Starting phenix.real_space_refine on Sun Jun 8 07:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8blb_16105/06_2025/8blb_16105.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blb_16105/06_2025/8blb_16105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8blb_16105/06_2025/8blb_16105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blb_16105/06_2025/8blb_16105.map" model { file = "/net/cci-nas-00/data/ceres_data/8blb_16105/06_2025/8blb_16105.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blb_16105/06_2025/8blb_16105.cif" } resolution = 3.3 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= -0.001 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 6115 2.51 5 N 1515 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 9400 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "F" 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.28, per 1000 atoms: 0.67 Number of scatterers: 9400 At special positions: 0 Unit cell: (96.9, 94.62, 79.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1740 8.00 N 1515 7.00 C 6115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 104 " " NAG B 501 " - " ASN B 104 " " NAG C 501 " - " ASN C 104 " " NAG D 501 " - " ASN D 104 " " NAG E 501 " - " ASN E 104 " " NAG F 1 " - " ASN A 186 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 186 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 186 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 186 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 186 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 952.1 milliseconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 14.7% alpha, 52.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 32 through 43 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 163 through 166 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 163 through 166 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 163 through 166 Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'E' and resid 32 through 43 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 192 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 154 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR A 136 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A 148 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 72 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 83 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 70 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TRP A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR A 68 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG A 87 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 66 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR A 89 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP A 64 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR A 91 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER A 62 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU A 211 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 154 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR B 136 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR B 148 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 72 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 83 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE B 70 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N TRP B 85 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 68 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG B 87 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE B 66 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR B 89 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP B 64 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR B 91 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N SER B 62 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.871A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 211 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 154 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR C 136 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR C 148 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 72 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR C 83 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE C 70 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP C 85 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR C 68 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ARG C 87 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE C 66 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR C 89 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP C 64 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR C 91 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER C 62 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU C 211 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 7.021A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 154 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 7.021A pdb=" N TYR D 136 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR D 148 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 72 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR D 83 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE