Starting phenix.real_space_refine on Sat Sep 12 14:39:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22qs_68607/09_2026/22qs_68607.cif Found real_map, /net/cci-nas-00/data/ceres_data/22qs_68607/09_2026/22qs_68607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22qs_68607/09_2026/22qs_68607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22qs_68607/09_2026/22qs_68607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22qs_68607/09_2026/22qs_68607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22qs_68607/09_2026/22qs_68607.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 10475 2.51 5 N 2553 2.21 5 O 2915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16026 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3209 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3061 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 356} Chain breaks: 1 Chain: "B" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3209 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3209 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3061 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 356} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.44, per 1000 atoms: 0.21 Number of scatterers: 16026 At special positions: 0 Unit cell: (99.17, 96.005, 142.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 2915 8.00 N 2553 7.00 C 10475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 601 " - " ASN A 96 " " NAG A 602 " - " ASN A 224 " " NAG B 601 " - " ASN B 224 " " NAG C 601 " - " ASN C 224 " " NAG C 602 " - " ASN C 96 " " NAG F 1 " - " ASN A 52 " " NAG G 1 " - " ASN D 125 " " NAG H 1 " - " ASN D 198 " " NAG I 1 " - " ASN B 52 " " NAG J 1 " - " ASN C 52 " " NAG K 1 " - " ASN E 125 " " NAG L 1 " - " ASN E 198 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 711.8 milliseconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3718 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 44.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.932A pdb=" N TYR A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.753A pdb=" N GLU A 95 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.637A pdb=" N THR A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 245 through 263 removed outlier: 3.890A pdb=" N THR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.799A pdb=" N MET A 269 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 removed outlier: 3.531A pdb=" N GLY A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 332 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 496 through 548 removed outlier: 3.605A pdb=" N ASN A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 266 through 273 Processing helix chain 'D' and resid 273 through 289 Processing helix chain 'D' and resid 301 through 319 Processing helix chain 'D' and resid 331 through 359 Processing helix chain 'D' and resid 511 through 556 Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 85 through 88 removed outlier: 4.181A pdb=" N TYR B 88 " --> pdb=" O GLU B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 88' Processing helix chain 'B' and resid 90 through 95 removed outlier: 4.222A pdb=" N GLU B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 245 through 262 Processing helix chain 'B' and resid 273 through 292 Processing helix chain 'B' and resid 303 through 331 Processing helix chain 'B' and resid 332 through 336 Processing helix chain 'B' and resid 340 through 355 Processing helix chain 'B' and resid 496 through 546 Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 85 through 88 removed outlier: 3.897A pdb=" N TYR C 88 " --> pdb=" O GLU C 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 88' Processing helix chain 'C' and resid 90 through 95 removed outlier: 4.044A pdb=" N GLU C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.633A pdb=" N ILE C 107 " --> pdb=" O TYR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'C' and resid 245 through 262 Processing helix chain 'C' and resid 274 through 291 removed outlier: 3.520A pdb=" N VAL C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 332 Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 496 through 548 removed outlier: 3.857A pdb=" N VAL C 502 " --> pdb=" O ARG C 498 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 548 " --> pdb=" O VAL C 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 164 through 167 Processing helix chain 'E' and resid 266 through 273 Processing helix chain 'E' and resid 273 through 289 Processing helix chain 'E' and resid 301 through 319 Processing helix chain 'E' and resid 331 through 359 Processing helix chain 'E' and resid 511 through 556 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 5.719A pdb=" N ASN A 130 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A 147 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N TRP A 77 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N TYR A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE A 79 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASP A 58 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ARG A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N SER A 56 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N PHE A 83 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N SER A 54 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.690A pdb=" N CYS A 170 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER A 176 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 226 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN A 208 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG A 235 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE A 206 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 126 through 130 removed outlier: 5.496A pdb=" N ASN D 157 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU D 176 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN D 102 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE D 89 " --> pdb=" O ASN D 102 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N TRP D 104 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N TYR D 87 " --> pdb=" O TRP D 104 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE D 106 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER D 85 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS D 108 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 83 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ARG D 110 " --> pdb=" O HIS D 81 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N HIS D 81 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 139 through 141 removed outlier: 