Starting phenix.real_space_refine on Sat Feb 17 14:33:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6k_27921/02_2024/8e6k_27921.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6k_27921/02_2024/8e6k_27921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6k_27921/02_2024/8e6k_27921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6k_27921/02_2024/8e6k_27921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6k_27921/02_2024/8e6k_27921.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e6k_27921/02_2024/8e6k_27921.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 120 5.16 5 C 11908 2.51 5 N 3200 2.21 5 O 3704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18932 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "B" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "I" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "C" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "D" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2963 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 928 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" 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: "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: 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: "D" 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 Time building chain proxies: 9.85, per 1000 atoms: 0.52 Number of scatterers: 18932 At special positions: 0 Unit cell: (166.025, 166.025, 82.65, 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 120 16.00 O 3704 8.00 N 3200 7.00 C 11908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.02 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 336 " distance=2.05 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.04 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.02 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 336 " distance=2.05 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.02 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 336 " distance=2.05 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.04 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.02 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 336 " distance=2.05 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 146 " " NAG B 501 " - " ASN B 146 " " NAG C 501 " - " ASN C 146 " " NAG D 501 " - " ASN D 146 " Time building additional restraints: 7.33 Conformation dependent library (CDL) restraints added in 3.7 seconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 44 sheets defined 5.2% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER A 145 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 412A through 414 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER B 145 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 146 " --> pdb=" O LYS B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 412A through 414 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER C 145 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 146 " --> pdb=" O LYS C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'C' and resid 412A through 414 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.512A pdb=" N SER D 145 " --> pdb=" O ASP D 142 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D 146 " --> pdb=" O LYS D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 412A through 414 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.550A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS A 102 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA A 203 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 205 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR A 252 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU A 267 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 254 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS A 256 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER A 372 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 400 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET A 376 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP A 396 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP A 378 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG A 394 " --> pdb=" O TRP A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP H 35A" --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS B 102 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA B 203 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU B 205 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR B 252 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU B 267 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 254 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS B 256 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER