Starting phenix.real_space_refine on Mon Jun 16 16:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bqh_44799/06_2025/9bqh_44799_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bqh_44799/06_2025/9bqh_44799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bqh_44799/06_2025/9bqh_44799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bqh_44799/06_2025/9bqh_44799.map" model { file = "/net/cci-nas-00/data/ceres_data/9bqh_44799/06_2025/9bqh_44799_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bqh_44799/06_2025/9bqh_44799_trim.cif" } resolution = 2.27 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 6027 2.51 5 N 1521 2.21 5 O 2205 1.98 5 H 8664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18483 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5838 Chain: "B" Number of atoms: 5824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5838 Chain: "C" Number of atoms: 5824 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5799 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5838 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 147 Unusual residues: {'LMT': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'LMT': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Unusual residues: {'LMT': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 19 " occ=0.57 ... (46 atoms not shown) pdb="HH22BARG A 19 " occ=0.43 residue: pdb=" N AARG B 19 " occ=0.57 ... (46 atoms not shown) pdb="HH22BARG B 19 " occ=0.43 residue: pdb=" N AARG C 19 " occ=0.57 ... (46 atoms not shown) pdb="HH22BARG C 19 " occ=0.43 Time building chain proxies: 19.62, per 1000 atoms: 1.06 Number of scatterers: 18483 At special positions: 0 Unit cell: (91.368, 86.184, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 2205 8.00 N 1521 7.00 C 6027 6.00 H 8664 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.04 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 401 " - " ASN A 110 " " NAG A 402 " - " ASN A 153 " " NAG A 403 " - " ASN A 199 " " NAG B 402 " - " ASN B 110 " " NAG B 403 " - " ASN B 153 " " NAG B 404 " - " ASN B 199 " " NAG C 402 " - " ASN C 110 " " NAG C 403 " - " ASN C 153 " " NAG C 404 " - " ASN C 199 " " NAG D 1 " - " ASN A 75 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN B 75 " " NAG H 1 " - " ASN B 184 " " NAG I 1 " - " ASN B 208 " " NAG J 1 " - " ASN C 75 " " NAG K 1 " - " ASN C 184 " " NAG L 1 " - " ASN C 208 " Time building additional restraints: 4.97 Conformation dependent library (CDL) restraints added in 2.3 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 21 sheets defined 29.5% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.832A pdb=" N VAL A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.645A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 4.299A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'B' and resid 4 through 13 Processing helix chain 'B' and resid 25 through 46 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.833A pdb=" N VAL B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.646A pdb=" N THR B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 removed outlier: 4.299A pdb=" N THR B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 25 through 46 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.832A pdb=" N VAL C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 331 through 346 removed outlier: 3.646A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 360 removed outlier: 4.298A pdb=" N THR C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 4.795A pdb=" N ARG B 24 " --> pdb=" O VAL C 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 372 through 375 removed outlier: 4.795A pdb=" N ARG A 24 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 76 Processing sheet with id=AA7, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 372 through 375 removed outlier: 6.525A