D 70 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TRP D 85 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR D 68 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG D 87 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE D 66 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR D 89 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ASP D 64 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR D 91 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER D 62 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 211 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL E 154 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 7.020A pdb=" N TYR E 136 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR E 148 " --> pdb=" O TYR E 136 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 72 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR E 83 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE E 70 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TRP E 85 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR E 68 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG E 87 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE E 66 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR E 89 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP E 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N THR E 91 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N SER E 62 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 211 " --> pdb=" O ARG E 239 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2855 1.34 - 1.46: 2599 1.46 - 1.58: 4171 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9675 Sorted by residual: bond pdb=" C12 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 1.404 1.453 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C12 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C12 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.70e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12914 1.95 - 3.90: 251 3.90 - 5.86: 20 5.86 - 7.81: 10 7.81 - 9.76: 10 Bond angle restraints: 13205 Sorted by residual: angle pdb=" C15 VTX E 502 " pdb=" C14 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 109.33 119.09 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C15 VTX D 502 " pdb=" C14 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 109.33 119.06 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX A 502 " pdb=" C14 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 109.33 119.05 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX B 502 " pdb=" C14 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX C 502 " pdb=" C14 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 13200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.13: 5689 25.13 - 50.25: 316 50.25 - 75.38: 35 75.38 - 100.51: 10 100.51 - 125.63: 5 Dihedral angle restraints: 6055 sinusoidal: 2875 harmonic: 3180 Sorted by residual: dihedral pdb=" C15 VTX A 502 " pdb=" C17 VTX A 502 " pdb=" N16 VTX A 502 " pdb=" C18 VTX A 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.31 -125.63 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX C 502 " pdb=" C17 VTX C 502 " pdb=" N16 VTX C 502 " pdb=" C18 VTX C 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.30 -125.62 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX D 502 " pdb=" C17 VTX D 502 " pdb=" N16 VTX D 502 " pdb=" C18 VTX D 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.29 -125.61 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 892 0.029 - 0.057: 348 0.057 - 0.086: 57 0.086 - 0.115: 135 0.115 - 0.143: 58 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 186 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 170 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 186 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1487 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 98 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 99 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 98 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.52e+00 pdb=" N PRO E 99 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 99 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 98 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO D 99 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.038 5.00e-02 4.00e+02 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 362 2.72 - 3.26: 8911 3.26 - 3.81: 14685 3.81 - 4.35: 18995 4.35 - 4.90: 33164 Nonbonded interactions: 76117 Sorted by model distance: nonbonded pdb=" OH TYR D 136 " pdb=" O VAL E 117 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR C 136 " pdb=" O VAL D 117 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG D 219 " pdb=" OE2 GLU D 231 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG A 219 " pdb=" OE2 GLU A 231 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG C 219 " pdb=" OE2 GLU C 231 " model vdw 2.298 3.120 ... (remaining 76112 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.220 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.004 0.049 9705 Z= 0.208 Angle : 0.663 9.759 13290 Z= 0.291 Chirality : 0.048 0.143 1490 Planarity : 0.005 0.069 1620 