Starting phenix.real_space_refine on Wed Mar 4 08:28:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5g_10696/03_2026/6y5g_10696.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5g_10696/03_2026/6y5g_10696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y5g_10696/03_2026/6y5g_10696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5g_10696/03_2026/6y5g_10696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5g_10696/03_2026/6y5g_10696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5g_10696/03_2026/6y5g_10696.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.245 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 57 5.16 5 C 7482 2.51 5 N 2058 2.21 5 O 2439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12036 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.95, per 1000 atoms: 0.25 Number of scatterers: 12036 At special positions: 0 Unit cell: (87.2, 87.2, 150.42, 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 57 16.00 O 2439 8.00 N 2058 7.00 C 7482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.09 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.93 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.09 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 38 " " NAG A 410 " - " ASN A 81 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 38 " " NAG C 410 " - " ASN C 81 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 38 " " NAG E 410 " - " ASN E 81 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 285 " " NAG I 1 " - " ASN B 154 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 285 " " NAG L 1 " - " ASN E 165 " " NAG M 1 " - " ASN E 285 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN F 154 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 528.9 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 24.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 3.578A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.690A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.579A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.690A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.578A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 removed outlier: 3.689A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.131A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS A 139 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.603A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.130A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC7, first strand: chain 'F' and resid 22 through 27 removed outlier: 3.815A pdb=" N ILE F 140 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.130A pdb=" N PHE E 87 " --> pdb=" O MET E 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS E 139 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 146 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY E 144 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 287 414 hydrogen bonds defined for protein. 1143 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: 1.63 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3966 1.34 - 1.46: 2924 1.46 - 1.58: 5308 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 12276 Sorted by residual: bond pdb=" N ILE B 10 " pdb=" CA ILE B 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.13e+00 bond pdb=" N ILE F 10 " pdb=" CA ILE F 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N ILE D 10 " pdb=" CA ILE D 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N GLU D 11 " pdb=" CA GLU D 11 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.98e+00 bond pdb=" N GLU F 11 " pdb=" CA GLU F 11 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.96e+00 ... (remaining 12271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 15794 1.33 - 2.67: 717 2.67 - 4.00: 83 4.00 - 5.34: 32 5.34 - 6.67: 21 Bond angle restraints: 16647 Sorted by residual: angle pdb=" CA LYS D 39 " pdb=" CB LYS D 39 " pdb=" CG LYS D 39 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.28e+00 angle pdb=" CA LYS B 39 " pdb=" CB LYS B 39 " pdb=" CG LYS B 39 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 angle pdb=" CA LYS F 39 " pdb=" CB LYS F 39 " pdb=" CG LYS