc_start: 0.6819 (t70) cc_final: 0.6253 (t0) REVERT: D 481 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.5602 (m-80) outliers start: 48 outliers final: 25 residues processed: 287 average time/residue: 1.3191 time to fit residues: 418.0352 Evaluate side-chains 303 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15496 Z= 0.488 Angle : 0.652 7.669 20984 Z= 0.346 Chirality : 0.049 0.164 2324 Planarity : 0.005 0.035 2716 Dihedral : 5.024 21.806 2104 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.54 % Allowed : 19.60 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.19), residues: 1964 helix: 1.30 (0.18), residues: 804 sheet: 0.29 (0.26), residues: 400 loop : -0.25 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 178 HIS 0.005 0.002 HIS C 30 PHE 0.017 0.003 PHE B 483 TYR 0.024 0.003 TYR D 351 ARG 0.009 0.001 ARG C 321 *********************** 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 330 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 273 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7321 (m-30) cc_final: 0.6651 (p0) REVERT: A 48 GLU cc_start: 0.5879 (tt0) cc_final: 0.5651 (tt0) REVERT: A 53 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 54 GLU cc_start: 0.6982 (tt0) cc_final: 0.6306 (tp30) REVERT: A 57 LYS cc_start: 0.6681 (tttm) cc_final: 0.6308 (tttt) REVERT: A 84 GLU cc_start: 0.6414 (tp30) cc_final: 0.5596 (mp0) REVERT: A 97 GLU cc_start: 0.6518 (tt0) cc_final: 0.6172 (tt0) REVERT: A 107 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.4825 (mm-30) REVERT: A 110 ASN cc_start: 0.7614 (t0) cc_final: 0.7164 (t0) REVERT: A 238 ASP cc_start: 0.7191 (t70) cc_final: 0.6803 (t0) REVERT: A 240 ASP cc_start: 0.7524 (m-30) cc_final: 0.7172 (m-30) REVERT: A 285 ASP cc_start: 0.6521 (t0) cc_final: 0.6239 (p0) REVERT: A 293 HIS cc_start: 0.6299 (m-70) cc_final: 0.4873 (t-90) REVERT: A 313 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6214 (pm20) REVERT: A 321 ARG cc_start: 0.6578 (ttp80) cc_final: 0.6243 (ttp-110) REVERT: A 325 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6934 (tp30) REVERT: A 329 LYS cc_start: 0.6715 (mttt) cc_final: 0.6109 (mtpm) REVERT: A 352 ASP cc_start: 0.6887 (m-30) cc_final: 0.6538 (m-30) REVERT: A 353 LYS cc_start: 0.5834 (ttpp) cc_final: 0.5198 (mttp) REVERT: A 357 LEU cc_start: 0.5989 (mt) cc_final: 0.5538 (mt) REVERT: A 367 LYS cc_start: 0.6947 (tttt) cc_final: 0.6549 (tttm) REVERT: A 380 TYR cc_start: 0.6457 (m-80) cc_final: 0.5958 (m-80) REVERT: A 409 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6626 (mtm) REVERT: A 436 ASP cc_start: 0.6799 (t70) cc_final: 0.6232 (t0) REVERT: A 481 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.5655 (m-80) REVERT: B 31 ASP cc_start: 0.7320 (m-30) cc_final: 0.6650 (p0) REVERT: B 48 GLU cc_start: 0.5881 (tt0) cc_final: 0.5652 (tt0) REVERT: B 53 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 54 GLU cc_start: 0.6980 (tt0) cc_final: 0.6305 (tp30) REVERT: B 57 LYS cc_start: 0.6686 (tttm) cc_final: 0.6295 (tttt) REVERT: B 84 GLU cc_start: 0.6431 (tp30) cc_final: 0.5609 (mp0) REVERT: B 97 GLU cc_start: 0.6515 (tt0) cc_final: 0.6169 (tt0) REVERT: B 107 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5398 (mm-30) REVERT: B 110 ASN cc_start: 0.7617 (t0) cc_final: 0.7166 (t0) REVERT: B 238 ASP cc_start: 0.7192 (t70) cc_final: 0.6802 (t0) REVERT: B 240 ASP cc_start: 0.7524 (m-30) cc_final: 0.7172 (m-30) REVERT: B 285 ASP cc_start: 0.6520 (t0) cc_final: 0.6234 (p0) REVERT: B 293 HIS cc_start: 0.6297 (m-70) cc_final: 0.4873 (t-90) REVERT: B 313 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: B 321 ARG cc_start: 0.6579 (ttp80) cc_final: 0.6243 (ttp-110) REVERT: B 325 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6935 (tp30) REVERT: B 329 LYS cc_start: 0.6717 (mttt) cc_final: 0.6110 (mtpm) REVERT: B 352 ASP cc_start: 0.6890 (m-30) cc_final: 0.6541 (m-30) REVERT: B 353 LYS cc_start: 0.5836 (ttpp) cc_final: 0.5201 (mttp) REVERT: B 357 LEU cc_start: 0.5991 (mt) cc_final: 0.5539 (mt) REVERT: B 367 LYS cc_start: 0.6947 (tttt) cc_final: 0.6545 (tttm) REVERT: B 380 TYR cc_start: 0.6458 (m-80) cc_final: 0.5958 (m-80) REVERT: B 409 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6620 (mtm) REVERT: B 436 ASP cc_start: 0.6798 (t70) cc_final: 0.6232 (t0) REVERT: B 481 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.5653 (m-80) REVERT: C 31 ASP cc_start: 0.7320 (m-30) cc_final: 0.6650 (p0) REVERT: C 48 GLU cc_start: 0.5881 (tt0) cc_final: 0.5653 (tt0) REVERT: C 53 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7168 (mm-30) REVERT: C 54 GLU cc_start: 0.6980 (tt0) cc_final: 0.6303 (tp30) REVERT: C 57 LYS cc_start: 0.6683 (tttm) cc_final: 0.6309 (tttt) REVERT: C 84 GLU cc_start: 0.6412 (tp30) cc_final: 0.5595 (mp0) REVERT: C 97 GLU cc_start: 0.6519 (tt0) cc_final: 0.6171 (tt0) REVERT: C 107 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5395 (mm-30) REVERT: C 110 ASN cc_start: 0.7632 (t0) cc_final: 0.7180 (t0) REVERT: C 238 ASP cc_start: 0.7193 (t70) cc_final: 0.6788 (t0) REVERT: C 240 ASP cc_start: 0.7522 (m-30) cc_final: 0.7168 (m-30) REVERT: C 285 ASP cc_start: 0.6521 (t0) cc_final: 0.6239 (p0) REVERT: C 293 HIS cc_start: 0.6299 (m-70) cc_final: 0.4875 (t-90) REVERT: C 313 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6210 (pm20) REVERT: C 321 ARG cc_start: 0.6570 (ttp80) cc_final: 0.6235 (ttp-110) REVERT: C 329 LYS cc_start: 0.6853 (mttt) cc_final: 0.6236 (mtpm) REVERT: C 352 ASP cc_start: 0.6889 (m-30) cc_final: 0.6540 (m-30) REVERT: C 353 LYS cc_start: 0.5838 (ttpp) cc_final: 0.5202 (mttp) REVERT: C 357 LEU cc_start: 0.5993 (mt) cc_final: 0.5541 (mt) REVERT: C 367 LYS cc_start: 0.6948 (tttt) cc_final: 0.6550 (tttm) REVERT: C 380 TYR cc_start: 0.6458 (m-80) cc_final: 0.5960 (m-80) REVERT: C 409 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.6623 (mtm) REVERT: C 436 ASP cc_start: 0.6806 (t70) cc_final: 0.6253 (t0) REVERT: C 481 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.5656 (m-80) REVERT: D 31 ASP cc_start: 0.7319 (m-30) cc_final: 0.6651 (p0) REVERT: D 48 GLU cc_start: 0.5881 (tt0) cc_final: 0.5653 (tt0) REVERT: D 53 