Dihedral : 15.177 125.633 3980 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.27), residues: 1045 helix: -0.07 (0.57), residues: 95 sheet: -0.49 (0.25), residues: 395 loop : -0.63 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 97 HIS 0.001 0.000 HIS A 180 PHE 0.003 0.001 PHE B 125 TYR 0.007 0.001 TYR E 89 ARG 0.003 0.000 ARG C 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 15) link_NAG-ASN : angle 0.83541 ( 45) link_BETA1-4 : bond 0.00280 ( 10) link_BETA1-4 : angle 1.12812 ( 30) hydrogen bonds : bond 0.22231 ( 290) hydrogen bonds : angle 9.23933 ( 1020) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.12941 ( 10) covalent geometry : bond 0.00429 ( 9675) covalent geometry : angle 0.66116 (13205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.350 Fit side-chains REVERT: A 239 ARG cc_start: 0.6314 (ptm160) cc_final: 0.4596 (ptt180) REVERT: B 140 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7417 (mtp180) REVERT: B 239 ARG cc_start: 0.6186 (ptm160) cc_final: 0.4666 (ptt180) REVERT: C 103 ASP cc_start: 0.7337 (t70) cc_final: 0.7041 (t0) REVERT: D 103 ASP cc_start: 0.7270 (t70) cc_final: 0.7054 (t0) REVERT: D 212 LEU cc_start: 0.8629 (mt) cc_final: 0.8405 (mt) REVERT: D 239 ARG cc_start: 0.5887 (ptm160) cc_final: 0.5417 (ptm-80) REVERT: E 239 ARG cc_start: 0.6219 (ptm160) cc_final: 0.4521 (ptt180) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.4063 time to fit residues: 61.6030 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN C 152 GLN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.133746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.114593 restraints weight = 10675.142| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.16 r_work: 0.3044 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9705 Z= 0.139 Angle : 0.722 13.573 13290 Z= 0.345 Chirality : 0.050 0.193 1490 Planarity : 0.005 0.053 1620 Dihedral : 11.379 118.633 1795 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.56 % Allowed : 12.87 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 1045 helix: 0.31 (0.55), residues: 95 sheet: -0.34 (0.24), residues: 400 loop : -0.72 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 90 HIS 0.002 0.001 HIS E 180 PHE 0.015 0.001 PHE B 221 TYR 0.011 0.001 TYR D 138 ARG 0.007 0.000 ARG D 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 15) link_NAG-ASN : angle 6.00196 ( 45) link_BETA1-4 : bond 0.00211 ( 10) link_BETA1-4 : angle 1.32042 ( 30) hydrogen bonds : bond 0.04548 ( 290) hydrogen bonds : angle 5.93707 ( 1020) SS BOND : bond 0.00356 ( 5) SS BOND : angle 0.69220 ( 10) covalent geometry : bond 0.00310 ( 9675) covalent geometry : angle 0.63082 (13205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7335 (mtm-85) REVERT: A 205 ASN cc_start: 0.7535 (m-40) cc_final: 0.7168 (m-40) REVERT: A 239 ARG cc_start: 0.6033 (ptm160) cc_final: 0.4140 (ptt180) REVERT: B 47 LYS cc_start: 0.9021 (ptmt) cc_final: 0.8780 (ptmt) REVERT: B 103 ASP cc_start: 0.7660 (t70) cc_final: 0.7401 (t0) REVERT: B 107 LYS cc_start: 0.8753 (ptmt) cc_final: 0.8545 (ptmt) REVERT: B 140 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7290 (mtp180) REVERT: B 239 ARG cc_start: 0.5974 (ptm160) cc_final: 0.4259 (ptt180) REVERT: C 56 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6934 (mtm-85) REVERT: C 103 ASP cc_start: 0.7704 (t70) cc_final: 0.7311 (t0) REVERT: C 205 ASN cc_start: 0.7728 (m-40) cc_final: 0.7285 (m-40) REVERT: D 47 LYS cc_start: 0.8796 (ptpp) cc_final: 0.8514 (ptmt) REVERT: D 56 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6502 (mtt90) REVERT: D 103 ASP cc_start: 0.7771 (t70) cc_final: 0.7335 (t0) REVERT: D 212 LEU cc_start: 0.8626 (mt) cc_final: 0.8334 (mt) REVERT: D 239 ARG cc_start: 0.5680 (ptm160) cc_final: 0.5171 (ptm-80) REVERT: E 56 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.7168 (mtm-85) REVERT: E 77 ASN cc_start: 0.8548 (m-40) cc_final: 0.8128 (m110) REVERT: E 197 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7561 (ttmt) REVERT: E 239 ARG cc_start: 0.6283 (ptm160) cc_final: 0.4363 (ptt180) outliers start: 36 outliers final: 22 residues processed: 145 average time/residue: 0.3220 time to fit residues: 59.2183 Evaluate side-chains 134 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 56 ARG Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.131749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.112309 restraints weight = 10751.982| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.17 r_work: 0.3010 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9705 Z= 0.130 Angle : 0.667 13.047 13290 Z= 0.315 Chirality : 0.048 0.132 1490 Planarity : 0.005 0.046 1620 Dihedral : 11.245 116.835 1795 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.56 % Allowed : 13.96 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1045 helix: 0.45 (0.56), residues: 95 sheet: -0.55 (0.23), residues: 395 loop : -0.79 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.002 0.001 HIS C 180 PHE 0.012 0.001 PHE E 221 TYR 0.013 0.001 TYR B 45 ARG 0.004 0.000 ARG D 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00918 ( 15) link_NAG-ASN : angle 5.55656 ( 45) link_BETA1-4 : bond 0.00366 ( 10) link_BETA1-4 : angle 1.29373 ( 30) hydrogen bonds : bond 0.03789 ( 290) hydrogen bonds : angle 5.38551 ( 1020) SS BOND : bond 0.00262 ( 5) SS BOND : angle 0.68047 ( 10) covalent geometry : bond 0.00285 ( 9675) covalent geometry : angle 0.58184 (13205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 205 ASN cc_start: 0.7744 (m-40) cc_final: 0.7453 (m-40) REVERT: A 239 ARG cc_start: 0.6003 (ptm160) cc_final: 0.4153 (ptt180) REVERT: B 78 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8077 (mm-40) REVERT: B 103 ASP cc_start: 0.7689 (t70) cc_final: 0.7356 (t0) REVERT: B 107 LYS cc_start: 0.8888 (ptmt) cc_final: 0.8611 (ptmt) REVERT: B 140 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7288 (mtp180) REVERT: B 239 ARG cc_start: 0.5849 (ptm160) cc_final: 0.4399 (ptt180) REVERT: C 56 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7431 (mtm-85) REVERT: C 103 ASP cc_start: 0.7764 (t70) cc_final: 0.7307 (t0) REVERT: C 140 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7426 (mtt90) REVERT: C 198 SER cc_start: 0.8007 (p) cc_final: 0.7772 (m) REVERT: C 239 ARG cc_start: 0.6018 (ptm160) cc_final: 0.4223 (ptt180) REVERT: D 56 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6519 (mtt90) REVERT: D 103 ASP cc_start: 0.7730 (t70) cc_final: 0.7273 (t0) REVERT: D 212 LEU cc_start: 0.8582 (mt) cc_final: 0.8338 (mt) REVERT: D 239 ARG cc_start: 0.5842 (ptm160) cc_final: 0.5402 (ptm-80) REVERT: E 64 ASP cc_start: 0.9047 (t0) cc_final: 0.8527 (t0) REVERT: E 101 ASP cc_start: 0.7959 (t0) cc_final: 0.7602 (t0) REVERT: E 197 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7420 (ttmt) REVERT: E 239 ARG cc_start: 0.6408 (ptm160) cc_final: 0.4505 (ptt180) outliers start: 36 outliers final: 23 residues processed: 155 average time/residue: 0.3029 time to fit residues: 60.2965 Evaluate side-chains 142 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.129598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.110474 restraints weight = 10666.413| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.07 r_work: 0.3000 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9705 Z= 0.127 Angle : 0.653 12.524 13290 Z= 0.306 Chirality : 0.048 0.132 1490 Planarity : 0.005 0.043 1620 Dihedral : 11.201 116.457 1795 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.95 % Allowed : 14.75 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1045 helix: 0.40 (0.56), residues: 95 sheet: -0.75 (0.23), residues: 395 loop : -0.78 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 90 HIS 0.002 0.001 HIS C 180 PHE 0.012 0.001 PHE D 166 TYR 0.011 0.001 TYR B 45 ARG 0.008 0.000 ARG C 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 15) link_NAG-ASN : angle 5.27134 ( 45) link_BETA1-4 : bond 0.00282 ( 10) link_BETA1-4 : angle 1.24516 ( 30) hydrogen bonds : bond 0.03240 ( 290) hydrogen bonds : angle 5.04482 ( 1020) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.61053 ( 10) covalent geometry : bond 0.00286 ( 9675) covalent geometry : angle 0.57466 (13205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 142 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7907 (t0) cc_final: 0.7373 (t0) REVERT: A 127 ASP cc_start: 0.8319 (t0) cc_final: 0.7918 (t0) REVERT: A 205 ASN cc_start: 0.7672 (m-40) cc_final: 0.7453 (m-40) REVERT: A 239 ARG cc_start: 0.5993 (ptm160) cc_final: 0.4212 (ptt180) REVERT: B 78 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8132 (mm-40) REVERT: B 101 ASP cc_start: 0.8214 (t0) cc_final: 0.7978 (t0) REVERT: B 103 ASP cc_start: 0.7665 (t70) cc_final: 0.7386 (t0) REVERT: B 239 ARG cc_start: 0.5914 (ptm160) cc_final: 0.4472 (ptt180) REVERT: C 45 TYR cc_start: 0.7626 (t80) cc_final: 0.7348 (t80) REVERT: C 56 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7481 (mtm-85) REVERT: C 103 ASP cc_start: 0.7781 (t70) cc_final: 0.7480 (t0) REVERT: C 114 SER cc_start: 0.9240 (m) cc_final: 0.8989 (m) REVERT: C 239 ARG cc_start: 0.5999 (ptm160) cc_final: 0.4367 (ptt180) REVERT: D 56 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: D 64 ASP cc_start: 0.9084 (t0) cc_final: 0.8862 (t70) REVERT: D 103 ASP cc_start: 0.7656 (t70) cc_final: 0.7293 (t0) REVERT: D 200 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7371 (mtp-110) REVERT: D 206 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7937 (mm-40) REVERT: D 239 ARG cc_start: 0.5720 (ptm160) cc_final: 0.5299 (ptm-80) REVERT: E 101 ASP cc_start: 0.7955 (t0) cc_final: 0.7553 (t0) REVERT: E 136 TYR cc_start: 0.8925 (m-80) cc_final: 0.8718 (m-80) REVERT: E 197 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7260 (mtmt) REVERT: E 239 ARG cc_start: 0.6338 (ptm160) cc_final: 0.4412 (ptt180) outliers start: 50 outliers final: 29 residues processed: 184 average time/residue: 0.2628 time to fit residues: 64.1080 Evaluate side-chains 162 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 146 GLN B 146 GLN C 206 GLN D 78 GLN D 146 GLN E 146 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.103236 restraints weight = 10944.259| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.98 r_work: 0.2937 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9705 Z= 0.175 Angle : 0.698 12.239 13290 Z= 0.331 Chirality : 0.050 0.306 1490 Planarity : 0.005 0.046 1620 