F 39 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.11e+00 angle pdb=" O GLU B 85 " pdb=" C GLU B 85 " pdb=" N ASP B 86 " ideal model delta sigma weight residual 122.07 124.70 -2.63 1.03e+00 9.43e-01 6.53e+00 angle pdb=" O GLU F 85 " pdb=" C GLU F 85 " pdb=" N ASP F 86 " ideal model delta sigma weight residual 122.07 124.66 -2.59 1.03e+00 9.43e-01 6.31e+00 ... (remaining 16642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 7287 22.13 - 44.27: 411 44.27 - 66.40: 72 66.40 - 88.53: 42 88.53 - 110.66: 15 Dihedral angle restraints: 7827 sinusoidal: 3609 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.60 -79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.61 -79.39 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.64 -79.36 1 1.00e+01 1.00e-02 7.83e+01 ... (remaining 7824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 1920 0.314 - 0.627: 6 0.627 - 0.941: 3 0.941 - 1.255: 3 1.255 - 1.568: 3 Chirality restraints: 1935 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.15e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 ... (remaining 1932 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 73 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 74 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO E 74 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 73 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO C 74 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.026 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 886 2.73 - 3.27: 10349 3.27 - 3.82: 18279 3.82 - 4.36: 22695 4.36 - 4.90: 40185 Nonbonded interactions: 92394 Sorted by model distance: nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.189 3.120 nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.189 3.120 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLU F 131 " pdb=" OH TYR F 141 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLU B 131 " pdb=" OH TYR B 141 " model vdw 2.280 3.040 ... (remaining 92389 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 12330 Z= 0.278 Angle : 1.805 59.392 16791 Z= 0.658 Chirality : 0.101 1.568 1935 Planarity : 0.004 0.047 2130 Dihedral : 15.738 110.663 5067 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.94 % Allowed : 12.65 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.18), residues: 1458 helix: -0.38 (0.26), residues: 366 sheet: -1.23 (0.33), residues: 228 loop : -3.05 (0.15), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 54 TYR 0.010 0.001 TYR E 161 PHE 0.013 0.001 PHE F 9 TRP 0.008 0.001 TRP C 234 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00522 (12276) covalent geometry : angle 0.66089 (16647) SS BOND : bond 0.03120 ( 18) SS BOND : angle 1.53718 ( 36) hydrogen bonds : bond 0.16548 ( 414) hydrogen bonds : angle 6.16138 ( 1143) link_ALPHA1-3 : bond 0.06558 ( 3) link_ALPHA1-3 : angle 30.53201 ( 9) link_ALPHA1-6 : bond 0.06532 ( 3) link_ALPHA1-6 : angle 19.34584 ( 9) link_BETA1-4 : bond 0.06544 ( 12) link_BETA1-4 : angle 31.34804 ( 36) link_NAG-ASN : bond 0.00313 ( 18) link_NAG-ASN : angle 2.07196 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 111 LEU cc_start: 0.8585 (tt) cc_final: 0.8269 (tp) REVERT: A 119 GLU cc_start: 0.8087 (tt0) cc_final: 0.7866 (tt0) REVERT: B 46 ASP cc_start: 0.7801 (m-30) cc_final: 0.7480 (m-30) REVERT: C 62 ILE cc_start: 0.8819 (mt) cc_final: 0.8579 (mp) REVERT: C 82 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8093 (mm-30) REVERT: E 27 LYS cc_start: 0.8307 (mttt) cc_final: 0.7933 (mtmm) REVERT: E 111 LEU cc_start: 0.8684 (tt) cc_final: 0.8319 (tt) REVERT: E 119 GLU cc_start: 0.8184 (tt0) cc_final: 0.7955 (tt0) REVERT: E 139 CYS cc_start: 0.7879 (t) cc_final: 0.7368 (t) REVERT: D 49 ASN cc_start: 0.7872 (m-40) cc_final: 0.7542 (m-40) REVERT: D 62 LYS cc_start: 0.8304 (mttt) cc_final: 0.7958 (mmtt) REVERT: D 115 MET cc_start: 0.8653 (tpt) cc_final: 0.8397 (mmm) REVERT: D 121 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7449 (ttmm) REVERT: D 139 LYS cc_start: 0.8239 (tttp) cc_final: 0.7941 (tptm) REVERT: F 115 MET cc_start: 0.8851 (tpt) cc_final: 0.8648 (mmm) REVERT: F 139 LYS cc_start: 0.8220 (tttp) cc_final: 0.7976 (tptm) REVERT: F 168 ASN cc_start: 0.7901 (t0) cc_final: 0.7488 (m-40) outliers start: 12 outliers final: 0 residues processed: 237 average time/residue: 0.7153 time to fit residues: 181.3358 Evaluate side-chains 166 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 125 GLN C 33 GLN C 216 ASN E 17 HIS E 54 ASN E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099692 restraints weight = 14244.792| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.90 r_work: 0.2903 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12330 Z= 0.189 Angle : 0.645 6.814 16791 Z= 0.323 Chirality : 0.048 0.209 1935 Planarity : 0.005 0.045 2130 Dihedral : 10.867 92.862 2322 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.36 % Allowed : 15.07 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.19), residues: 1458 helix: 0.68 (0.28), residues: 375 sheet: -0.73 (0.33), residues: 234 loop : -2.53 (0.16), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.010 0.002 TYR A 308 PHE 0.019 0.002 PHE D 9 TRP 0.009 0.001 TRP A 234 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00456 (12276) covalent geometry : angle 0.61347 (16647) SS BOND : bond 0.00760 ( 18) SS BOND : angle 2.19311 ( 36) hydrogen bonds : bond 0.06355 ( 414) hydrogen bonds : angle 4.78244 ( 1143) link_ALPHA1-3 : bond 0.01074 ( 3) link_ALPHA1-3 : angle 2.29598 ( 9) link_ALPHA1-6 : bond 0.00505 ( 3) link_ALPHA1-6 : angle 2.58052 ( 9) link_BETA1-4 : bond 0.00269 ( 12) link_BETA1-4 : angle 2.36488 ( 36) link_NAG-ASN : bond 0.00319 ( 18) link_NAG-ASN : angle 2.13183 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.6995 (t0) REVERT: A 101 ASP cc_start: 0.8860 (p0) cc_final: 0.8651 (p0) REVERT: A 111 LEU cc_start: 0.8644 (tt) cc_final: 0.8384 (tp) REVERT: A 321 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7949 (ttt180) REVERT: B 54 ARG cc_start: 0.7954 (tpt90) cc_final: 0.5457 (tmt-80) REVERT: B 72 GLU cc_start: 0.7645 (mp0) cc_final: 0.7251 (mp0) REVERT: C 41 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: C 62 ILE cc_start: 0.8834 (mt) cc_final: 0.8558 (mp) REVERT: C 82 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 321 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7983 (ttt180) REVERT: C 325 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7345 (mt-10) REVERT: E 27 LYS cc_start: 0.8517 (mttt) cc_final: 0.8072 (mtmm) REVERT: E 41 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: E 111 LEU cc_start: 0.8615 (tt) cc_final: 0.8323 (tt) REVERT: E 139 CYS cc_start: 0.8268 (t) cc_final: 0.7761 (t) REVERT: E 321 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7833 (ttt180) REVERT: D 49 ASN cc_start: 0.7905 (m-40) cc_final: 0.7618 (m-40) REVERT: D 62 LYS cc_start: 0.8369 (mttt) cc_final: 0.7905 (mmtt) REVERT: D 115 MET cc_start: 0.8899 (tpt) cc_final: 0.8560 (mmm) REVERT: D 121 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7606 (ttmm) REVERT: D 131 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: D 139 LYS cc_start: 0.8474 (tttp) cc_final: 0.8165 (tptm) REVERT: F 37 ASP cc_start: 0.8362 (t0) cc_final: 0.8031 (t70) REVERT: F 115 MET cc_start: 0.9079 (tpt) cc_final: 0.8672 (mmm) REVERT: F 139 LYS cc_start: 0.8575 (tttp) cc_final: 0.8208 (tptm) REVERT: F 150 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6663 (tt0) REVERT: F 160 ASP cc_start: 0.8206 (m-30) cc_final: 0.7991 (m-30) REVERT: F 168 ASN cc_start: 0.8256 (t0) cc_final: 0.7618 (m-40) outliers start: 43 outliers final: 16 residues processed: 202 average time/residue: 0.7218 time to fit residues: 156.1082 Evaluate side-chains 185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN C 216 ASN E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.117137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.099173 restraints weight = 14565.410| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.92 r_work: 0.2886 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12330 Z= 0.181 Angle : 0.631 7.130 16791 Z= 0.322 Chirality : 0.047 0.231 1935 Planarity : 0.004 0.038 2130 Dihedral : 9.835 87.117 2322 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.98 % Allowed : 15.93 