4.670A pdb=" N SER D 205 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL D 254 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 236 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN D 263 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL D 234 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 103 removed outlier: 5.695A pdb=" N ASN B 130 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU B 147 " --> pdb=" O ASN B 130 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N TRP B 77 " --> pdb=" O TYR B 60 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N TYR B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ILE B 79 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP B 58 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ARG B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N SER B 56 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE B 83 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N SER B 54 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.773A pdb=" N SER B 176 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR B 226 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 235 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE B 206 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 99 through 102 removed outlier: 6.849A pdb=" N TYR C 71 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU C 64 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE C 62 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN C 75 " --> pdb=" O TYR C 60 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE C 83 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN C 52 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.692A pdb=" N CYS C 170 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N SER C 176 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR C 226 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 208 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG C 235 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE C 206 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 126 through 130 removed outlier: 5.362A pdb=" N ASN E 157 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU E 176 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN E 102 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE E 89 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TRP E 104 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TYR E 87 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE E 106 " --> pdb=" O SER E 85 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER E 85 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS E 108 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER E 83 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ARG E 110 " --> pdb=" O HIS E 81 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N HIS E 81 " --> pdb=" O ARG E 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 139 through 141 removed outlier: 4.662A pdb=" N SER E 205 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL E 254 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E 236 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN E 263 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL E 234 " --> pdb=" O GLN E 263 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2532 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: 2.53 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4857 1.35 - 1.46: 4220 1.46 - 1.58: 7217 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 16432 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 ... (remaining 16427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 22117 2.12 - 4.23: 223 4.23 - 6.35: 31 6.35 - 8.46: 1 8.46 - 10.58: 3 Bond angle restraints: 22375 Sorted by residual: angle pdb=" CA ILE D 275 " pdb=" C ILE D 275 " pdb=" N PRO D 276 " ideal model delta sigma weight residual 120.83 117.31 3.52 6.10e-01 2.69e+00 3.34e+01 angle pdb=" CB MET B 269 " pdb=" CG MET B 269 " pdb=" SD MET B 269 " ideal model delta sigma weight residual 112.70 123.28 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N VAL E 319 " pdb=" CA VAL E 319 " pdb=" C VAL E 319 " ideal model delta sigma weight residual 112.29 109.13 3.16 9.40e-01 1.13e+00 1.13e+01 angle pdb=" C ILE D 275 " pdb=" CA ILE D 275 " pdb=" CB ILE D 275 " ideal model delta sigma weight residual 114.00 109.62 4.38 1.31e+00 5.83e-01 1.12e+01 angle pdb=" O ILE D 275 " pdb=" C ILE D 275 " pdb=" N PRO D 276 " ideal model delta sigma weight residual 120.42 122.41 -1.99 6.40e-01 2.44e+00 9.66e+00 ... (remaining 22370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 9224 21.63 - 43.27: 643 43.27 - 64.90: 115 64.90 - 86.54: 18 86.54 - 108.17: 5 Dihedral angle restraints: 10005 sinusoidal: 4276 harmonic: 5729 Sorted by residual: dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.46 108.17 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.43 106.05 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" CA CYS A 170 " pdb=" C CYS A 170 " pdb=" N THR A 171 " pdb=" CA THR A 171 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 10002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2172 0.055 - 0.109: 397 0.109 - 0.164: 59 0.164 - 0.218: 7 0.218 - 0.273: 3 Chirality restraints: 2638 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 52 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 52 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2635 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 49 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO D 50 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 221 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO B 222 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 222 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 222 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 94 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.63e+00 pdb=" N PRO E 95 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " -0.018 5.00e-02 4.00e+02 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3906 2.80 - 3.32: 14456 3.32 - 3.85: 28366 3.85 - 4.37: 33670 4.37 - 4.90: 56567 Nonbonded interactions: 136965 Sorted by model distance: nonbonded pdb=" O MET D 156 " pdb=" ND2 ASN D 157 " model vdw 2.274 3.120 nonbonded pdb=" O SER A 275 " pdb=" OG1 THR A 279 " model vdw 2.284 3.040 nonbonded pdb=" O THR D 286 " pdb=" OG1 THR D 290 " model vdw 2.287 3.040 nonbonded pdb=" O GLY B 259 " pdb=" OG1 THR B 263 " model vdw 2.303 3.040 nonbonded pdb=" N GLU E 62 " pdb=" OE1 GLU E 62 " model vdw 2.306 3.120 ... (remaining 136960 