pdb=" N LYS A 373 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG C 24 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL A 375 " --> pdb=" O ARG C 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 55 through 59 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB3, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB4, first strand: chain 'B' and resid 72 through 76 Processing sheet with id=AB5, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.223A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.223A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 55 through 59 Processing sheet with id=AB8, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB9, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AC1, first strand: chain 'C' and resid 72 through 76 Processing sheet with id=AC2, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.224A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1299 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: 7.38 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8649 1.02 - 1.22: 15 1.22 - 1.42: 3900 1.42 - 1.62: 5643 1.62 - 1.82: 90 Bond restraints: 18297 Sorted by residual: bond pdb=" ND2 ASN C 142 " pdb="HD22 ASN C 142 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN A 142 " pdb="HD22 ASN A 142 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN C 142 " pdb="HD21 ASN C 142 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN B 142 " pdb="HD22 ASN B 142 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 142 " pdb="HD21 ASN A 142 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 ... (remaining 18292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 32399 2.21 - 4.43: 265 4.43 - 6.64: 24 6.64 - 8.85: 18 8.85 - 11.06: 6 Bond angle restraints: 32712 Sorted by residual: angle pdb=" C2 LMT B 405 " pdb=" C3 LMT B 405 " pdb=" C4 LMT B 405 " ideal model delta sigma weight residual 117.09 106.03 11.06 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C2 LMT A 404 " pdb=" C3 LMT A 404 " pdb=" C4 LMT A 404 " ideal model delta sigma weight residual 117.09 106.04 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C2 LMT A 405 " pdb=" C3 LMT A 405 " pdb=" C4 LMT A 405 " ideal model delta sigma weight residual 117.09 106.08 11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ASN B 142 " pdb=" CA ASN B 142 " pdb=" C ASN B 142 " ideal model delta sigma weight residual 113.23 109.07 4.16 1.24e+00 6.50e-01 1.12e+01 angle pdb=" N ASN C 142 " pdb=" CA ASN C 142 " pdb=" C ASN C 142 " ideal model delta sigma weight residual 113.23 109.08 4.15 1.24e+00 6.50e-01 1.12e+01 ... (remaining 32707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 8640 21.31 - 42.63: 516 42.63 - 63.94: 177 63.94 - 85.25: 33 85.25 - 106.57: 12 Dihedral angle restraints: 9378 sinusoidal: 5469 harmonic: 3909 Sorted by residual: dihedral pdb=" O4 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C5 BMA L 3 " pdb=" O5 BMA L 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.86 106.57 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.85 106.56 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C5 BMA I 3 " pdb=" O5 BMA I 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.84 106.55 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 9375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1300 0.057 - 0.114: 217 0.114 - 0.171: 73 0.171 - 0.228: 0 0.228 - 0.285: 9 Chirality restraints: 1599 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1596 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 142 " -0.042 2.00e-02 2.50e+03 4.08e-02 2.50e+01 pdb=" CG ASN C 142 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN C 142 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN C 142 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 142 " 0.057 2.00e-02 2.50e+03 pdb="HD22 ASN C 142 