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7167 (mm-30) REVERT: D 54 GLU cc_start: 0.6983 (tt0) cc_final: 0.6302 (tp30) REVERT: D 57 LYS cc_start: 0.6684 (tttm) cc_final: 0.6294 (tttt) REVERT: D 84 GLU cc_start: 0.6432 (tp30) cc_final: 0.5608 (mp0) REVERT: D 97 GLU cc_start: 0.6514 (tt0) cc_final: 0.6169 (tt0) REVERT: D 107 GLU cc_start: 0.6169 (OUTLIER) cc_final: 0.4822 (mm-30) REVERT: D 110 ASN cc_start: 0.7613 (t0) cc_final: 0.7164 (t0) REVERT: D 238 ASP cc_start: 0.7191 (t70) cc_final: 0.6787 (t0) REVERT: D 240 ASP cc_start: 0.7520 (m-30) cc_final: 0.7166 (m-30) REVERT: D 285 ASP cc_start: 0.6521 (t0) cc_final: 0.6238 (p0) REVERT: D 293 HIS cc_start: 0.6299 (m-70) cc_final: 0.4875 (t-90) REVERT: D 313 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6210 (pm20) REVERT: D 321 ARG cc_start: 0.6570 (ttp80) cc_final: 0.6236 (ttp-110) REVERT: D 329 LYS cc_start: 0.6852 (mttt) cc_final: 0.6234 (mtpm) REVERT: D 352 ASP cc_start: 0.6889 (m-30) cc_final: 0.6539 (m-30) REVERT: D 353 LYS cc_start: 0.5837 (ttpp) cc_final: 0.5200 (mttp) REVERT: D 357 LEU cc_start: 0.5992 (mt) cc_final: 0.5540 (mt) REVERT: D 367 LYS cc_start: 0.6945 (tttt) cc_final: 0.6548 (tttm) REVERT: D 380 TYR cc_start: 0.6457 (m-80) cc_final: 0.5957 (m-80) REVERT: D 409 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6619 (mtm) REVERT: D 436 ASP cc_start: 0.6805 (t70) cc_final: 0.6251 (t0) REVERT: D 481 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.5656 (m-80) outliers start: 57 outliers final: 30 residues processed: 302 average time/residue: 1.2975 time to fit residues: 436.1375 Evaluate side-chains 319 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 273 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15496 Z= 0.209 Angle : 0.512 6.673 20984 Z= 0.272 Chirality : 0.043 0.166 2324 Planarity : 0.004 0.033 2716 Dihedral : 4.616 20.203 2104 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.23 % Allowed : 20.29 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.19), residues: 1964 helix: 1.82 (0.19), residues: 800 sheet: 0.20 (0.27), residues: 384 loop : -0.06 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 453 HIS 0.002 0.001 HIS A 30 PHE 0.007 0.001 PHE A 483 TYR 0.017 0.002 TYR B 351 ARG 0.008 0.001 ARG D 321 ********************** 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 306 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 254 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7314 (m-30) cc_final: 0.6624 (p0) REVERT: A 48 GLU cc_start: 0.5835 (tt0) cc_final: 0.5580 (tt0) REVERT: A 53 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7160 (mm-30) REVERT: A 54 GLU cc_start: 0.7012 (tt0) cc_final: 0.6237 (tp30) REVERT: A 57 LYS cc_start: 0.6500 (tttm) cc_final: 0.6199 (tttt) REVERT: A 69 GLN cc_start: 0.7001 (tp-100) cc_final: 0.6488 (tm-30) REVERT: A 84 GLU cc_start: 0.6379 (tp30) cc_final: 0.5557 (mm-30) REVERT: A 97 GLU cc_start: 0.6501 (tt0) cc_final: 0.6161 (tt0) REVERT: A 107 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5441 (tp30) REVERT: A 110 ASN cc_start: 0.7543 (t0) cc_final: 0.6972 (t0) REVERT: A 240 ASP cc_start: 0.7480 (m-30) cc_final: 0.7129 (m-30) REVERT: A 285 ASP cc_start: 0.6486 (t0) cc_final: 0.6207 (p0) REVERT: A 313 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6144 (pm20) REVERT: A 325 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6803 (tp30) REVERT: A 329 LYS cc_start: 0.6623 (mttt) cc_final: 0.6012 (mtpm) REVERT: A 352 ASP cc_start: 0.6939 (m-30) cc_final: 0.6593 (m-30) REVERT: A 353 LYS cc_start: 0.5673 (ttpp) cc_final: 0.5064 (mttp) REVERT: A 357 LEU cc_start: 0.5907 (mt) cc_final: 0.5460 (mt) REVERT: A 367 LYS cc_start: 0.6899 (tttt) cc_final: 0.6483 (tttm) REVERT: A 409 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6387 (mtm) REVERT: A 436 ASP cc_start: 0.6827 (t70) cc_final: 0.6278 (t0) REVERT: A 481 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.5726 (m-80) REVERT: B 31 ASP cc_start: 0.7312 (m-30) cc_final: 0.6623 (p0) REVERT: B 48 GLU cc_start: 0.5838 (tt0) cc_final: 0.5584 (tt0) REVERT: B 53 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7159 (mm-30) REVERT: B 54 GLU cc_start: 0.7011 (tt0) cc_final: 0.6236 (tp30) REVERT: B 57 LYS cc_start: 0.6490 (tttm) cc_final: 0.6189 (tttt) REVERT: B 69 GLN cc_start: 0.6970 (tp-100) cc_final: 0.6453 (tm-30) REVERT: B 84 GLU cc_start: 0.6448 (tp30) cc_final: 0.5635 (mm-30) REVERT: B 97 GLU cc_start: 0.6504 (tt0) cc_final: 0.6161 (tt0) REVERT: B 107 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5442 (tp30) REVERT: B 110 ASN cc_start: 0.7542 (t0) cc_final: 0.6970 (t0) REVERT: B 240 ASP cc_start: 0.7480 (m-30) cc_final: 0.7129 (m-30) REVERT: B 285 ASP cc_start: 0.6480 (t0) cc_final: 0.6205 (p0) REVERT: B 313 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6127 (pm20) REVERT: B 325 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6804 (tp30) REVERT: B 329 LYS cc_start: 0.6622 (mttt) cc_final: 0.6013 (mtpm) REVERT: B 352 ASP cc_start: 0.6941 (m-30) cc_final: 0.6595 (m-30) REVERT: B 353 LYS cc_start: 0.5675 (ttpp) cc_final: 0.5064 (mttp) REVERT: B 357 LEU cc_start: 0.5914 (mt) cc_final: 0.5464 (mt) REVERT: B 367 LYS cc_start: 0.6898 (tttt) cc_final: 0.6482 (tttm) REVERT: B 409 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6395 (mtm) REVERT: B 436 ASP cc_start: 0.6828 (t70) cc_final: 0.6280 (t0) REVERT: B 481 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.5725 (m-80) REVERT: C 31 ASP cc_start: 0.7313 (m-30) cc_final: 0.6624 (p0) REVERT: C 48 GLU cc_start: 0.5837 (tt0) cc_final: 0.5581 (tt0) REVERT: C 53 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7160 (mm-30) REVERT: C 54 GLU cc_start: 0.7011 (tt0) cc_final: 0.6234 (tp30) REVERT: C 57 LYS cc_start: 0.6502 (tttm) cc_final: 0.6185 (tttt) REVERT: C 69 GLN cc_start: 0.6998 (tp-100) cc_final: 0.6486 (tm-30) REVERT: C 84 GLU cc_start: 0.6379 (tp30) cc_final: 0.5557 (mm-30) REVERT: C 97 GLU cc_start: 0.6505 (tt0) cc_final: 0.6163 (tt0) REVERT: C 107 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5439 (tp30) REVERT: C 110 ASN cc_start: 0.7528 (t0) cc_final: 0.6945 (t0) REVERT: C 240 ASP cc_start: 0.7478 (m-30) cc_final: 0.7125 (m-30) REVERT: C 313 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6138 (pm20) REVERT: C 329 LYS cc_start: 0.6795 (mttt) cc_final: 0.6076 (mtpm) REVERT: C 352 ASP cc_start: 0.6939 (m-30) cc_final: 0.6594 (m-30) REVERT: C 353 LYS cc_start: 0.5675 (ttpp) cc_final: 0.5064 (mttp) REVERT: C 357 LEU cc_start: 0.5908 (mt) cc_final: 0.5461 (mt) REVERT: C 367 LYS cc_start: 0.6901 (tttt) cc_final: 0.6480 (tttm) REVERT: C 409 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6314 (mtm) REVERT: C 436 ASP cc_start: 0.6820 (t70) cc_final: 0.6258 (t0) REVERT: C 481 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5728 (m-80) REVERT: D 31 ASP cc_start: 0.7312 (m-30) cc_final: 0.6624 (p0) REVERT: D 48 GLU cc_start: 0.5837 (tt0) cc_final: 0.5581 (tt0) REVERT: D 53 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7157 (mm-30) REVERT: D 54 GLU cc_start: 0.7011 (tt0) cc_final: 0.6232 (tp30) REVERT: D 57 LYS cc_start: 0.6490 (tttm) cc_final: 0.6190 (tttt) REVERT: D 69 GLN cc_start: 0.6999 (tp-100) cc_final: 0.6487 (tm-30) REVERT: D 84 GLU cc_start: 0.6448 (tp30) cc_final: 0.5637 (mm-30) REVERT: D 97 GLU cc_start: 0.6501 (tt0) cc_final: 0.6162 (tt0) REVERT: D 107 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5440 (tp30) REVERT: D 110 ASN cc_start: 0.7540 (t0) cc_final: 0.6970 (t0) REVERT: D 240 ASP cc_start: 0.7477 (m-30) cc_final: 0.7124 (m-30) REVERT: D 313 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6137 (pm20) REVERT: D 329 LYS cc_start: 0.6794 (mttt) cc_final: 0.6073 (mtpm) REVERT: D 352 ASP cc_start: 0.6938 (m-30) cc_final: 0.6593 (m-30) REVERT: D 353 LYS cc_start: 0.5672 (ttpp) cc_final: 0.5062 (mttp) REVERT: D 357 LEU cc_start: 0.5908 (mt) cc_final: 0.5460 (mt) REVERT: D 367 LYS cc_start: 0.6900 (tttt) cc_final: 0.6479 (tttm) REVERT: D 409 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.6317 (mtm) REVERT: D 436 ASP cc_start: 0.6819 (t70) cc_final: 0.6256 (t0) REVERT: D 481 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5727 (m-80) outliers start: 52 outliers final: 25 residues processed: 289 average time/residue: 1.3118 time to fit residues: 417.6965 Evaluate side-chains 290 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 249 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117932 restraints weight = 15504.232| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.49 r_work: 0.3146 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15496 Z= 0.205 Angle : 0.497 6.750 20984 Z= 0.264 Chirality : 0.043 0.159 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.453 19.668 2104 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.79 % Allowed : 20.10 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.19), residues: 1964 helix: 2.01 (0.19), residues: 800 sheet: 0.24 (0.27), residues: 384 loop : 0.02 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.002 0.001 HIS D 30 PHE 0.007 0.001 PHE C 310 TYR 0.014 0.002 TYR B 351 ARG 0.008 0.001 ARG C 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7105.07 seconds wall clock time: 127 minutes 38.36 seconds (7658.36 seconds total)