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 23 through 601) selection = chain 'B' selection = (chain 'C' and resid 23 through 601) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.840 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.000 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16457 Z= 0.150 Angle : 0.558 10.579 22445 Z= 0.284 Chirality : 0.044 0.273 2638 Planarity : 0.004 0.045 2716 Dihedral : 14.989 108.171 6272 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.91 % Allowed : 16.36 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 1904 helix: 2.48 (0.19), residues: 743 sheet: 0.84 (0.24), residues: 423 loop : -0.39 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 514 TYR 0.013 0.001 TYR B 71 PHE 0.015 0.001 PHE B 533 TRP 0.022 0.001 TRP C 539 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16432) covalent geometry : angle 0.54849 / 0.28 (22375) SS BOND : bond 0.00159 / 0.08 ( 5) SS BOND : angle 0.84420 / 0.50 ( 10) hydrogen bonds : bond 0.13187 / 8.71 ( 877) hydrogen bonds : angle 5.78825 / 3.88 ( 2532) link_BETA1-4 : bond 0.00938 / 0.63 ( 8) link_BETA1-4 : angle 2.74508 / 2.07 ( 24) link_NAG-ASN : bond 0.00212 / 0.16 ( 12) link_NAG-ASN : angle 1.39874 / 0.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7787 (mt-10) REVERT: A 161 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7756 (mtm-85) REVERT: A 269 MET cc_start: 0.7591 (tmt) cc_final: 0.7377 (ttp) REVERT: A 288 MET cc_start: 0.7287 (mmm) cc_final: 0.6737 (mmm) REVERT: A 290 MET cc_start: 0.5501 (mtp) cc_final: 0.5258 (mtp) REVERT: A 324 SER cc_start: 0.7808 (m) cc_final: 0.7571 (m) REVERT: A 526 ILE cc_start: 0.7482 (mm) cc_final: 0.7213 (mt) REVERT: D 75 LYS cc_start: 0.7644 (mmtt) cc_final: 0.7177 (mptt) REVERT: D 150 ASP cc_start: 0.7955 (m-30) cc_final: 0.7736 (m-30) REVERT: D 231 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8283 (mt-10) REVERT: D 303 ASN cc_start: 0.7651 (t0) cc_final: 0.7352 (m-40) REVERT: D 312 MET cc_start: 0.6828 (mmm) cc_final: 0.6513 (mmm) REVERT: D 318 MET cc_start: 0.5810 (mtp) cc_final: 0.5468 (mtp) REVERT: D 349 PHE cc_start: 0.7185 (m-10) cc_final: 0.6909 (m-80) REVERT: D 543 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6083 (tt) REVERT: D 548 ARG cc_start: 0.5808 (mmm160) cc_final: 0.4933 (ttt180) REVERT: B 290 MET cc_start: 0.8067 (ttm) cc_final: 0.7598 (ttp) REVERT: B 304 LEU cc_start: 0.8492 (tp) cc_final: 0.8034 (mt) REVERT: B 524 PHE cc_start: 0.8265 (t80) cc_final: 0.7996 (t80) REVERT: B 532 ASN cc_start: 0.6865 (m-40) cc_final: 0.6605 (m-40) REVERT: C 172 MET cc_start: 0.9089 (mtm) cc_final: 0.8756 (mtm) REVERT: C 269 MET cc_start: 0.7809 (ppp) cc_final: 0.7395 (tmm) REVERT: C 271 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: C 288 MET cc_start: 0.7028 (mtp) cc_final: 0.6828 (mtm) REVERT: C 504 GLU cc_start: 0.6574 (tt0) cc_final: 0.6355 (mt-10) REVERT: E 47 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7133 (mtpt) REVERT: E 94 GLU cc_start: 0.8277 (mp0) cc_final: 0.8053 (mm-30) REVERT: E 168 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7151 (mm-30) REVERT: E 273 LEU cc_start: 0.8550 (tt) cc_final: 0.8221 (tm) REVERT: E 316 MET cc_start: 0.5500 (ppp) cc_final: 0.5298 (pp-130) REVERT: E 346 ILE cc_start: 0.7674 (mm) cc_final: 0.7449 (mt) REVERT: E 545 LEU cc_start: 0.7685 (mp) cc_final: 0.7199 (mm) outliers start: 16 outliers final: 6 residues processed: 240 average time/residue: 0.6053 time to fit residues: 161.4076 Evaluate side-chains 210 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain C residue 271 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN B 75 ASN C 223 ASN E 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114028 restraints weight = 16822.232| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.63 r_work: 0.3228 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16457 Z= 0.256 Angle : 0.680 7.346 22445 Z= 0.345 Chirality : 0.049 0.458 2638 Planarity : 0.005 0.060 2716 Dihedral : 7.695 79.366 2536 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.94 % Allowed : 15.01 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.19), residues: 1904 helix: 2.31 (0.19), residues: 742 sheet: 0.72 (0.24), residues: 462 loop : -0.29 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 514 TYR 0.019 0.002 TYR B 71 PHE 0.021 0.002 PHE B 533 TRP 0.019 0.002 TRP D 116 HIS 0.007 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.26 (16432) covalent geometry : angle 0.66833 / 0.34 (22375) SS BOND : bond 0.00214 / 0.11 ( 5) SS BOND : angle 2.37302 / 1.42 ( 10) hydrogen bonds : bond 0.05246 / 3.42 ( 877) hydrogen bonds : angle 4.83121 / 3.27 ( 2532) link_BETA1-4 : bond 0.00549 / 0.34 ( 8) link_BETA1-4 : angle 2.60028 / 1.91 ( 24) link_NAG-ASN : bond 0.00461 / 0.25 ( 12) link_NAG-ASN : angle 2.10174 / 1.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 123 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8070 (t70) REVERT: A 161 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7918 (mtm-85) REVERT: A 269 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7599 (ttp) REVERT: A 288 MET cc_start: 0.8085 (mmm) cc_final: 0.7633 (mmm) REVERT: A 526 ILE cc_start: 0.8001 (mm) cc_final: 0.7776 (mt) REVERT: D 75 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7340 (mptt) REVERT: D 150 ASP cc_start: 0.8018 (m-30) cc_final: 0.7794 (m-30) REVERT: D 231 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8488 (mt-10) REVERT: D 302 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7533 (mm) REVERT: D 312 MET cc_start: 0.7377 (mmm) cc_final: 0.7010 (mmm) REVERT: D 349 PHE cc_start: 0.7657 (m-10) cc_final: 0.7376 (m-80) REVERT: D 543 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6707 (tt) REVERT: D 548 ARG cc_start: 0.6364 (mmm160) cc_final: 0.5492 (ttt180) REVERT: B 200 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: B 212 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8401 (tttm) REVERT: B 224 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7824 (m110) REVERT: B 269 MET cc_start: 0.5344 (tpp) cc_final: 0.4538 (tpp) REVERT: B 290 MET cc_start: 0.8572 (ttm) cc_final: 0.8050 (ttp) REVERT: B 304 LEU cc_start: 0.8609 (tp) cc_final: 0.8189 (mt) REVERT: B 524 PHE cc_start: 0.8581 (t80) cc_final: 0.8381 (t80) REVERT: B 532 ASN cc_start: 0.7238 (m-40) cc_final: 0.6962 (m-40) REVERT: C 269 MET cc_start: 0.8170 (ppp) cc_final: 0.7780 (tmm) REVERT: C 504 GLU cc_start: 0.7040 (tt0) cc_final: 0.6776 (tt0) REVERT: E 43 ASP cc_start: 0.7759 (m-30) cc_final: 0.7529 (m-30) REVERT: E 47 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7496 (mtpt) REVERT: E 168 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7757 (mm-30) REVERT: E 304 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7548 (mt) REVERT: E 346 ILE cc_start: 0.8256 (mm) cc_final: 0.8022 (mt) REVERT: E 545 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7784 (mm) REVERT: E 548 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7015 (mtt90) outliers start: 52 outliers final: 15 residues processed: 230 average time/residue: 0.6066 time to fit residues: 154.6098 Evaluate side-chains 213 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 224 GLN D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116487 restraints weight = 16967.235| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.63 r_work: 0.3284 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16457 Z= 0.141 Angle : 0.552 8.167 22445 Z= 0.282 Chirality : 0.044 0.263 2638 Planarity : 0.004 0.038 2716 Dihedral : 6.423 69.806 2528 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.83 % Allowed : 15.57 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 1904 helix: 2.51 (0.19), residues: 742 sheet: 0.60 (0.24), residues: 462 loop : -0.30 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 514 TYR 0.014 0.001 TYR B 71 PHE 0.019 0.001 PHE B 533 TRP 0.017 0.001 TRP B 539 HIS 0.003 0.001 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16432) covalent geometry : angle 0.54367 / 0.28 (22375) SS BOND : bond 0.00695 / 0.35 ( 5) SS BOND : angle 1.23497 / 0.74 ( 10) hydrogen bonds : bond 0.04399 / 2.88 ( 877) hydrogen bonds : angle 4.59861 / 3.11 ( 2532) link_BETA1-4 : bond 0.00679 / 0.45 ( 8) link_BETA1-4 : angle 2.41975 / 1.77 ( 24) link_NAG-ASN : bond 0.00127 / 0.08 ( 12) link_NAG-ASN : angle 1.29547 / 0.91 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7995 (mt-10) REVERT: A 123 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7982 (t70) REVERT: A 161 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: A 170 CYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5483 (t) REVERT: A 269 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7553 (ttp) REVERT: A 288 MET cc_start: 0.8194 (mmm) cc_final: 0.7761 (mmm) REVERT: A 290 MET cc_start: 0.6977 (mtp) cc_final: 0.6700 (mtp) REVERT: A 526 ILE cc_start: 0.7928 (mm) cc_final: 0.7704 (mt) REVERT: D 46 MET cc_start: 0.7721 (ttp) cc_final: 0.7443 (ttt) REVERT: D 75 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7290 (mptt) REVERT: D 150 ASP cc_start: 0.8081 (m-30) cc_final: 0.7853 (m-30) REVERT: D 231 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8472 (mt-10) REVERT: D 312 MET cc_start: 0.7309 (mmm) cc_final: 0.7000 (mmm) REVERT: D 349 PHE cc_start: 0.7679 (m-10) cc_final: 0.7366 (m-80) REVERT: D 543 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6407 (tp) REVERT: D 548 ARG cc_start: 0.6314 (mmm160) cc_final: 0.5451 (ttt180) REVERT: B 200 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: B 212 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8423 (tttm) REVERT: B 224 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7782 (m-40) REVERT: B 269 MET cc_start: 0.5482 (tpp) cc_final: 0.4822 (tpp) REVERT: B 290 MET cc_start: 0.8552 (ttm) cc_final: 0.8198 (ttp) REVERT: B 304 LEU cc_start: 0.8523 (tp) cc_final: 0.8096 (mt) REVERT: B 330 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: B 524 PHE cc_start: 0.8552 (t80) cc_final: 0.8343 (t80) REVERT: B 532 ASN cc_start: 0.7232 (m-40) cc_final: 0.6970 (m-40) REVERT: C 170 CYS cc_start: 0.6819 (OUTLIER) cc_final: 0.6503 (t) REVERT: C 269 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7815 (tmm) REVERT: C 504 GLU cc_start: 0.7031 (tt0) cc_final: 0.6715 (mt-10) REVERT: E 43 ASP cc_start: 0.7757 (m-30) cc_final: 0.7507 (m-30) REVERT: E 47 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7512 (mtpt) REVERT: E 168 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7770 (mm-30) REVERT: E 304 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7541 (mt) REVERT: E 346 ILE cc_start: 0.8258 (mm) cc_final: 0.8039 (mt) REVERT: E 545 LEU cc_start: 0.8193 (mp) cc_final: 0.7855 (mm) REVERT: E 548 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6895 (mtt90) outliers start: 50 outliers final: 22 residues processed: 224 average time/residue: 0.6131 time to fit residues: 152.4368 Evaluate side-chains 224 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN D 117 ASN D 157 ASN D 303 ASN C 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118227 restraints weight = 16862.865| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.61 r_work: 0.3324 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16457 Z= 0.117 Angle : 0.516 6.932 22445 Z= 0.265 Chirality : 0.043 0.242 2638 Planarity : 0.003 0.037 2716 Dihedral : 5.719 67.136 2528 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.83 % Allowed : 15.57 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.19), residues: 1904 helix: 2.67 (0.19), residues: 744 sheet: 0.57 (0.23), residues: 462 loop : -0.30 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 514 TYR 0.012 0.001 TYR B 71 PHE 0.021 0.001 PHE B 533 TRP 0.017 0.001 TRP A 539 HIS 0.002 0.000 HIS E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16432) covalent geometry : angle 0.50915 / 0.26 (22375) SS BOND : bond 0.00151 / 0.08 ( 5) SS BOND : angle 1.22354 / 0.74 ( 10) hydrogen bonds : bond 0.04042 / 2.64 ( 877) hydrogen bonds : angle 4.44408 / 3.01 ( 2532) link_BETA1-4 : bond 0.00656 / 0.43 ( 8) link_BETA1-4 : angle 2.26568 / 1.66 ( 24) link_NAG-ASN : bond 0.00141 / 0.09 ( 12) link_NAG-ASN : angle 1.10303 / 0.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.648 Fit side-chains REVERT: A 78 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8987 (mm) REVERT: A 99 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8016 (mt-10) REVERT: A 161 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7903 (mtm-85) REVERT: A 170 CYS cc_start: 0.6197 (OUTLIER) cc_final: 0.5183 (t) REVERT: A 269 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7540 (ttp) REVERT: A 288 MET cc_start: 0.8212 (mmm) cc_final: 0.7830 (mmm) REVERT: A 290 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6712 (mtp) REVERT: A 526 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7690 (mt) REVERT: D 75 LYS cc_start: 0.7826 (mmtt) cc_final: 0.7310 (mptt) REVERT: D 150 ASP cc_start: 0.8042 (m-30) cc_final: 0.7814 (m-30) REVERT: D 231 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8478 (mt-10) REVERT: D 312 MET cc_start: 0.7197 (mmm) cc_final: 0.6891 (mmm) REVERT: D 346 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7516 (mm) REVERT: D 349 PHE