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 142 " 0.042 2.00e-02 2.50e+03 4.07e-02 2.49e+01 pdb=" CG ASN B 142 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B 142 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 142 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 142 " -0.057 2.00e-02 2.50e+03 pdb="HD22 ASN B 142 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 142 " 0.042 2.00e-02 2.50e+03 4.07e-02 2.49e+01 pdb=" CG ASN A 142 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN A 142 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 142 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 142 " -0.057 2.00e-02 2.50e+03 pdb="HD22 ASN A 142 " 0.058 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1005 2.20 - 2.80: 36055 2.80 - 3.40: 48106 3.40 - 4.00: 70815 4.00 - 4.60: 104617 Nonbonded interactions: 260598 Sorted by model distance: nonbonded pdb="HH22 ARG A 301 " pdb=" OE1 GLN C 308 " model vdw 1.601 2.450 nonbonded pdb=" OE1 GLN B 308 " pdb="HH22 ARG C 301 " model vdw 1.601 2.450 nonbonded pdb=" OE1 GLN A 308 " pdb="HH22 ARG B 301 " model vdw 1.602 2.450 nonbonded pdb=" HH TYR A 300 " pdb=" O HOH A 501 " model vdw 1.606 2.450 nonbonded pdb=" O HIS A 286 " pdb="HH22 ARG C 203 " model vdw 1.625 2.450 ... (remaining 260593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 18 or resid 20 through 253 or resid 255 through \ 376 or resid 402 through 403)) selection = (chain 'B' and (resid 3 through 18 or resid 20 through 253 or resid 255 through \ 376 or resid 402 through 403)) selection = (chain 'C' and (resid 3 through 18 or resid 20 through 253 or resid 255 through \ 376 or resid 402 through 403)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' 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=0.43 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: 18.590 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: 0.450 Extract box with map and model: 1.030 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 53.780 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 0.049 9675 Z= 0.281 Angle : 0.842 11.064 13188 Z= 0.381 Chirality : 0.053 0.285 1599 Planarity : 0.004 0.036 1581 Dihedral : 16.674 106.566 4233 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: -0.51 (0.24), residues: 1125 helix: 0.18 (0.30), residues: 321 sheet: 0.12 (0.27), residues: 357 loop : -0.99 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 164 HIS 0.001 0.000 HIS C 241 PHE 0.011 0.001 PHE B 276 TYR 0.009 0.001 TYR B 299 ARG 0.001 0.000 ARG C 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 18) link_NAG-ASN : angle 4.44346 ( 54) link_BETA1-4 : bond 0.00441 ( 12) link_BETA1-4 : angle 2.43063 ( 36) hydrogen bonds : bond 0.17922 ( 406) hydrogen bonds : angle 7.36474 ( 1299) SS BOND : bond 0.00322 ( 12) SS BOND : angle 1.18796 ( 24) covalent geometry : bond 0.00575 ( 9633) covalent geometry : angle 0.78434 (13074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8452 (mtmt) cc_final: 0.7901 (mppt) REVERT: A 148 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7016 (mtm-85) REVERT: A 157 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7767 (mtmt) REVERT: A 326 LYS cc_start: 0.8424 (mttt) cc_final: 0.8152 (mmmt) REVERT: B 69 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7868 (mppt) REVERT: B 109 MET cc_start: 0.7929 (mmm) cc_final: 0.7716 (mmm) REVERT: B 148 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7050 (mtm-85) REVERT: B 197 LYS cc_start: 0.8418 (tttt) cc_final: 0.8181 (tttt) REVERT: B 326 LYS cc_start: 0.8427 (mttt) cc_final: 0.8188 (mmmt) REVERT: C 148 ARG cc_start: 0.7686 (mtm110) cc_final: 0.6990 (mtm-85) REVERT: C 326 LYS cc_start: 0.8425 (mttt) cc_final: 0.8168 (mmmt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 3.1342 time to fit residues: 366.0210 Evaluate side-chains 101 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.0370 