Dihedral : 11.278 116.681 1795 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.25 % Allowed : 15.25 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1045 helix: 0.32 (0.56), residues: 95 sheet: -1.09 (0.22), residues: 480 loop : -0.67 (0.32), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 85 HIS 0.002 0.001 HIS C 141 PHE 0.011 0.001 PHE A 166 TYR 0.014 0.002 TYR B 45 ARG 0.008 0.000 ARG C 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00729 ( 15) link_NAG-ASN : angle 5.13039 ( 45) link_BETA1-4 : bond 0.00194 ( 10) link_BETA1-4 : angle 1.42921 ( 30) hydrogen bonds : bond 0.03421 ( 290) hydrogen bonds : angle 5.15823 ( 1020) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.75946 ( 10) covalent geometry : bond 0.00412 ( 9675) covalent geometry : angle 0.62884 (13205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7963 (t0) cc_final: 0.7413 (t0) REVERT: A 127 ASP cc_start: 0.8298 (t0) cc_final: 0.7867 (t0) REVERT: A 134 ILE cc_start: 0.8376 (mm) cc_final: 0.8098 (mm) REVERT: A 239 ARG cc_start: 0.5813 (ptm160) cc_final: 0.4020 (ptt180) REVERT: B 101 ASP cc_start: 0.8252 (t0) cc_final: 0.7884 (t0) REVERT: B 103 ASP cc_start: 0.7650 (t70) cc_final: 0.7348 (t0) REVERT: B 107 LYS cc_start: 0.9085 (ptmt) cc_final: 0.8255 (ptmt) REVERT: B 239 ARG cc_start: 0.5957 (ptm160) cc_final: 0.4268 (ptt180) REVERT: C 45 TYR cc_start: 0.7827 (t80) cc_final: 0.7374 (t80) REVERT: C 56 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7515 (mtm-85) REVERT: C 103 ASP cc_start: 0.7796 (t70) cc_final: 0.7373 (t0) REVERT: C 114 SER cc_start: 0.9202 (m) cc_final: 0.8931 (m) REVERT: C 197 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7094 (ttmt) REVERT: C 239 ARG cc_start: 0.5922 (ptm160) cc_final: 0.4238 (ptt180) REVERT: D 56 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7734 (mtm-85) REVERT: D 101 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8037 (t0) REVERT: D 103 ASP cc_start: 0.7677 (t70) cc_final: 0.7322 (t0) REVERT: D 108 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8417 (pt) REVERT: D 205 ASN cc_start: 0.7544 (m-40) cc_final: 0.7092 (m-40) REVERT: D 206 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8127 (mm-40) REVERT: D 239 ARG cc_start: 0.5528 (ptm160) cc_final: 0.3865 (ptt180) REVERT: E 101 ASP cc_start: 0.8117 (t0) cc_final: 0.7715 (t0) REVERT: E 103 ASP cc_start: 0.7717 (t70) cc_final: 0.7291 (t0) REVERT: E 107 LYS cc_start: 0.9092 (ptmt) cc_final: 0.8614 (ptmt) REVERT: E 197 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7152 (mtmt) REVERT: E 239 ARG cc_start: 0.5964 (ptm160) cc_final: 0.4125 (ptt180) outliers start: 53 outliers final: 39 residues processed: 190 average time/residue: 0.2472 time to fit residues: 63.0318 Evaluate side-chains 179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 103 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.120702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.103015 restraints weight = 10921.007| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.98 r_work: 0.2931 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9705 Z= 0.154 Angle : 0.659 11.034 13290 Z= 0.312 Chirality : 0.049 0.221 1490 Planarity : 0.005 0.045 1620 Dihedral : 11.316 117.185 1795 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.75 % Allowed : 15.64 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.27), residues: 1045 helix: 0.47 (0.55), residues: 95 sheet: -1.17 (0.22), residues: 485 loop : -0.58 (0.32), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.002 0.001 HIS C 180 PHE 0.009 0.001 PHE C 221 TYR 0.011 0.002 TYR A 86 ARG 0.005 0.000 ARG C 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00613 ( 15) link_NAG-ASN : angle 4.75309 ( 45) link_BETA1-4 : bond 0.00253 ( 10) link_BETA1-4 : angle 1.29332 ( 30) hydrogen bonds : bond 0.03137 ( 290) hydrogen bonds : angle 5.10665 ( 1020) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.75365 ( 10) covalent geometry : bond 0.00362 ( 9675) covalent geometry : angle 0.59675 (13205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.997 Fit side-chains REVERT: A 101 ASP cc_start: 0.8002 (t0) cc_final: 0.7798 (t0) REVERT: A 134 ILE cc_start: 0.8422 (mm) cc_final: 0.8141 (mm) REVERT: A 239 ARG cc_start: 0.5909 (ptm160) cc_final: 0.4089 (ptt180) REVERT: B 78 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7887 (mm-40) REVERT: B 101 ASP cc_start: 0.8243 (t0) cc_final: 0.7872 (t0) REVERT: B 103 ASP cc_start: 0.7760 (t70) cc_final: 0.7414 (t0) REVERT: B 107 LYS cc_start: 0.9117 (ptmt) cc_final: 0.8291 (ptmt) REVERT: B 239 ARG cc_start: 0.5819 (ptm160) cc_final: 0.4106 (ptt180) REVERT: C 56 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7791 (mtm-85) REVERT: C 103 ASP cc_start: 0.7806 (t70) cc_final: 0.7412 (t0) REVERT: C 197 LYS cc_start: 0.7405 (ttmm) cc_final: 0.7069 (ttmt) REVERT: C 223 MET cc_start: 0.8487 (mmm) cc_final: 0.8250 (mmm) REVERT: C 239 ARG cc_start: 0.5811 (ptm160) cc_final: 0.4186 (ptt180) REVERT: D 56 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7910 (mtm-85) REVERT: D 101 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7978 (t0) REVERT: D 103 ASP cc_start: 0.7618 (t70) cc_final: 0.7264 (t0) REVERT: D 108 