cc_start: 0.7652 (m-10) cc_final: 0.7346 (m-80) REVERT: D 526 ARG cc_start: 0.3994 (OUTLIER) cc_final: 0.2895 (tmt170) REVERT: D 543 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6478 (tt) REVERT: D 548 ARG cc_start: 0.6270 (mmm160) cc_final: 0.5404 (ttt180) REVERT: B 200 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: B 224 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7829 (m-40) REVERT: B 269 MET cc_start: 0.5597 (tpp) cc_final: 0.5017 (tpp) REVERT: B 290 MET cc_start: 0.8563 (ttm) cc_final: 0.8263 (ttp) REVERT: B 304 LEU cc_start: 0.8450 (tp) cc_final: 0.8008 (mt) REVERT: B 330 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: B 532 ASN cc_start: 0.7266 (m-40) cc_final: 0.7019 (m-40) REVERT: C 170 CYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6369 (t) REVERT: C 189 TYR cc_start: 0.8723 (m-80) cc_final: 0.8123 (m-10) REVERT: C 269 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: C 294 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7074 (mm-40) REVERT: C 504 GLU cc_start: 0.7035 (tt0) cc_final: 0.6769 (mt-10) REVERT: E 47 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7491 (mtpt) REVERT: E 168 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7757 (mm-30) REVERT: E 243 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: E 304 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7566 (mt) REVERT: E 346 ILE cc_start: 0.8249 (mm) cc_final: 0.8033 (mt) REVERT: E 545 LEU cc_start: 0.8194 (mp) cc_final: 0.7863 (mm) REVERT: E 548 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6909 (mtt90) outliers start: 50 outliers final: 17 residues processed: 223 average time/residue: 0.6065 time to fit residues: 150.2010 Evaluate side-chains 223 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 142 optimal weight: 0.0370 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 28 optimal weight: 0.0670 chunk 21 optimal weight: 5.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120174 restraints weight = 16927.577| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.63 r_work: 0.3355 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16457 Z= 0.099 Angle : 0.488 7.522 22445 Z= 0.250 Chirality : 0.042 0.218 2638 Planarity : 0.003 0.039 2716 Dihedral : 5.261 64.007 2523 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.72 % Allowed : 16.19 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 1904 helix: 2.82 (0.18), residues: 744 sheet: 0.55 (0.24), residues: 462 loop : -0.25 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 514 TYR 0.011 0.001 TYR A 71 PHE 0.020 0.001 PHE B 533 TRP 0.016 0.001 TRP C 539 HIS 0.002 0.000 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (16432) covalent geometry : angle 0.48162 / 0.25 (22375) SS BOND : bond 0.00031 / 0.02 ( 5) SS BOND : angle 0.84318 / 0.51 ( 10) hydrogen bonds : bond 0.03789 / 2.48 ( 877) hydrogen bonds : angle 4.33039 / 2.94 ( 2532) link_BETA1-4 : bond 0.00632 / 0.41 ( 8) link_BETA1-4 : angle 2.06176 / 1.52 ( 24) link_NAG-ASN : bond 0.00156 / 0.10 ( 12) link_NAG-ASN : angle 1.11228 / 0.77 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.637 Fit side-chains REVERT: A 78 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8883 (mm) REVERT: A 99 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8024 (mt-10) REVERT: A 161 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7860 (mtm-85) REVERT: A 170 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.4930 (t) REVERT: A 288 MET cc_start: 0.8085 (mmm) cc_final: 0.7537 (mmm) REVERT: A 290 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6594 (mtp) REVERT: A 526 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7526 (mt) REVERT: D 75 LYS cc_start: 0.7770 (mmtt) cc_final: 0.7233 (mptt) REVERT: D 150 ASP cc_start: 0.7996 (m-30) cc_final: 0.7775 (m-30) REVERT: D 231 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8418 (mt-10) REVERT: D 312 MET cc_start: 0.7115 (mmm) cc_final: 0.6761 (mmm) REVERT: D 349 PHE cc_start: 0.7514 (m-10) cc_final: 0.7172 (m-80) REVERT: D 526 ARG cc_start: 0.3851 (OUTLIER) cc_final: 0.2714 (tmt170) REVERT: D 548 ARG cc_start: 0.6149 (mmm160) cc_final: 0.5291 (ttt180) REVERT: B 121 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7805 (ttpt) REVERT: B 161 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8232 (mtm-85) REVERT: B 224 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7859 (m-40) REVERT: B 269 MET cc_start: 0.5677 (tpp) cc_final: 0.5120 (tpp) REVERT: B 290 MET cc_start: 0.8509 (ttm) cc_final: 0.8231 (ttp) REVERT: B 330 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: B 532 ASN cc_start: 0.7071 (m-40) cc_final: 0.6785 (m-40) REVERT: B 545 GLU cc_start: 0.7015 (pt0) cc_final: 0.6749 (pt0) REVERT: C 95 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8008 (pm20) REVERT: C 170 CYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5984 (t) REVERT: C 189 TYR cc_start: 0.8690 (m-80) cc_final: 0.8119 (m-10) REVERT: C 269 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7943 (tmm) REVERT: C 294 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.6927 (mm-40) REVERT: E 168 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7573 (mm-30) REVERT: E 304 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7455 (mt) REVERT: E 323 MET cc_start: 0.5174 (OUTLIER) cc_final: 0.4080 (tmt) REVERT: E 543 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7753 (tt) REVERT: E 545 LEU cc_start: 0.7907 (mp) cc_final: 0.7589 (mm) REVERT: E 548 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6790 (mtt90) outliers start: 48 outliers final: 16 residues processed: 225 average time/residue: 0.6175 time to fit residues: 154.0771 Evaluate side-chains 219 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN D 224 GLN D 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.150230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114488 restraints weight = 16770.490| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.62 r_work: 0.3254 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16457 Z= 0.227 Angle : 0.647 18.144 22445 Z= 0.324 Chirality : 0.047 0.231 2638 Planarity : 0.004 0.047 2716 Dihedral : 5.845 67.589 2523 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.11 % Allowed : 16.53 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.19), residues: 1904 helix: 2.50 (0.18), residues: 742 sheet: 0.58 (0.23), residues: 462 loop : -0.29 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 514 TYR 0.019 0.002 TYR D 337 PHE 0.021 0.002 PHE E 192 TRP 0.016 0.002 TRP D 116 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (16432) covalent geometry : angle 0.63791 / 0.32 (22375) SS BOND : bond 0.00189 / 0.08 ( 5) SS BOND : angle 2.18561 / 1.31 ( 10) hydrogen bonds : bond 0.04687 / 3.06 ( 877) hydrogen bonds : angle 4.59582 / 3.10 ( 2532) link_BETA1-4 : bond 0.00604 / 0.39 ( 8) link_BETA1-4 : angle 2.65223 / 1.97 ( 24) link_NAG-ASN : bond 0.00315 / 0.21 ( 12) link_NAG-ASN : angle 1.44367 / 1.05 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9030 (mm) REVERT: A 99 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8027 (mt-10) REVERT: A 123 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7934 (t70) REVERT: A 217 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8064 (tptm) REVERT: A 288 MET cc_start: 0.8187 (mmm) cc_final: 0.7683 (mmm) REVERT: A 290 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6661 (mtp) REVERT: A 526 ILE cc_start: 0.7933 (mm) cc_final: 0.7723 (mt) REVERT: D 75 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7265 (mptt) REVERT: D 150 ASP cc_start: 0.8095 (m-30) cc_final: 0.7882 (m-30) REVERT: D 231 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8481 (mt-10) REVERT: D 312 MET cc_start: 0.7326 (mmm) cc_final: 0.6972 (mmm) REVERT: D 316 MET cc_start: 0.4479 (tpp) cc_final: 0.4224 (tpp) REVERT: D 349 PHE cc_start: 0.7636 (m-10) cc_final: 0.7329 (m-80) REVERT: D 526 ARG cc_start: 0.3815 (OUTLIER) cc_final: 0.2717 (ttt-90) REVERT: D 548 ARG cc_start: 0.6197 (mmm160) cc_final: 0.5326 (ttt180) REVERT: B 121 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7920 (ttpt) REVERT: B 200 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: B 224 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7841 (m-40) REVERT: B 269 MET cc_start: 0.5699 (tpp) cc_final: 0.5271 (tpp) REVERT: B 290 MET cc_start: 0.8568 (ttm) cc_final: 0.8258 (ttp) REVERT: B 304 LEU cc_start: 0.8572 (tp) cc_final: 0.8219 (mt) REVERT: B 330 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: B 514 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6312 (mtp85) REVERT: B 532 ASN cc_start: 0.7233 (m-40) cc_final: 0.6944 (m-40) REVERT: C 28 ARG cc_start: 0.7931 (mtp180) cc_final: 0.7636 (mtp180) REVERT: C 189 TYR cc_start: 0.8693 (m-80) cc_final: 0.8186 (m-80) REVERT: C 269 MET cc_start: 0.8226 (ppp) cc_final: 0.7897 (tmm) REVERT: C 294 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7036 (mm-40) REVERT: E 47 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7498 (mtpt) REVERT: E 169 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8425 (tptp) REVERT: E 304 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7475 (mt) REVERT: E 543 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8046 (tt) REVERT: E 545 LEU cc_start: 0.8101 (mp) cc_final: 0.7764 (mm) REVERT: E 548 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6940 (mtt90) outliers start: 55 outliers final: 28 residues processed: 228 average time/residue: 0.5814 time to fit residues: 147.5399 Evaluate side-chains 227 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 2 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.8187 > 50:) overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.152423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116794 restraints weight = 16684.144| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.62 r_work: 0.3290 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16457 Z= 0.139 Angle : 0.548 8.723 22445 Z= 0.279 Chirality : 0.043 0.223 2638 Planarity : 0.004 0.038 2716 Dihedral : 5.623 68.168 2523 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.06 % Allowed : 16.76 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 1904 helix: 2.63 (0.18), residues: 742 sheet: 0.53 (0.23), residues: 462 loop : -0.28 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.021 0.001 TYR D 337 PHE 0.019 0.001 PHE B 533 TRP 0.017 0.001 TRP B 539 HIS 0.003 0.001 HIS C 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16432) covalent geometry : angle 0.53954 / 0.28 (22375) SS BOND : bond 0.00101 / 0.04 ( 5) SS BOND : angle 1.32887 / 0.80 ( 10) hydrogen bonds : bond 0.04181 / 2.74 ( 877) hydrogen bonds : angle 4.48766 / 3.03 ( 2532) link_BETA1-4 : bond 0.00663 / 0.43 ( 8) link_BETA1-4 : angle 2.35578 / 1.76 ( 24) link_NAG-ASN : bond 0.00177 / 0.10 ( 12) link_NAG-ASN : angle 1.45722 / 1.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 0.559 Fit side-chains REVERT: A 99 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 123 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7956 (t70) REVERT: A 170 CYS cc_start: 0.6486 (OUTLIER) cc_final: 0.5655 (m) REVERT: A 288 MET cc_start: 0.8195 (mmm) cc_final: 0.7712 (mmm) REVERT: A 290 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6446 (mtp) REVERT: A 324 SER cc_start: 0.7855 (m) cc_final: 0.7504 (p) REVERT: A 526 ILE cc_start: 0.7898 (mm) cc_final: 0.7673 (mt) REVERT: D 75 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7247 (mptt) REVERT: D 150 ASP cc_start: 0.8052 (m-30) cc_final: 0.7848 (m-30) REVERT: D 231 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8463 (mt-10) REVERT: D 312 MET cc_start: 0.7177 (mmm) cc_final: 0.6913 (mmm) REVERT: D 346 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7347 (mp) REVERT: D 526 ARG cc_start: 0.3909 (OUTLIER) cc_final: 0.2747 (ttt-90) REVERT: D 548 ARG cc_start: 0.6184 (mmm160) cc_final: 0.5315 (ttt180) REVERT: B 121 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7877 (ttpt) REVERT: B 200 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: B 224 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7802 (m-40) REVERT: B 269 MET cc_start: 0.5790 (tpp) cc_final: 0.5328 (tpp) REVERT: B 290 MET cc_start: 0.8561 (ttm) cc_final: 0.8287 (ttp) REVERT: B 304 LEU cc_start: 0.8402 (tp) cc_final: 0.8015 (mt) REVERT: B 330 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: B 514 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6330 (mtp85) REVERT: B 532 ASN cc_start: 0.7117 (m-40) cc_final: 0.6815 (m-40) REVERT: C 95 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7973 (pm20) REVERT: C 170 CYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6687 (t) REVERT: C 189 TYR cc_start: 0.8699 (m-80) cc_final: 0.8253 (m-80) REVERT: C 269 MET cc_start: 0.8273 (ppp) cc_final: 0.7957 (tmm) REVERT: C 294 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.6999 (mm-40) REVERT: E 47 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7465 (mtpt) REVERT: E 168 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7435 (mm-30) REVERT: E 243 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8437 (mt-10) REVERT: E 304 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7493 (mt) REVERT: E 543 