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.108339 restraints weight = 30080.146| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.11 r_work: 0.3110 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9675 Z= 0.137 Angle : 0.607 5.139 13188 Z= 0.315 Chirality : 0.047 0.201 1599 Planarity : 0.004 0.034 1581 Dihedral : 11.027 58.309 2226 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.95 % Allowed : 11.78 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.09 (0.25), residues: 1125 helix: 0.80 (0.30), residues: 309 sheet: 0.32 (0.28), residues: 330 loop : -0.50 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 259 HIS 0.004 0.001 HIS C 241 PHE 0.013 0.001 PHE B 276 TYR 0.009 0.002 TYR A 42 ARG 0.003 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 18) link_NAG-ASN : angle 2.04648 ( 54) link_BETA1-4 : bond 0.00285 ( 12) link_BETA1-4 : angle 1.91498 ( 36) hydrogen bonds : bond 0.04677 ( 406) hydrogen bonds : angle 5.63909 ( 1299) SS BOND : bond 0.00461 ( 12) SS BOND : angle 1.36783 ( 24) covalent geometry : bond 0.00294 ( 9633) covalent geometry : angle 0.58432 (13074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8882 (mtmt) cc_final: 0.7830 (mppt) REVERT: A 148 ARG cc_start: 0.7467 (mtm110) cc_final: 0.6434 (mtm-85) REVERT: A 157 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7320 (mtmt) REVERT: A 197 LYS cc_start: 0.8471 (tttt) cc_final: 0.8129 (tttt) REVERT: A 326 LYS cc_start: 0.8607 (mttt) cc_final: 0.8153 (mmmt) REVERT: B 148 ARG cc_start: 0.7463 (mtm110) cc_final: 0.6452 (mtm-85) REVERT: B 197 LYS cc_start: 0.8451 (tttt) cc_final: 0.8168 (tttt) REVERT: B 326 LYS cc_start: 0.8584 (mttt) cc_final: 0.8076 (mmmt) REVERT: C 148 ARG cc_start: 0.7419 (mtm110) cc_final: 0.6350 (mtm-85) REVERT: C 326 LYS cc_start: 0.8599 (mttt) cc_final: 0.8032 (mmmt) outliers start: 9 outliers final: 3 residues processed: 97 average time/residue: 3.2465 time to fit residues: 335.2424 Evaluate side-chains 93 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110146 restraints weight = 39444.240| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.32 r_work: 0.3053 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9675 Z= 0.134 Angle : 0.562 4.273 13188 Z= 0.297 Chirality : 0.045 0.181 1599 Planarity : 0.004 0.035 1581 Dihedral : 9.192 59.146 2226 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.95 % Allowed : 11.25 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.05 (0.25), residues: 1125 helix: 0.95 (0.30), residues: 309 sheet: 0.00 (0.27), residues: 360 loop : -0.45 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 259 HIS 0.003 0.001 HIS C 241 PHE 0.015 0.001 PHE A 276 TYR 0.010 0.002 TYR B 89 ARG 0.002 0.000 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 18) link_NAG-ASN : angle 1.94027 ( 54) link_BETA1-4 : bond 0.00212 ( 12) link_BETA1-4 : angle 1.92536 ( 36) hydrogen bonds : bond 0.04718 ( 406) hydrogen bonds : angle 5.41525 ( 1299) SS BOND : bond 0.00492 ( 12) SS BOND : angle 1.28599 ( 24) covalent geometry : bond 0.00292 ( 9633) covalent geometry : angle 0.53783 (13074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7609 (tp) REVERT: A 69 LYS cc_start: 0.8954 (mtmt) cc_final: 0.7971 (mppt) REVERT: A 140 HIS cc_start: 0.5636 (m-70) cc_final: 0.5319 (m-70) REVERT: A 148 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6448 (mtm-85) REVERT: A 157 LYS cc_start: 0.7602 (mtmm) cc_final: 0.7289 (mtmt) REVERT: A 197 LYS cc_start: 0.8586 (tttt) cc_final: 0.8276 (tttt) REVERT: A 326 LYS cc_start: 0.8671 (mttt) cc_final: 0.8262 (mttt) REVERT: B 148 ARG cc_start: 0.7457 (mtm110) cc_final: 0.6410 (mtm-85) REVERT: B 197 LYS cc_start: 0.8568 (tttt) cc_final: 0.8267 (tttt) REVERT: B 260 ASP cc_start: 0.8120 (m-30) cc_final: 0.7910 (m-30) REVERT: B 326 LYS cc_start: 0.8645 (mttt) cc_final: 0.8165 (mmmt) REVERT: C 38 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7503 (tp) REVERT: C 326 LYS cc_start: 0.8675 (mttt) cc_final: 0.8224 (mttt) outliers start: 9 outliers final: 3 residues processed: 99 average time/residue: 2.9896 time to fit residues: 315.1659 Evaluate side-chains 95 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106573 restraints weight = 29928.451| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.09 r_work: 0.3087 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9675 Z= 0.154 Angle : 0.592 4.296 13188 Z= 0.312 Chirality : 0.046 0.203 1599 Planarity : 0.004 0.035 1581 Dihedral : 9.129 56.771 2226 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.84 % Allowed : 11.88 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.00 (0.25), residues: 1125 helix: 0.87 (0.30), residues: 309 sheet: -0.03 (0.27), residues: 360 loop : -0.44 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 259 HIS 0.003 0.001 HIS C 241 PHE 0.017 0.002 PHE B 276 TYR 0.011 0.002 TYR A 89 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 18) link_NAG-ASN : angle 1.95976 ( 54) link_BETA1-4 : bond 0.00137 ( 12) link_BETA1-4 : angle 2.00335 ( 36) hydrogen bonds : bond 0.04545 ( 406) hydrogen bonds : angle 5.38617 ( 1299) SS BOND : bond 0.00542 ( 12) SS BOND : angle 1.39021 ( 24) covalent geometry : bond 0.00343 ( 9633) covalent geometry : angle 0.56888 (13074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.528 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7486 (tp) REVERT: A 56 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6931 (pt0) REVERT: A 69 LYS cc_start: 0.8913 (mtmt) cc_final: 0.7875 (mppt) REVERT: A 148 ARG cc_start: 0.7434 (mtm110) cc_final: 0.6411 (mtm-85) REVERT: A 157 LYS cc_start: 0.7582 (mtmm) cc_final: 0.7256 (mtmt) REVERT: A 197 LYS cc_start: 0.8493 (tttt) cc_final: 0.8137 (tttt) REVERT: A 326 LYS cc_start: 0.8601 (mttt) cc_final: 0.8157 (mttt) REVERT: B 140 HIS cc_start: 0.5614 (m-70) cc_final: 0.5404 (m-70) REVERT: B 148 ARG cc_start: 0.7422 (mtm110) cc_final: 0.6372 (mtm-85) REVERT: B 197 LYS cc_start: 0.8484 (tttt) cc_final: 0.8178 (tttt) REVERT: B 326 LYS cc_start: 0.8575 (mttt) cc_final: 0.8036 (mmmt) REVERT: C 38 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7346 (tp) REVERT: C 326 LYS cc_start: 0.8591 (mttt) cc_final: 0.8043 (mmmt) outliers start: 8 outliers final: 3 residues processed: 90 average time/residue: 3.1819 time to fit residues: 304.4244 Evaluate side-chains 92 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.150914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.105639 restraints weight = 38159.762| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.33 r_work: 0.3071 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9675 Z= 0.134 Angle : 0.555 4.274 13188 Z= 0.295 Chirality : 0.045 0.188 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.871 58.949 2226 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.95 % Allowed : 12.30 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.03 (0.25), residues: 1125 helix: 0.96 (0.30), residues: 309 sheet: -0.04 (0.27), residues: 360 loop : -0.44 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 PHE 0.015 0.001 PHE B 276 TYR 0.010 0.002 TYR B 299 ARG 0.002 0.000 ARG B 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 18) link_NAG-ASN : angle 1.77821 ( 54) link_BETA1-4 : bond 0.00174 ( 12) link_BETA1-4 : angle 1.91007 ( 36) hydrogen bonds : bond 0.04357 ( 406) hydrogen bonds : angle 5.28746 ( 1299) SS BOND : bond 0.00472 ( 12) SS BOND : angle 1.29824 ( 24) covalent geometry : bond 0.00295 ( 9633) covalent geometry : angle 0.53304 (13074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7499 (tp) REVERT: A 69 LYS cc_start: 0.8926 (mtmt) cc_final: 0.7880 (mppt) REVERT: A 148 ARG cc_start: 0.7404 (mtm110) cc_final: 0.6381 (mtm-85) REVERT: A 157 LYS