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8427 (pt) REVERT: D 205 ASN cc_start: 0.7384 (m-40) cc_final: 0.7169 (m-40) REVERT: D 206 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8062 (mm-40) REVERT: D 223 MET cc_start: 0.8586 (mmm) cc_final: 0.8292 (mmm) REVERT: D 239 ARG cc_start: 0.5617 (ptm160) cc_final: 0.3858 (ptt180) REVERT: E 101 ASP cc_start: 0.8171 (t0) cc_final: 0.7792 (t0) REVERT: E 103 ASP cc_start: 0.7655 (t70) cc_final: 0.7215 (t0) REVERT: E 107 LYS cc_start: 0.9127 (ptmt) cc_final: 0.8857 (ptmt) REVERT: E 197 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7123 (mtmt) REVERT: E 239 ARG cc_start: 0.5913 (ptm160) cc_final: 0.4081 (ptt180) outliers start: 48 outliers final: 40 residues processed: 187 average time/residue: 0.2515 time to fit residues: 62.4041 Evaluate side-chains 179 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN D 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.103316 restraints weight = 10983.274| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.06 r_work: 0.2945 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9705 Z= 0.137 Angle : 0.647 10.359 13290 Z= 0.307 Chirality : 0.048 0.209 1490 Planarity : 0.004 0.038 1620 Dihedral : 11.276 116.738 1795 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.36 % Allowed : 16.24 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.27), residues: 1045 helix: -0.77 (0.47), residues: 125 sheet: -1.17 (0.22), residues: 490 loop : -0.59 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 55 HIS 0.002 0.001 HIS C 141 PHE 0.008 0.001 PHE A 166 TYR 0.011 0.001 TYR B 86 ARG 0.005 0.000 ARG B 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 15) link_NAG-ASN : angle 4.50732 ( 45) link_BETA1-4 : bond 0.00262 ( 10) link_BETA1-4 : angle 1.29302 ( 30) hydrogen bonds : bond 0.03017 ( 290) hydrogen bonds : angle 5.05327 ( 1020) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.63890 ( 10) covalent geometry : bond 0.00319 ( 9675) covalent geometry : angle 0.58952 (13205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.065 Fit side-chains REVERT: A 101 ASP cc_start: 0.8026 (t0) cc_final: 0.7824 (t0) REVERT: A 134 ILE cc_start: 0.8507 (mm) cc_final: 0.8225 (mm) REVERT: A 239 ARG cc_start: 0.6022 (ptm160) cc_final: 0.4236 (ptt180) REVERT: B 101 ASP cc_start: 0.8270 (t0) cc_final: 0.8020 (t0) REVERT: B 103 ASP cc_start: 0.7763 (t70) cc_final: 0.7525 (t0) REVERT: B 107 LYS cc_start: 0.9099 (ptmt) cc_final: 0.8330 (ptmt) REVERT: B 197 LYS cc_start: 0.7647 (ttmm) cc_final: 0.7403 (ttmm) REVERT: B 239 ARG cc_start: 0.5861 (ptm160) cc_final: 0.4244 (ptt180) REVERT: C 45 TYR cc_start: 0.7910 (t80) cc_final: 0.7454 (t80) REVERT: C 56 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7949 (mtm-85) REVERT: C 103 ASP cc_start: 0.7834 (t70) cc_final: 0.7517 (t0) REVERT: C 166 PHE cc_start: 0.8086 (m-80) cc_final: 0.7884 (m-80) REVERT: C 223 MET cc_start: 0.8527 (mmm) cc_final: 0.8321 (mmm) REVERT: C 239 ARG cc_start: 0.5844 (ptm160) cc_final: 0.4263 (ptt180) REVERT: D 45 TYR cc_start: 0.7528 (t80) cc_final: 0.7314 (t80) REVERT: D 56 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8022 (mtm-85) REVERT: D 101 ASP cc_start: 0.8224 (m-30) cc_final: 0.7983 (t0) REVERT: D 103 ASP cc_start: 0.7661 (t70) cc_final: 0.7301 (t0) REVERT: D 108 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8499 (pt) REVERT: D 205 ASN cc_start: 0.7483 (m-40) cc_final: 0.7225 (m-40) REVERT: D 206 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8028 (mm-40) REVERT: D 223 MET cc_start: 0.8609 (mmm) cc_final: 0.8377 (mmm) REVERT: D 239 ARG cc_start: 0.5647 (ptm160) cc_final: 0.3982 (ptt180) REVERT: D 241 ARG cc_start: 0.7793 (ptt180) cc_final: 0.7390 (ptt180) REVERT: E 64 ASP cc_start: 0.8988 (t70) cc_final: 0.8648 (t0) REVERT: E 101 ASP cc_start: 0.8210 (t0) cc_final: 0.7826 (t0) REVERT: E 103 ASP cc_start: 0.7638 (t70) cc_final: 0.7253 (t0) REVERT: E 107 LYS cc_start: 0.9174 (ptmt) cc_final: 0.8915 (ptmt) REVERT: E 197 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7251 (mtmt) REVERT: E 239 ARG cc_start: 0.6033 (ptm160) cc_final: 0.4243 (ptt180) outliers start: 44 outliers final: 39 residues processed: 181 average time/residue: 0.2616 time to fit residues: 63.6033 Evaluate side-chains 178 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.121596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.105253 restraints weight = 11063.280| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.80 r_work: 0.2977 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9705 Z= 0.115 Angle : 0.643 12.743 13290 Z= 0.303 Chirality : 0.049 0.364 1490 Planarity : 0.004 0.035 1620 Dihedral : 11.308 116.157 1795 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.46 % Allowed : 16.44 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.27), residues: 1045 helix: -0.71 (0.47), residues: 125 sheet: -1.28 (0.22), residues: 505 loop : -0.52 (0.34), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.002 0.000 HIS C 180 PHE 0.012 0.001 PHE E 221 TYR 0.012 0.001 TYR B 45 ARG 0.005 0.000 ARG D 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 15) link_NAG-ASN : angle 4.64993 ( 45) link_BETA1-4 : bond 0.00307 ( 10) link_BETA1-4 : angle 1.21400 ( 