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8000 (tt) REVERT: E 545 LEU cc_start: 0.8062 (mp) cc_final: 0.7736 (mm) REVERT: E 548 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6962 (mtt90) outliers start: 54 outliers final: 22 residues processed: 222 average time/residue: 0.5556 time to fit residues: 136.7181 Evaluate side-chains 221 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 63 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117794 restraints weight = 16835.772| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.62 r_work: 0.3324 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16457 Z= 0.123 Angle : 0.524 6.652 22445 Z= 0.268 Chirality : 0.043 0.211 2638 Planarity : 0.004 0.039 2716 Dihedral : 5.426 66.862 2523 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.60 % Allowed : 17.10 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.19), residues: 1904 helix: 2.73 (0.18), residues: 742 sheet: 0.53 (0.23), residues: 458 loop : -0.28 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 514 TYR 0.021 0.001 TYR D 337 PHE 0.018 0.001 PHE B 533 TRP 0.016 0.001 TRP C 539 HIS 0.002 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (16432) covalent geometry : angle 0.51673 / 0.27 (22375) SS BOND : bond 0.00081 / 0.03 ( 5) SS BOND : angle 1.15277 / 0.70 ( 10) hydrogen bonds : bond 0.03998 / 2.62 ( 877) hydrogen bonds : angle 4.41774 / 2.99 ( 2532) link_BETA1-4 : bond 0.00676 / 0.43 ( 8) link_BETA1-4 : angle 2.25619 / 1.69 ( 24) link_NAG-ASN : bond 0.00147 / 0.09 ( 12) link_NAG-ASN : angle 1.22178 / 0.86 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8875 (mm) REVERT: A 99 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 123 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (t70) REVERT: A 288 MET cc_start: 0.8148 (mmm) cc_final: 0.7762 (mmm) REVERT: A 290 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6562 (mtp) REVERT: A 324 SER cc_start: 0.7890 (m) cc_final: 0.7544 (p) REVERT: A 526 ILE cc_start: 0.7844 (mm) cc_final: 0.7591 (mt) REVERT: D 46 MET cc_start: 0.7865 (ttt) cc_final: 0.7422 (ttp) REVERT: D 75 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7260 (mptt) REVERT: D 150 ASP cc_start: 0.8069 (m-30) cc_final: 0.7866 (m-30) REVERT: D 231 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8443 (mt-10) REVERT: D 346 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7298 (mp) REVERT: D 526 ARG cc_start: 0.4010 (OUTLIER) cc_final: 0.2795 (ttt-90) REVERT: D 548 ARG cc_start: 0.6171 (mmm160) cc_final: 0.5303 (ttt180) REVERT: B 121 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.7815 (ttpt) REVERT: B 200 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: B 269 MET cc_start: 0.5696 (tpp) cc_final: 0.5274 (tpp) REVERT: B 290 MET cc_start: 0.8548 (ttm) cc_final: 0.8268 (ttp) REVERT: B 330 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: B 532 ASN cc_start: 0.7118 (m-40) cc_final: 0.6816 (m-40) REVERT: C 28 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7688 (mtp180) REVERT: C 95 GLU cc_start: 0.8513 (mt-10) cc_final: 0.7986 (pm20) REVERT: C 170 CYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6470 (t) REVERT: C 189 TYR cc_start: 0.8757 (m-80) cc_final: 0.8302 (m-10) REVERT: C 269 MET cc_start: 0.8205 (ppp) cc_final: 0.7940 (tmm) REVERT: C 294 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.6964 (mm-40) REVERT: E 47 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7455 (mtpt) REVERT: E 168 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7330 (mm-30) REVERT: E 243 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: E 304 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7526 (mt) REVERT: E 543 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7940 (tt) REVERT: E 545 LEU cc_start: 0.8057 (mp) cc_final: 0.7730 (mm) REVERT: E 548 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6943 (mtt90) outliers start: 46 outliers final: 23 residues processed: 215 average time/residue: 0.6496 time to fit residues: 154.2994 Evaluate side-chains 220 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 182 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN D 303 ASN B 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118810 restraints weight = 16875.732| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.62 r_work: 0.3317 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16457 Z= 0.111 Angle : 0.511 8.602 22445 Z= 0.261 Chirality : 0.042 0.203 2638 Planarity : 0.003 0.040 2716 Dihedral : 5.295 65.645 2523 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.43 % Allowed : 17.55 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.19), residues: 1904 helix: 2.78 (0.18), residues: 742 sheet: 0.52 (0.23), residues: 462 loop : -0.25 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.021 0.001 TYR D 337 PHE 0.019 0.001 PHE D 336 TRP 0.017 0.001 TRP C 539 HIS 0.002 0.000 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16432) covalent geometry : angle 0.50456 / 0.26 (22375) SS BOND : bond 0.00075 / 0.03 ( 5) SS BOND : angle 1.01450 / 0.61 ( 10) hydrogen bonds : bond 0.03873 / 2.53 ( 877) hydrogen bonds : angle 4.36824 / 2.96 ( 2532) link_BETA1-4 : bond 0.00657 / 0.43 ( 8) link_BETA1-4 : angle 2.16287 / 1.61 ( 24) link_NAG-ASN : bond 0.00146 / 0.09 ( 12) link_NAG-ASN : angle 1.12482 / 0.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 123 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7875 (t70) REVERT: A 170 CYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5194 (t) REVERT: A 288 MET cc_start: 0.8115 (mmm) cc_final: 0.7758 (mmm) REVERT: A 290 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6604 (mtp) REVERT: A 526 ILE cc_start: 0.7788 (mm) cc_final: 0.7545 (mt) REVERT: D 46 MET cc_start: 0.7859 (ttt) cc_final: 0.7411 (ttp) REVERT: D 75 LYS cc_start: 0.7789 (mmtt) cc_final: 0.7265 (mptt) REVERT: D 150 ASP cc_start: 0.8047 (m-30) cc_final: 0.7844 (m-30) REVERT: D 231 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8480 (mt-10) REVERT: D 346 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7305 (mp) REVERT: D 526 ARG cc_start: 0.4189 (OUTLIER) cc_final: 0.2954 (ttt-90) REVERT: D 548 ARG cc_start: 0.6157 (mmm160) cc_final: 0.5289 (ttt180) REVERT: B 121 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7818 (ttpt) REVERT: B 161 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8251 (mtm-85) REVERT: B 200 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7225 (mm-30) REVERT: B 269 MET cc_start: 0.5839 (tpp) cc_final: 0.5397 (tpp) REVERT: B 290 MET cc_start: 0.8557 (ttm) cc_final: 0.8266 (ttp) REVERT: B 330 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: B 532 ASN cc_start: 0.7118 (m-40) cc_final: 0.6817 (m-40) REVERT: C 28 ARG cc_start: 0.8011 (mtp180) cc_final: 0.7688 (mtp180) REVERT: C 95 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7947 (pm20) REVERT: C 170 CYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6247 (t) REVERT: C 189 TYR cc_start: 0.8764 (m-80) cc_final: 0.8299 (m-10) REVERT: C 269 MET cc_start: 0.8180 (ppp) cc_final: 0.7975 (tmm) REVERT: C 294 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.6909 (mm-40) REVERT: E 47 LYS cc_start: 0.8027 (mtmt) cc_final: 0.7460 (mtpt) REVERT: E 168 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7373 (mm-30) REVERT: E 243 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8366 (mt-10) REVERT: E 304 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7504 (mt) REVERT: E 543 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7855 (tt) REVERT: E 545 LEU cc_start: 0.8041 (mp) cc_final: 0.7717 (mm) REVERT: E 548 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6977 (mtt90) outliers start: 43 outliers final: 21 residues processed: 219 average time/residue: 0.6080 time to fit residues: 147.8254 Evaluate side-chains 221 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 38 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118031 restraints weight = 16762.847| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.61 r_work: 0.3328 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16457 Z= 0.130 Angle : 0.546 18.347 22445 Z= 0.274 Chirality : 0.043 0.201 2638 Planarity : 0.003 0.039 2716 Dihedral : 5.331 66.003 2523 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.27 % Allowed : 17.72 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.19), residues: 1904 helix: 2.77 (0.18), residues: 742 sheet: 0.54 (0.23), residues: 458 loop : -0.25 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.019 0.001 TYR D 337 PHE 0.017 0.001 PHE D 336 TRP 0.014 0.001 TRP C 539 HIS 0.002 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (16432) covalent geometry : angle 0.53952 / 0.27 (22375) SS BOND : bond 0.00073 / 0.03 ( 5) SS BOND : angle 1.21810 / 0.74 ( 10) hydrogen bonds : bond 0.03974 / 2.60 ( 877) hydrogen bonds : angle 4.37514 / 2.96 ( 2532) link_BETA1-4 : bond 0.00637 / 0.41 ( 8) link_BETA1-4 : angle 2.22873 / 1.66 ( 24) link_NAG-ASN : bond 0.00157 / 0.10 ( 12) link_NAG-ASN : angle 1.16133 / 0.83 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8023 (mt-10) REVERT: A 123 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7896 (t70) REVERT: A 288 MET cc_start: 0.8118 (mmm) cc_final: 0.7757 (mmm) REVERT: A 290 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6606 (mtp) REVERT: A 526 ILE cc_start: 0.7805 (mm) cc_final: 0.7568 (mt) REVERT: D 46 MET cc_start: 0.7880 (ttt) cc_final: 0.7402 (ttp) REVERT: D 75 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7257 (mptt) REVERT: D 150 ASP cc_start: 0.8047 (m-30) cc_final: 0.7842 (m-30) REVERT: D 231 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8468 (mt-10) REVERT: D 346 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7319 (mp) REVERT: D 526 ARG cc_start: 0.4217 (OUTLIER) cc_final: 0.2955 (ttt-90) REVERT: D 548 ARG cc_start: 0.6147 (mmm160) cc_final: 0.5272 (ttt180) REVERT: B 121 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7856 (ttpt) REVERT: B 161 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8232 (mtm-85) REVERT: B 200 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: B 269 MET cc_start: 0.5721 (tpp) cc_final: 0.5298 (tpp) REVERT: B 290 MET cc_start: 0.8558 (ttm) cc_final: 0.8280 (ttp) REVERT: B 330 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: B 532 ASN cc_start: 0.7111 (m-40) cc_final: 0.6805 (m-40) REVERT: C 28 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7684 (mtp180) REVERT: C 95 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7934 (pm20) REVERT: C 170 CYS cc_start: 0.6851 (OUTLIER) cc_final: 0.6408 (t) REVERT: C 189 TYR cc_start: 0.8755 (m-80) cc_final: 0.8272 (m-10) REVERT: C 269 MET cc_start: 0.8172 (ppp) cc_final: 0.7949 (tmm) REVERT: C 294 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.6890 (mm-40) REVERT: E 47 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7441 (mtpt) REVERT: E 168 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7364 (mm-30) REVERT: E 243 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8407 (mt-10) REVERT: E 304 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7515 (mt) REVERT: E 543 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7896 (tt) REVERT: E 545 LEU cc_start: 0.8058 (mp) cc_final: 0.7727 (mm) REVERT: E 548 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6965 (mtt90) outliers start: 40 outliers final: 21 residues processed: 206 average time/residue: 0.6332 time to fit residues: 144.2631 Evaluate side-chains 215 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain D residue 220 GLU Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 526 ARG Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 170 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 548 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 22 optimal weight: 0.6980 chunk 2 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 66.9795 > 50:) chunk 169 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 117 ASN D 157 ASN D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118257 restraints weight = 16764.361| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.61 r_work: 0.3330 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16457 Z= 0.122 Angle : 0.550 20.561 22445 Z= 0.273 Chirality : 0.043 0.198 2638 Planarity : 0.003 0.040 2716 Dihedral : 5.323 66.038 2523 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.38 % Allowed : 17.61 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1904 helix: 2.77 (0.18), residues: 742 sheet: 0.53 (0.23), residues: 458 loop : -0.24 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 514 TYR 0.019 0.001 TYR D 337 PHE 0.020 0.001 PHE B 533 TRP 0.015 0.001 TRP C 539 HIS 0.002 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (16432) covalent geometry : angle 0.54264 / 0.27 (22375) SS BOND : bond 0.00068 / 0.03 ( 5) SS BOND : angle 1.15268 / 0.70 ( 10) hydrogen bonds : bond 0.03940 / 2.59 ( 877) hydrogen bonds : angle 4.35520 / 2.94 ( 2532) link_BETA1-4 : bond 0.00629 / 0.41 ( 8) link_BETA1-4 : angle 2.20343 / 1.64 ( 24) link_NAG-ASN : bond 0.00163 / 0.10 ( 12) link_NAG-ASN : angle 1.37070 / 0.93 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5733.84 seconds wall clock time: 98 minutes 28.72 seconds (5908.72 seconds total)