cc_start: 0.7532 (mtmm) cc_final: 0.7200 (mtmt) REVERT: A 197 LYS cc_start: 0.8501 (tttt) cc_final: 0.8190 (tttt) REVERT: A 326 LYS cc_start: 0.8611 (mttt) cc_final: 0.8155 (mttt) REVERT: B 140 HIS cc_start: 0.5564 (m-70) cc_final: 0.5335 (m-70) REVERT: B 197 LYS cc_start: 0.8488 (tttt) cc_final: 0.8226 (tttt) REVERT: B 285 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: B 326 LYS cc_start: 0.8565 (mttt) cc_final: 0.8083 (mttt) REVERT: C 38 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7364 (tp) REVERT: C 326 LYS cc_start: 0.8599 (mttt) cc_final: 0.8114 (mttt) outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 3.1526 time to fit residues: 308.6440 Evaluate side-chains 92 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN C 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106323 restraints weight = 37614.036| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.63 r_work: 0.3058 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9675 Z= 0.141 Angle : 0.566 4.269 13188 Z= 0.300 Chirality : 0.045 0.196 1599 Planarity : 0.004 0.033 1581 Dihedral : 8.816 58.973 2226 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.95 % Allowed : 12.09 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.04 (0.25), residues: 1125 helix: 1.00 (0.30), residues: 306 sheet: -0.02 (0.27), residues: 360 loop : -0.47 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 PHE 0.016 0.001 PHE B 276 TYR 0.010 0.002 TYR A 299 ARG 0.002 0.000 ARG C 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 18) link_NAG-ASN : angle 1.84047 ( 54) link_BETA1-4 : bond 0.00137 ( 12) link_BETA1-4 : angle 1.92278 ( 36) hydrogen bonds : bond 0.04374 ( 406) hydrogen bonds : angle 5.27487 ( 1299) SS BOND : bond 0.00486 ( 12) SS BOND : angle 1.32560 ( 24) covalent geometry : bond 0.00315 ( 9633) covalent geometry : angle 0.54381 (13074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7619 (tp) REVERT: A 69 LYS cc_start: 0.8960 (mtmt) cc_final: 0.7997 (mppt) REVERT: A 148 ARG cc_start: 0.7440 (mtm110) cc_final: 0.6471 (mtm-85) REVERT: A 157 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7281 (mtmt) REVERT: A 197 LYS cc_start: 0.8564 (tttt) cc_final: 0.8278 (tttt) REVERT: A 326 LYS cc_start: 0.8694 (mttt) cc_final: 0.8267 (mttt) REVERT: B 197 LYS cc_start: 0.8585 (tttt) cc_final: 0.8331 (tttt) REVERT: B 260 ASP cc_start: 0.8150 (m-30) cc_final: 0.7938 (m-30) REVERT: B 326 LYS cc_start: 0.8657 (mttt) cc_final: 0.8255 (mttt) REVERT: C 38 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7497 (tp) REVERT: C 326 LYS cc_start: 0.8693 (mttt) cc_final: 0.8251 (mttt) outliers start: 9 outliers final: 3 residues processed: 90 average time/residue: 3.2157 time to fit residues: 308.2722 Evaluate side-chains 90 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.146631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104074 restraints weight = 33471.611| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.04 r_work: 0.3056 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9675 Z= 0.120 Angle : 0.531 4.267 13188 Z= 0.283 Chirality : 0.044 0.180 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.523 57.187 2226 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.84 % Allowed : 12.30 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.10 (0.25), residues: 1125 helix: 1.12 (0.31), residues: 306 sheet: -0.00 (0.27), residues: 360 loop : -0.47 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 PHE 0.014 0.001 PHE B 276 TYR 0.009 0.001 TYR A 89 ARG 0.002 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 18) link_NAG-ASN : angle 1.64232 ( 54) link_BETA1-4 : bond 0.00200 ( 12) link_BETA1-4 : angle 1.79473 ( 36) hydrogen bonds : bond 0.04116 ( 406) hydrogen bonds : angle 5.18439 ( 1299) SS BOND : bond 0.00429 ( 12) SS BOND : angle 1.25119 ( 24) covalent geometry : bond 0.00263 ( 