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.20), residues: 1458 helix: 1.37 (0.29), residues: 357 sheet: -0.13 (0.36), residues: 204 loop : -2.24 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 57 TYR 0.009 0.002 TYR C 308 PHE 0.017 0.002 PHE B 9 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00440 (12276) covalent geometry : angle 0.59968 (16647) SS BOND : bond 0.00831 ( 18) SS BOND : angle 2.66407 ( 36) hydrogen bonds : bond 0.06150 ( 414) hydrogen bonds : angle 4.56179 ( 1143) link_ALPHA1-3 : bond 0.00720 ( 3) link_ALPHA1-3 : angle 1.49032 ( 9) link_ALPHA1-6 : bond 0.00642 ( 3) link_ALPHA1-6 : angle 2.01500 ( 9) link_BETA1-4 : bond 0.00395 ( 12) link_BETA1-4 : angle 2.09696 ( 36) link_NAG-ASN : bond 0.00325 ( 18) link_NAG-ASN : angle 2.06654 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: A 77 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7140 (t0) REVERT: A 111 LEU cc_start: 0.8678 (tt) cc_final: 0.8413 (tp) REVERT: A 280 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8210 (mm-30) REVERT: A 321 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8036 (ttt180) REVERT: A 325 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7055 (mt-10) REVERT: B 54 ARG cc_start: 0.7943 (tpt90) cc_final: 0.5421 (tmt-80) REVERT: B 72 GLU cc_start: 0.7546 (mp0) cc_final: 0.7221 (mp0) REVERT: C 62 ILE cc_start: 0.8778 (mt) cc_final: 0.8477 (mp) REVERT: C 82 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8342 (mm-30) REVERT: C 321 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8119 (ttt180) REVERT: C 325 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7370 (mt-10) REVERT: E 27 LYS cc_start: 0.8524 (mttt) cc_final: 0.8100 (mtmm) REVERT: E 31 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.7014 (t0) REVERT: E 41 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: E 70 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8435 (tp) REVERT: E 104 ASP cc_start: 0.8122 (m-30) cc_final: 0.7888 (m-30) REVERT: E 111 LEU cc_start: 0.8682 (tt) cc_final: 0.8393 (tt) REVERT: E 321 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7950 (ttt180) REVERT: E 325 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6849 (mt-10) REVERT: D 38 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7634 (mt) REVERT: D 49 ASN cc_start: 0.8077 (m-40) cc_final: 0.7768 (m-40) REVERT: D 62 LYS cc_start: 0.8401 (mttt) cc_final: 0.7984 (mmtt) REVERT: D 120 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: D 139 LYS cc_start: 0.8585 (tttp) cc_final: 0.8191 (tptm) REVERT: F 37 ASP cc_start: 0.8407 (t0) cc_final: 0.8096 (t70) REVERT: F 115 MET cc_start: 0.9107 (tpt) cc_final: 0.8749 (mmm) REVERT: F 121 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7672 (tttp) REVERT: F 150 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6774 (tt0) REVERT: F 160 ASP cc_start: 0.8296 (m-30) cc_final: 0.8077 (m-30) REVERT: F 168 ASN cc_start: 0.8353 (t0) cc_final: 0.7702 (m-40) outliers start: 51 outliers final: 18 residues processed: 202 average time/residue: 0.7019 time to fit residues: 154.1466 Evaluate side-chains 186 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 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 33 GLN A 295 GLN E 295 GLN D 28 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.100351 restraints weight = 14323.536| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.90 r_work: 0.2856 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12330 Z= 0.157 Angle : 0.617 8.524 16791 Z= 0.313 Chirality : 0.047 0.249 1935 Planarity : 0.004 0.046 2130 Dihedral : 8.793 77.169 2322 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.59 % Allowed : 17.33 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.20), residues: 1458 helix: 1.59 (0.29), residues: 357 sheet: 0.03 (0.36), residues: 204 loop : -2.09 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 57 TYR 0.008 0.001 TYR C 308 PHE 0.017 0.001 PHE D 9 TRP 0.008 0.001 TRP E 234 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00376 (12276) covalent geometry : angle 0.58377 (16647) SS BOND : bond 0.00812 ( 18) SS BOND : angle 3.00343 ( 36) hydrogen bonds : bond 0.05708 ( 414) hydrogen bonds : angle 