B 372 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE B 400 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET B 376 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP B 396 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP B 378 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG B 394 " --> pdb=" O TRP B 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'E' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER E 50 " --> pdb=" O TRP E 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP E 35A" --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR E 52 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR E 34 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS C 102 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA C 203 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR C 214 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 205 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR C 252 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU C 267 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 254 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS C 256 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER C 372 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE C 400 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET C 376 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP C 396 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP C 378 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG C 394 " --> pdb=" O TRP C 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'F' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER F 50 " --> pdb=" O TRP F 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP F 35A" --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR F 52 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR F 34 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.558A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS D 102 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N SER D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.765A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.564A pdb=" N ALA D 203 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR D 214 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 205 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 231 through 233 removed outlier: 6.848A pdb=" N TYR D 252 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU D 267 " --> pdb=" O TYR D 252 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 254 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS D 256 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.562A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 353 through 356 removed outlier: 5.681A pdb=" N SER D 372 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE D 400 " --> pdb=" O SER D 372 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET D 376 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP D 396 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N TRP D 378 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG D 394 " --> pdb=" O TRP D 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.714A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AE7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.525A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER G 50 " --> pdb=" O TRP G 35A" (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP G 35A" --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR G 52 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N TYR G 34 " --> pdb=" O TYR G 52 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.62 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6036 1.34 - 1.47: 5156 1.47 - 1.59: 8084 1.59 - 1.71: 0 1.71 - 1.84: 156 Bond restraints: 19432 Sorted by residual: bond pdb=" N VAL L 15 " pdb=" CA VAL L 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N VAL I 15 " pdb=" CA VAL I 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N VAL J 15 " pdb=" CA VAL J 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.27e-02 6.20e+03 8.70e+00 bond pdb=" N ARG J 18 " pdb=" CA ARG J 18 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.34e+00 ... (remaining 19427 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 936 107.12 - 113.86: 9988 113.86 - 120.60: 7660 120.60 - 127.34: 7520 127.34 - 134.09: 336 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N ASN C 299 " pdb=" CA ASN C 299 " pdb=" C ASN C 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" N ASN B 299 " pdb=" CA ASN B 299 " pdb=" C ASN B 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" N ASN A 299 " pdb=" CA ASN A 299 " pdb=" C ASN A 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" N ASN D 299 " pdb=" CA ASN D 299 " pdb=" C ASN D 299 " ideal model delta sigma weight residual 109.65 104.71 4.94 1.56e+00 4.11e-01 1.00e+01 angle pdb=" C CYS A 318 " pdb=" N SER A 319 " pdb=" CA SER A 319 " ideal model delta sigma weight residual 121.31 125.98 -4.67 1.49e+00 4.50e-01 9.81e+00 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 10448 15.95 - 31.89: 716 31.89 - 47.84: 240 47.84 - 63.79: 68 63.79 - 79.73: 20 Dihedral angle restraints: 11492 sinusoidal: 4520 harmonic: 6972 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.36 36.64 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.36 36.64 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.36 36.64 1 1.00e+01 1.00e-02 1.90e+01 ... (remaining 11489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1696 0.048 - 0.096: 736 0.096 - 0.144: 360 0.144 - 0.192: 52 0.192 - 0.240: 12 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2853 not shown) Planarity restraints: 3404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.135 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG D 501 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.179 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " -0.135 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG A 501 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.135 2.00e-02 2.50e+03 1.11e-01 1.55e+02 pdb=" C7 NAG B 501 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.101 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.179 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.018 2.00e-02 2.50e+03 ... (remaining 3401 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1008 2.71 - 3.26: 17576 3.26 - 3.81: 31552 3.81 - 4.35: 41908 4.35 - 4.90: 72448 Nonbonded interactions: 164492 Sorted by model distance: nonbonded pdb=" OD2 ASP D 293 " pdb=" OH TYR D 316 " model vdw 2.167 2.440 nonbonded pdb=" OD2 ASP B 293 " pdb=" OH TYR B 316 " model vdw 2.167 2.440 nonbonded pdb=" OD2 ASP A 293 " pdb=" OH TYR A 316 " model vdw 2.167 2.440 nonbonded pdb=" OD2 ASP C 293 " pdb=" OH TYR C 316 " model vdw 2.167 2.440 nonbonded pdb=" O GLN L 6 " pdb=" NE2 GLN L 100 " model vdw 2.259 2.520 ... (remaining 164487 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = 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: 4.710 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: 0.000 Extract box with map and model: 20.150 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.590 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.006 0.051 19432 Z= 0.418 Angle : 1.112 6.424 26440 Z= 0.622 Chirality : 0.064 0.240 2856 Planarity : 0.007 0.111 3400 Dihedral : 13.346 79.733 6948 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.19 % Allowed : 13.26 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2432 helix: 0.30 (0.83), residues: 24 sheet: 0.80 (0.16), residues: 944 loop : 0.08 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 456 HIS 0.006 0.002 HIS B 412A PHE 0.046 0.005 PHE A 410 TYR 0.047 0.004 TYR K 92 ARG 0.006 0.001 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 344 time to evaluate : 2.300 Fit side-chains REVERT: A 150 LYS cc_start: 0.7327 (ttpt) cc_final: 0.7033 (tppt) REVERT: B 150 LYS cc_start: 0.7327 (ttpt) cc_final: 0.7035 (tppt) REVERT: C 150 LYS cc_start: 0.7324 (ttpt) cc_final: 0.7033 (tppt) REVERT: D 150 LYS cc_start: 0.7328 (ttpt) cc_final: 0.7035 (tppt) outliers start: 4 outliers final: 0 residues processed: 348 average time/residue: 0.3008 time to fit residues: 161.8887 Evaluate side-chains 240 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.5980 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 97 optimal weight: 0.0060 chunk 188 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS H 59 ASN B 136 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN C 136 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS F 59 ASN D 136 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS G 59 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19432 Z= 0.195 Angle : 0.640 6.272 26440 Z= 0.347 Chirality : 0.048 0.144 2856 Planarity : 0.004 0.031 3400 Dihedral : 5.213 21.854 2728 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.03 % Allowed : 12.88 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2432 helix: -0.53 (0.69), residues: 28 sheet: 1.18 (0.16), residues: 916 loop : 0.31 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 456 HIS 0.006 0.002 HIS A 126 PHE 0.020 0.002 PHE B 410 TYR 0.018 0.002 TYR L 92 ARG 0.002 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 248 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.7075 (ttpt) cc_final: 0.6801 (tppt) REVERT: B 150 LYS cc_start: 0.7077 (ttpt) cc_final: 0.6802 (tppt) REVERT: C 150 LYS cc_start: 0.7078 (ttpt) cc_final: 0.6804 (tppt) REVERT: D 150 LYS cc_start: 0.7072 (ttpt) cc_final: 0.6800 (tppt) outliers start: 64 outliers final: 40 residues processed: 296 average time/residue: 0.2677 time to fit residues: 128.4479 Evaluate side-chains 264 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 19432 Z= 0.382 Angle : 0.680 6.223 26440 Z= 0.366 Chirality : 0.051 0.156 2856 Planarity : 0.005 0.031 3400 Dihedral : 5.418 29.370 2728 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.36 % Allowed : 13.68 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2432 helix: -1.11 (0.73), residues: 28 sheet: 1.02 (0.17), residues: 856 loop : 0.01 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 456 HIS 0.007 0.003 HIS A 296 PHE 0.023 0.003 PHE B 410 TYR 0.020 0.002 TYR L 92 ARG 0.002 0.000 ARG D 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 220 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7579 (p90) REVERT: H 7 SER cc_start: 0.8050 (t) cc_final: 0.7748 (m) REVERT: B 155 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7584 (p90) REVERT: E 7 SER cc_start: 0.8051 (t) cc_final: 0.7750 (m) REVERT: C 155 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7586 (p90) REVERT: F 7 SER cc_start: 0.8050 (t) cc_final: 0.7747 (m) REVERT: D 155 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7578 (p90) REVERT: G 7 SER cc_start: 0.8052 (t) cc_final: 0.7748 (m) outliers start: 92 outliers final: 72 residues processed: 292 average time/residue: 0.2770 time to fit residues: 129.4050 Evaluate side-chains 272 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 196 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.1980 chunk 164 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19432 Z= 0.188 Angle : 0.572 6.063 26440 Z= 0.308 Chirality : 0.047 0.144 2856 Planarity : 0.004 0.029 3400 Dihedral : 5.112 31.197 2728 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.46 % Allowed : 15.34 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2432 helix: -0.86 (0.73), residues: 28 sheet: 1.02 (0.17), residues: 868 loop : 0.01 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 178 HIS 0.003 0.001 HIS A 296 PHE 0.015 0.002 PHE D 410 TYR 0.011 0.001 TYR L 92 ARG 0.003 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 208 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8336 (tpt) cc_final: 0.8092 (tpt) REVERT: A 416 ASP cc_start: 0.7372 (t0) cc_final: 0.7076 (t0) REVERT: B 376 MET cc_start: 0.8341 (tpt) cc_final: 0.8096 (tpt) REVERT: B 416 ASP cc_start: 0.7370 (t0) cc_final: 0.7076 (t0) REVERT: C 376 MET cc_start: 0.8342 (tpt) cc_final: 0.8091 (tpt) REVERT: C 416 ASP cc_start: 0.7368 (t0) cc_final: 0.7074 (t0) REVERT: D 376 MET cc_start: 0.8336 (tpt) cc_final: 0.8090 (tpt) REVERT: D 416 ASP cc_start: 0.7375 (t0) cc_final: 0.7077 (t0) outliers start: 52 outliers final: 40 residues processed: 252 average time/residue: 0.2827 time to fit residues: 116.1872 Evaluate side-chains 232 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 19432 Z= 0.381 Angle : 0.648 5.475 26440 Z= 0.347 Chirality : 0.050 0.156 2856 Planarity : 0.004 0.033 3400 Dihedral : 5.352 28.209 2728 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.39 % Rotamer: Outliers : 3.98 % Allowed : 14.77 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2432 helix: -0.59 (0.86), residues: 28 sheet: 0.81 (0.18), residues: 876 loop : -0.18 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 97 HIS 0.007 0.003 HIS D 296 PHE 0.019 0.003 PHE D 410 TYR 0.015 0.002 TYR K 92 ARG 0.003 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 224 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7521 (p90) REVERT: A 416 ASP cc_start: 0.7502 (t0) cc_final: 0.7216 (t0) REVERT: H 7 SER cc_start: 0.8099 (t) cc_final: 0.7834 (m) REVERT: B 155 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7525 (p90) REVERT: B 416 ASP cc_start: 0.7499 (t0) cc_final: 0.7214 (t0) REVERT: E 7 SER cc_start: 0.8102 (t) cc_final: 0.7836 (m) REVERT: C 155 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7525 (p90) REVERT: C 416 ASP cc_start: 0.7500 (t0) cc_final: 0.7212 (t0) REVERT: F 7 SER cc_start: 0.8101 (t) cc_final: 0.7833 (m) REVERT: D 155 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7520 (p90) REVERT: D 416 ASP cc_start: 0.7505 (t0) cc_final: 0.7216 (t0) REVERT: G 7 SER cc_start: 0.8099 (t) cc_final: 0.7833 (m) outliers start: 84 outliers final: 68 residues processed: 288 average time/residue: 0.2626 time to fit residues: 123.6346 Evaluate side-chains 264 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 192 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19432 Z= 0.293 Angle : 0.598 5.580 26440 Z= 0.320 Chirality : 0.048 0.150 2856 Planarity : 0.004 0.032 3400 Dihedral : 5.285 33.548 2728 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.29 % Favored : 96.38 % Rotamer: Outliers : 4.17 % Allowed : 15.53 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2432 helix: -0.66 (0.86), residues: 28 sheet: 0.77 (0.18), residues: 876 loop : -0.17 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 178 HIS 0.006 0.002 HIS B 296 PHE 0.016 0.002 PHE D 410 TYR 0.013 0.002 TYR I 96 ARG 0.001 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 216 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7479 (p90) REVERT: A 416 ASP cc_start: 0.7453 (t0) cc_final: 0.7243 (t0) REVERT: A 439 THR cc_start: 0.8893 (t) cc_final: 0.8588 (m) REVERT: H 7 SER cc_start: 0.8051 (t) cc_final: 0.7804 (m) REVERT: B 155 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7482 (p90) REVERT: B 416 ASP cc_start: 0.7451 (t0) cc_final: 0.7242 (t0) REVERT: B 439 THR cc_start: 0.8894 (t) cc_final: 0.8588 (m) REVERT: E 7 SER cc_start: 0.8052 (t) cc_final: 0.7804 (m) REVERT: C 155 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7486 (p90) REVERT: C 416 ASP cc_start: 0.7452 (t0) cc_final: 0.7241 (t0) REVERT: C 439 THR cc_start: 0.8892 (t) cc_final: 0.8588 (m) REVERT: F 7 SER cc_start: 0.8051 (t) cc_final: 0.7802 (m) REVERT: D 155 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7475 (p90) REVERT: D 416 ASP cc_start: 0.7458 (t0) cc_final: 0.7245 (t0) REVERT: D 439 THR cc_start: 0.8892 (t) cc_final: 0.8588 (m) REVERT: G 7 SER cc_start: 0.8051 (t) cc_final: 0.7803 (m) outliers start: 88 outliers final: 72 residues processed: 284 average time/residue: 0.2803 time to fit residues: 127.8777 Evaluate side-chains 280 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19432 Z= 0.205 Angle : 0.559 6.065 26440 Z= 0.297 Chirality : 0.047 0.147 2856 Planarity : 0.004 0.032 3400 Dihedral : 5.054 30.608 2728 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.29 % Favored : 96.38 % Rotamer: Outliers : 4.17 % Allowed : 15.53 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2432 helix: -0.70 (0.79), residues: 28 sheet: 0.78 (0.17), residues: 880 loop : -0.09 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 178 HIS 0.004 0.001 HIS B 296 PHE 0.013 0.002 PHE A 422 TYR 0.011 0.001 TYR L 96 ARG 0.001 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 228 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7403 (p90) REVERT: A 416 ASP cc_start: 0.7458 (t0) cc_final: 0.7241 (t0) REVERT: H 7 SER cc_start: 0.8065 (t) cc_final: 0.7822 (m) REVERT: B 155 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7409 (p90) REVERT: B 416 ASP cc_start: 0.7456 (t0) cc_final: 0.7239 (t0) REVERT: E 7 SER cc_start: 0.8066 (t) cc_final: 0.7822 (m) REVERT: C 155 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.7408 (p90) REVERT: C 416 ASP cc_start: 0.7456 (t0) cc_final: 0.7238 (t0) REVERT: F 7 SER cc_start: 0.8063 (t) cc_final: 0.7818 (m) REVERT: D 155 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7401 (p90) REVERT: D 416 ASP cc_start: 0.7458 (t0) cc_final: 0.7240 (t0) REVERT: G 7 SER cc_start: 0.8063 (t) cc_final: 0.7819 (m) outliers start: 88 outliers final: 72 residues processed: 296 average time/residue: 0.2771 time to fit residues: 131.5323 Evaluate side-chains 276 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 200 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19432 Z= 0.238 Angle : 0.567 5.576 26440 Z= 0.301 Chirality : 0.047 0.150 2856 Planarity : 0.004 0.032 3400 Dihedral : 5.026 29.284 2728 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.12 % Favored : 96.55 % Rotamer: Outliers : 3.98 % Allowed : 16.67 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2432 helix: -0.66 (0.79), residues: 28 sheet: 0.77 (0.17), residues: 880 loop : -0.11 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 178 HIS 0.004 0.001 HIS A 296 PHE 0.014 0.002 PHE C 410 TYR 0.015 0.002 TYR B 275 ARG 0.001 0.000 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 216 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7372 (p90) REVERT: A 416 ASP cc_start: 0.7472 (t0) cc_final: 0.7262 (t0) REVERT: A 439 THR cc_start: 0.8885 (t) cc_final: 0.8607 (m) REVERT: H 7 SER cc_start: 0.8060 (t) cc_final: 0.7811 (m) REVERT: B 155 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7378 (p90) REVERT: B 416 ASP cc_start: 0.7472 (t0) cc_final: 0.7262 (t0) REVERT: B 439 THR cc_start: 0.8885 (t) cc_final: 0.8607 (m) REVERT: E 7 SER cc_start: 0.8063 (t) cc_final: 0.7814 (m) REVERT: C 155 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7377 (p90) REVERT: C 416 ASP cc_start: 0.7471 (t0) cc_final: 0.7259 (t0) REVERT: C 439 THR cc_start: 0.8885 (t) cc_final: 0.8607 (m) REVERT: F 7 SER cc_start: 0.8060 (t) cc_final: 0.7808 (m) REVERT: D 155 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7372 (p90) REVERT: D 416 