9633) covalent geometry : angle 0.51106 (13074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7493 (mtm180) cc_final: 0.6570 (mtm-85) REVERT: A 157 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7366 (mtmt) REVERT: A 197 LYS cc_start: 0.8596 (tttt) cc_final: 0.8329 (tttt) REVERT: A 326 LYS cc_start: 0.8654 (mttt) cc_final: 0.8259 (mttt) REVERT: B 197 LYS cc_start: 0.8647 (tttt) cc_final: 0.8365 (tttt) REVERT: B 326 LYS cc_start: 0.8616 (mttt) cc_final: 0.8219 (mttt) REVERT: C 38 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7528 (tp) REVERT: C 326 LYS cc_start: 0.8629 (mttt) cc_final: 0.8212 (mttt) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 3.2372 time to fit residues: 307.1104 Evaluate side-chains 90 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103451 restraints weight = 35403.521| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.12 r_work: 0.3047 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9675 Z= 0.124 Angle : 0.535 4.268 13188 Z= 0.285 Chirality : 0.044 0.185 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.420 56.483 2226 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.53 % Allowed : 12.51 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.10 (0.25), residues: 1125 helix: 1.13 (0.31), residues: 306 sheet: -0.03 (0.27), residues: 360 loop : -0.46 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 259 HIS 0.002 0.001 HIS C 241 PHE 0.015 0.001 PHE B 276 TYR 0.009 0.001 TYR C 89 ARG 0.002 0.000 ARG C 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 18) link_NAG-ASN : angle 1.67565 ( 54) link_BETA1-4 : bond 0.00177 ( 12) link_BETA1-4 : angle 1.80463 ( 36) hydrogen bonds : bond 0.04133 ( 406) hydrogen bonds : angle 5.17180 ( 1299) SS BOND : bond 0.00434 ( 12) SS BOND : angle 1.25868 ( 24) covalent geometry : bond 0.00273 ( 9633) covalent geometry : angle 0.51501 (13074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8947 (mtmt) cc_final: 0.8042 (mppt) REVERT: A 148 ARG cc_start: 0.7482 (mtm180) cc_final: 0.6548 (mtm-85) REVERT: A 157 LYS cc_start: 0.7681 (mtmm) cc_final: 0.7361 (mtmt) REVERT: A 197 LYS cc_start: 0.8605 (tttt) cc_final: 0.8339 (tttt) REVERT: A 326 LYS cc_start: 0.8674 (mttt) cc_final: 0.8186 (mttt) REVERT: B 197 LYS cc_start: 0.8658 (tttt) cc_final: 0.8377 (tttt) REVERT: B 326 LYS cc_start: 0.8630 (mttt) cc_final: 0.8269 (mttt) REVERT: C 38 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7532 (tp) REVERT: C 326 LYS cc_start: 0.8640 (mttt) cc_final: 0.8217 (mttt) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 3.6631 time to fit residues: 349.8504 Evaluate side-chains 90 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.146789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103816 restraints weight = 35579.165| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.10 r_work: 0.3053 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9675 Z= 0.119 Angle : 0.526 4.260 13188 Z= 0.281 Chirality : 0.044 0.179 1599 Planarity : 0.004 0.032 1581 Dihedral : 8.279 58.896 2226 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.53 % Allowed : 12.62 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.11 (0.25), residues: 1125 helix: 1.16 (0.31), residues: 306 sheet: -0.02 (0.27), residues: 360 loop : -0.47 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 259 HIS 0.002 0.000 HIS C 241 PHE 0.014 0.001 PHE B 276 TYR 0.009 0.001 TYR C 89 ARG 0.002 0.000 ARG A 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 18) link_NAG-ASN : angle 1.61876 ( 54) link_BETA1-4 : bond 0.00187 ( 12) link_BETA1-4 : angle 1.76024 ( 36) hydrogen bonds : bond 0.04059 ( 406) hydrogen bonds : angle 5.14542 ( 1299) SS BOND : bond 0.00420 ( 12) SS BOND : angle 1.23993 ( 24) covalent geometry : bond 0.00261 ( 9633) covalent geometry : angle 0.50712 (13074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7496 (mtm180) cc_final: 0.6564 (mtm-85) REVERT: A 157 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7386 (mtmt) REVERT: A 197 LYS cc_start: 0.8591 (tttt) cc_final: 0.8328 (tttt) REVERT: A 326 LYS cc_start: 0.8669 (mttt) cc_final: 0.8182 (mttt) REVERT: B 197 LYS cc_start: 0.8646 (tttt) cc_final: 0.8367 (tttt) REVERT: B 326 LYS cc_start: 0.8616 (mttt) cc_final: 0.8254 (mttt) REVERT: C 38 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7546 (tp) REVERT: C 326 LYS cc_start: 0.8628 (mttt) cc_final: 0.8208 (mttt) outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 3.0114 time to fit residues: 272.5191 Evaluate side-chains 90 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104268 restraints weight = 34005.909| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.08 r_work: 0.3058 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9675 Z= 0.114 Angle : 0.518 4.251 13188 Z= 0.277 Chirality : 0.044 0.177 1599 Planarity : 0.003 0.031 1581 Dihedral : 8.122 59.006 2226 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.42 % Allowed : 12.83 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.15 (0.25), residues: 1125 helix: 1.20 (0.31), residues: 306 sheet: -0.01 (0.27), residues: 360 loop : -0.44 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 259 HIS 0.002 0.000 HIS C 241 PHE 0.013 0.001 PHE B 276 TYR 0.009 0.001 TYR C 89 ARG 0.002 0.000 ARG A 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 18) link_NAG-ASN : angle 1.57652 ( 54) link_BETA1-4 : bond 0.00220 ( 12) link_BETA1-4 : angle 1.72030 ( 36) hydrogen bonds : bond 0.03983 ( 406) hydrogen bonds : angle 5.10929 ( 1299) SS BOND : bond 0.00406 ( 12) SS BOND : angle 1.21634 ( 24) covalent geometry : bond 0.00250 ( 9633) covalent geometry : angle 0.49972 (13074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7500 (mtm180) cc_final: 0.6564 (mtm-85) REVERT: A 157 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7373 (mtmt) REVERT: A 197 LYS cc_start: 0.8592 (tttt) cc_final: 0.8330 (tttt) REVERT: A 326 LYS cc_start: 0.8659 (mttt) cc_final: 0.8172 (mttt) REVERT: B 197 LYS cc_start: 0.8648 (tttt) cc_final: 0.8371 (tttt) REVERT: B 326 LYS cc_start: 0.8615 (mttt) cc_final: 0.8253 (mttt) REVERT: C 38 LEU cc_start: 0.7791 (tp) cc_final: 0.7537 (tp) REVERT: C 326 LYS cc_start: 0.8627 (mttt) cc_final: 0.8209 (mttt) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 3.2289 time to fit residues: 291.3236 Evaluate side-chains 87 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain C residue 361 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.146903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103955 restraints weight = 34500.145| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.09 r_work: 0.3053 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9675 Z= 0.119 Angle : 0.526 4.262 13188 Z= 0.280 Chirality : 0.044 0.179 1599 Planarity : 0.004 0.031 1581 Dihedral : 8.048 58.099 2226 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.63 % Allowed : 12.62 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.13 (0.25), residues: 1125 helix: 1.19 (0.31), residues: 306 sheet: -0.01 (0.27), residues: 360 loop : -0.47 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 259 HIS 0.002 0.000 HIS C 241 PHE 0.014 0.001 PHE B 276 TYR 0.009 0.001 TYR A 299 ARG 0.002 0.000 ARG A 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 18) link_NAG-ASN : angle 1.61304 ( 54) link_BETA1-4 : bond 0.00189 ( 12) link_BETA1-4 : angle 1.74146 ( 36) hydrogen bonds : bond 0.04039 ( 406) hydrogen bonds : angle 5.12294 ( 1299) SS BOND : bond 0.00419 ( 12) SS BOND : angle 1.24575 ( 24) covalent geometry : bond 0.00261 ( 9633) covalent geometry : angle 0.50665 (13074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18868.70 seconds wall clock time: 326 minutes 16.75 seconds (19576.75 seconds total)