30) hydrogen bonds : bond 0.02885 ( 290) hydrogen bonds : angle 4.94156 ( 1020) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.51277 ( 10) covalent geometry : bond 0.00263 ( 9675) covalent geometry : angle 0.58266 (13205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8019 (t0) cc_final: 0.7817 (t0) REVERT: A 239 ARG cc_start: 0.5875 (ptm160) cc_final: 0.4098 (ptt180) REVERT: B 78 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7968 (mm-40) REVERT: B 101 ASP cc_start: 0.8240 (t0) cc_final: 0.7989 (t0) REVERT: B 103 ASP cc_start: 0.7720 (t70) cc_final: 0.7513 (t0) REVERT: B 107 LYS cc_start: 0.9028 (ptmt) cc_final: 0.8238 (ptmt) REVERT: B 134 ILE cc_start: 0.8166 (mm) cc_final: 0.7903 (mm) REVERT: B 197 LYS cc_start: 0.7581 (ttmm) cc_final: 0.7332 (ttmm) REVERT: B 239 ARG cc_start: 0.5740 (ptm160) cc_final: 0.4168 (ptt180) REVERT: C 45 TYR cc_start: 0.7782 (t80) cc_final: 0.7312 (t80) REVERT: C 56 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.8016 (mtm-85) REVERT: C 197 LYS cc_start: 0.7249 (ttmm) cc_final: 0.6648 (mtmt) REVERT: C 239 ARG cc_start: 0.5779 (ptm160) cc_final: 0.4197 (ptt180) REVERT: D 101 ASP cc_start: 0.8188 (m-30) cc_final: 0.7955 (t0) REVERT: D 103 ASP cc_start: 0.7604 (t70) cc_final: 0.7250 (t0) REVERT: D 108 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8403 (pt) REVERT: D 205 ASN cc_start: 0.7462 (m-40) cc_final: 0.7242 (m-40) REVERT: D 206 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8011 (mm-40) REVERT: D 223 MET cc_start: 0.8587 (mmm) cc_final: 0.8359 (mmm) REVERT: D 239 ARG cc_start: 0.5396 (ptm160) cc_final: 0.3856 (ptt180) REVERT: E 64 ASP cc_start: 0.8957 (t70) cc_final: 0.8617 (t0) REVERT: E 78 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8133 (mm-40) REVERT: E 101 ASP cc_start: 0.8176 (t0) cc_final: 0.7791 (t0) REVERT: E 103 ASP cc_start: 0.7600 (t70) cc_final: 0.7234 (t0) REVERT: E 107 LYS cc_start: 0.9051 (ptmt) cc_final: 0.8797 (ptmt) REVERT: E 197 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7273 (mtmt) REVERT: E 239 ARG cc_start: 0.5914 (ptm160) cc_final: 0.4071 (ptt180) outliers start: 45 outliers final: 41 residues processed: 172 average time/residue: 0.2495 time to fit residues: 57.7419 Evaluate side-chains 166 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 100 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 0.0010 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.123125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104297 restraints weight = 11046.092| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.15 r_work: 0.2995 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9705 Z= 0.108 Angle : 0.613 9.126 13290 Z= 0.297 Chirality : 0.047 0.169 1490 Planarity : 0.004 0.035 1620 Dihedral : 11.114 115.907 1795 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.26 % Allowed : 17.13 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.27), residues: 1045 helix: -0.66 (0.47), residues: 125 sheet: -1.29 (0.23), residues: 500 loop : -0.42 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.001 0.000 HIS C 180 PHE 0.010 0.001 PHE E 221 TYR 0.023 0.001 TYR D 45 ARG 0.005 0.000 ARG D 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 15) link_NAG-ASN : angle 3.79751 ( 45) link_BETA1-4 : bond 0.00317 ( 10) link_BETA1-4 : angle 1.17024 ( 30) hydrogen bonds : bond 0.02745 ( 290) hydrogen bonds : angle 4.87221 ( 1020) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.42824 ( 10) covalent geometry : bond 0.00243 ( 9675) covalent geometry : angle 0.57085 (13205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7374 (ttmm) cc_final: 0.6726 (mtpt) REVERT: A 239 ARG cc_start: 0.5996 (ptm160) cc_final: 0.4217 (ptt180) REVERT: B 78 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8023 (mm-40) REVERT: B 101 ASP cc_start: 0.8252 (t0) cc_final: 0.8004 (t0) REVERT: B 103 ASP cc_start: 0.7856 (t70) cc_final: 0.7647 (t0) REVERT: B 107 LYS cc_start: 0.9054 (ptmt) cc_final: 0.8258 (ptmt) REVERT: B 134 ILE cc_start: 0.8194 (mm) cc_final: 0.7961 (mm) REVERT: B 197 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7404 (ttmm) REVERT: B 239 ARG cc_start: 0.5877 (ptm160) cc_final: 0.4292 (ptt180) REVERT: C 45 TYR cc_start: 0.7742 (t80) cc_final: 0.7283 (t80) REVERT: C 56 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7933 (mtm-85) REVERT: C 197 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6715 (mtmt) REVERT: C 204 MET cc_start: 0.7533 (mtp) cc_final: 0.7332 (mtm) REVERT: C 223 MET cc_start: 0.8609 (mmm) cc_final: 0.8406 (mmm) REVERT: C 239 ARG cc_start: 0.5882 (ptm160) cc_final: 0.4262 (ptt180) REVERT: D 101 ASP cc_start: 0.8190 (m-30) cc_final: 0.7969 (t0) REVERT: D 103 ASP cc_start: 0.7600 (t70) cc_final: 0.7302 (t0) REVERT: D 108 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8472 (pt) REVERT: D 205 ASN cc_start: 0.7481 (m-40) cc_final: 0.7253 (m-40) REVERT: D 206 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7975 (mm-40) REVERT: D 223 MET cc_start: 0.8600 (mmm) cc_final: 0.8384 (mmm) REVERT: D 239 ARG cc_start: 0.5626 (ptm160) cc_final: 0.4012 (ptt180) REVERT: E 64 ASP cc_start: 0.8988 (t70) cc_final: 0.8697 (t0) REVERT: E 78 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8129 (mm-40) REVERT: E 101 ASP cc_start: 0.8160 (t0) cc_final: 0.7778 (t0) REVERT: E 103 ASP cc_start: 0.7772 (t70) cc_final: 0.7492 (t0) REVERT: E 107 LYS cc_start: 0.9092 (ptmt) cc_final: 0.8852 (ptmt) REVERT: E 197 LYS cc_start: 0.7790 (ttmm) cc_final: 0.7291 (mtmt) REVERT: E 239 ARG cc_start: 0.6202 (ptm160) cc_final: 0.4274 (ptt180) outliers start: 43 outliers final: 39 residues processed: 175 average time/residue: 0.2455 time to fit residues: 57.6147 Evaluate side-chains 175 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 56 ARG Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.121273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.102594 restraints weight = 11101.981| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.14 r_work: 0.2936 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9705 Z= 0.128 Angle : 0.637 10.627 13290 Z= 0.305 Chirality : 0.049 0.221 1490 Planarity : 0.004 0.034 1620 Dihedral : 11.122 116.542 1795 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.86 % Allowed : 17.62 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.27), residues: 1045 helix: -0.65 (0.47), residues: 125 sheet: -1.28 (0.23), residues: 500 loop : -0.42 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.001 0.000 HIS C 180 PHE 0.009 0.001 PHE E 221 TYR 0.022 0.001 TYR B 45 ARG 0.005 0.000 ARG D 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00709 ( 15) link_NAG-ASN : angle 4.15789 ( 45) link_BETA1-4 : bond 0.00293 ( 10) link_BETA1-4 : angle 1.24207 ( 30) hydrogen bonds : bond 0.02892 ( 290) hydrogen bonds : angle 4.87375 ( 1020) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.59973 ( 10) covalent geometry : bond 0.00297 ( 9675) covalent geometry : angle 0.58768 (13205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.7326 (ttmm) cc_final: 0.6681 (mtpt) REVERT: A 239 ARG cc_start: 0.5988 (ptm160) cc_final: 0.4168 (ptt180) REVERT: B 78 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7979 (mm-40) REVERT: B 101 ASP cc_start: 0.8260 (t0) cc_final: 0.8015 (t0) REVERT: B 103 ASP cc_start: 0.7816 (t70) cc_final: 0.7614 (t0) REVERT: B 107 LYS cc_start: 0.9049 (ptmt) cc_final: 0.8262 (ptmt) REVERT: B 134 ILE cc_start: 0.8174 (mm) cc_final: 0.7937 (mm) REVERT: B 197 LYS cc_start: 0.7658 (ttmm) cc_final: 0.7403 (ttmm) REVERT: B 239 ARG cc_start: 0.5846 (ptm160) cc_final: 0.4229 (ptt180) REVERT: C 45 TYR cc_start: 0.7827 (t80) cc_final: 0.7343 (t80) REVERT: C 107 LYS cc_start: 0.8937 (ptmt) cc_final: 0.8067 (ptmt) REVERT: C 197 LYS cc_start: 0.7230 (ttmm) cc_final: 0.6741 (mtmt) REVERT: C 204 MET cc_start: 0.7524 (mtp) cc_final: 0.7301 (mtm) REVERT: C 239 ARG cc_start: 0.5874 (ptm160) cc_final: 0.4291 (ptt180) REVERT: D 101 ASP cc_start: 0.8188 (m-30) cc_final: 0.7941 (t0) REVERT: D 103 ASP cc_start: 0.7619 (t70) cc_final: 0.7316 (t0) REVERT: D 108 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8496 (pt) REVERT: D 205 ASN cc_start: 0.7501 (m-40) cc_final: 0.7270 (m-40) REVERT: D 206 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8067 (mm-40) REVERT: D 223 MET cc_start: 0.8626 (mmm) cc_final: 0.8399 (mmm) REVERT: D 239 ARG cc_start: 0.5606 (ptm160) cc_final: 0.3988 (ptt180) REVERT: E 78 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8074 (mm-40) REVERT: E 101 ASP cc_start: 0.8183 (t0) cc_final: 0.7811 (t0) REVERT: E 103 ASP cc_start: 0.7783 (t70) cc_final: 0.7505 (t0) REVERT: E 107 LYS cc_start: 0.9014 (ptmt) cc_final: 0.8764 (ptmt) REVERT: E 197 LYS cc_start: 0.7811 (ttmm) cc_final: 0.7338 (mtmt) REVERT: E 239 ARG cc_start: 0.6174 (ptm160) cc_final: 0.4330 (ptt180) outliers start: 39 outliers final: 37 residues processed: 169 average time/residue: 0.2589 time to fit residues: 58.0105 Evaluate side-chains 173 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 138 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 222 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 54 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.122182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.103656 restraints weight = 10962.256| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.12 r_work: 0.2992 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9705 Z= 0.118 Angle : 0.609 8.327 13290 Z= 0.299 Chirality : 0.047 0.166 1490 Planarity : 0.004 0.034 1620 Dihedral : 11.059 116.208 1795 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.96 % Allowed : 17.72 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 1045 helix: -0.62 (0.47), residues: 125 sheet: -1.11 (0.25), residues: 440 loop : -0.64 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 90 HIS 0.001 0.000 HIS C 180 PHE 0.009 0.001 PHE E 221 TYR 0.021 0.001 TYR B 45 ARG 0.005 0.000 ARG D 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 15) link_NAG-ASN : angle 3.55344 ( 45) link_BETA1-4 : bond 0.00319 ( 10) link_BETA1-4 : angle 1.19068 ( 30) hydrogen bonds : bond 0.02765 ( 290) hydrogen bonds : angle 4.84327 ( 1020) SS BOND : bond 0.00185 ( 5) SS BOND : angle 0.51522 ( 10) covalent geometry : bond 0.00269 ( 9675) covalent geometry : angle 0.57177 (13205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4903.72 seconds wall clock time: 84 minutes 59.47 seconds (5099.47 seconds total)