ASP cc_start: 0.7475 (t0) cc_final: 0.7262 (t0) REVERT: D 439 THR cc_start: 0.8885 (t) cc_final: 0.8607 (m) REVERT: G 7 SER cc_start: 0.8058 (t) cc_final: 0.7809 (m) outliers start: 84 outliers final: 72 residues processed: 280 average time/residue: 0.2812 time to fit residues: 125.6387 Evaluate side-chains 292 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 216 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 SER Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19432 Z= 0.183 Angle : 0.542 6.209 26440 Z= 0.288 Chirality : 0.046 0.139 2856 Planarity : 0.004 0.031 3400 Dihedral : 4.932 35.840 2728 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.80 % Favored : 96.88 % Rotamer: Outliers : 2.98 % Allowed : 17.28 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2432 helix: -0.63 (0.77), residues: 28 sheet: 0.84 (0.17), residues: 876 loop : -0.12 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 178 HIS 0.003 0.001 HIS D 296 PHE 0.014 0.002 PHE C 422 TYR 0.015 0.001 TYR B 275 ARG 0.001 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 220 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7356 (p90) REVERT: H 7 SER cc_start: 0.8153 (t) cc_final: 0.7839 (m) REVERT: B 155 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7361 (p90) REVERT: E 7 SER cc_start: 0.8152 (t) cc_final: 0.7838 (m) REVERT: C 155 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7359 (p90) REVERT: F 7 SER cc_start: 0.8150 (t) cc_final: 0.7835 (m) REVERT: D 155 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7352 (p90) REVERT: G 7 SER cc_start: 0.8150 (t) cc_final: 0.7836 (m) outliers start: 63 outliers final: 52 residues processed: 263 average time/residue: 0.2916 time to fit residues: 122.1512 Evaluate side-chains 264 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 208 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 139 optimal weight: 0.1980 chunk 108 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 220 optimal weight: 0.2980 chunk 190 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19432 Z= 0.186 Angle : 0.550 6.076 26440 Z= 0.294 Chirality : 0.047 0.169 2856 Planarity : 0.004 0.031 3400 Dihedral : 4.888 35.107 2728 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.12 % Favored : 96.55 % Rotamer: Outliers : 3.27 % Allowed : 17.00 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2432 helix: -0.53 (0.81), residues: 28 sheet: 0.81 (0.17), residues: 880 loop : -0.14 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 178 HIS 0.003 0.001 HIS D 296 PHE 0.012 0.002 PHE B 422 TYR 0.015 0.001 TYR B 275 ARG 0.001 0.000 ARG D 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 229 time to evaluate : 2.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7339 (p90) REVERT: A 355 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8262 (ttt90) REVERT: H 7 SER cc_start: 0.8178 (t) cc_final: 0.7849 (m) REVERT: B 155 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7344 (p90) REVERT: B 355 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8263 (ttt90) REVERT: E 7 SER cc_start: 0.8178 (t) cc_final: 0.7848 (m) REVERT: C 155 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7341 (p90) REVERT: C 355 ARG cc_start: 0.8472 (ttt180) cc_final: 0.8259 (ttt90) REVERT: F 7 SER cc_start: 0.8177 (t) cc_final: 0.7845 (m) REVERT: D 155 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7338 (p90) REVERT: D 355 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8257 (ttt90) REVERT: G 7 SER cc_start: 0.8176 (t) cc_final: 0.7847 (m) outliers start: 69 outliers final: 64 residues processed: 274 average time/residue: 0.2805 time to fit residues: 122.2745 Evaluate side-chains 284 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 216 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 155 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.149368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131148 restraints weight = 22266.590| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.47 r_work: 0.3502 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19432 Z= 0.241 Angle : 0.576 6.357 26440 Z= 0.305 Chirality : 0.048 0.173 2856 Planarity : 0.004 0.031 3400 Dihedral : 4.955 35.352 2728 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.96 % Favored : 96.71 % Rotamer: Outliers : 3.22 % Allowed : 17.23 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2432 helix: -0.60 (0.81), residues: 28 sheet: 0.64 (0.17), residues: 888 loop : -0.13 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 97 HIS 0.004 0.001 HIS A 296 PHE 0.014 0.002 PHE D 410 TYR 0.017 0.002 TYR D 275 ARG 0.001 0.000 ARG B 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4551.00 seconds wall clock time: 83 minutes 42.92 seconds (5022.92 seconds total)