4.43841 ( 1143) link_ALPHA1-3 : bond 0.00920 ( 3) link_ALPHA1-3 : angle 1.39858 ( 9) link_ALPHA1-6 : bond 0.00879 ( 3) link_ALPHA1-6 : angle 1.74121 ( 9) link_BETA1-4 : bond 0.00287 ( 12) link_BETA1-4 : angle 1.95564 ( 36) link_NAG-ASN : bond 0.00357 ( 18) link_NAG-ASN : angle 2.01473 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: A 77 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7100 (t0) REVERT: A 111 LEU cc_start: 0.8674 (tt) cc_final: 0.8434 (tp) REVERT: B 54 ARG cc_start: 0.7948 (tpt90) cc_final: 0.5575 (tmt-80) REVERT: B 72 GLU cc_start: 0.7563 (mp0) cc_final: 0.7229 (mp0) REVERT: C 41 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: C 70 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8399 (tp) REVERT: C 73 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7835 (t70) REVERT: C 82 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8341 (mm-30) REVERT: C 321 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8155 (ttt180) REVERT: C 325 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7326 (mt-10) REVERT: E 27 LYS cc_start: 0.8527 (mttt) cc_final: 0.8103 (mtmm) REVERT: E 41 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: E 70 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8546 (tp) REVERT: E 104 ASP cc_start: 0.8112 (m-30) cc_final: 0.7896 (m-30) REVERT: E 111 LEU cc_start: 0.8697 (tt) cc_final: 0.8421 (tt) REVERT: E 321 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7977 (ttt180) REVERT: E 325 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6997 (mt-10) REVERT: D 38 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7585 (mt) REVERT: D 49 ASN cc_start: 0.7982 (m-40) cc_final: 0.7677 (m-40) REVERT: D 62 LYS cc_start: 0.8377 (mttt) cc_final: 0.7942 (mmtt) REVERT: D 120 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: D 139 LYS cc_start: 0.8583 (tttp) cc_final: 0.8190 (tptm) REVERT: F 37 ASP cc_start: 0.8419 (t0) cc_final: 0.8063 (t70) REVERT: F 115 MET cc_start: 0.9088 (tpt) cc_final: 0.8717 (mmm) REVERT: F 121 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7600 (tttp) REVERT: F 139 LYS cc_start: 0.8643 (tttm) cc_final: 0.8288 (tptm) REVERT: F 150 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6717 (tt0) REVERT: F 160 ASP cc_start: 0.8286 (m-30) cc_final: 0.8061 (m-30) REVERT: F 168 ASN cc_start: 0.8365 (t0) cc_final: 0.7670 (m-40) outliers start: 46 outliers final: 16 residues processed: 187 average time/residue: 0.6805 time to fit residues: 136.4402 Evaluate side-chains 180 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 34 GLN E 295 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.117656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.099912 restraints weight = 14529.176| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.91 r_work: 0.2849 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12330 Z= 0.169 Angle : 0.678 20.106 16791 Z= 0.341 Chirality : 0.049 0.367 1935 Planarity : 0.004 0.044 2130 Dihedral : 8.062 69.116 2322 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.14 % Allowed : 17.17 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1458 helix: 1.77 (0.29), residues: 354 sheet: 0.22 (0.39), residues: 174 loop : -1.98 (0.16), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 57 TYR 0.010 0.001 TYR A 195 PHE 0.017 0.002 PHE D 9 TRP 0.009 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00401 (12276) covalent geometry : angle 0.63536 (16647) SS BOND : bond 0.01041 ( 18) SS BOND : angle 4.08264 ( 36) hydrogen bonds : bond 0.05841 ( 414) hydrogen bonds : angle 4.42763 ( 1143) link_ALPHA1-3 : bond 0.00921 ( 3) link_ALPHA1-3 : angle 1.33500 ( 9) link_ALPHA1-6 : bond 0.00956 ( 3) link_ALPHA1-6 : angle 1.64431 ( 9) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.94088 ( 36) link_NAG-ASN : bond 0.00364 ( 18) link_NAG-ASN : angle 2.04565 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: A 77 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7128 (t0) REVERT: A 111 LEU cc_start: 0.8705 (tt) cc_final: 0.8475 (tp) REVERT: A 280 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: B 72 GLU cc_start: 0.7500 (mp0) cc_final: 0.7139 (mp0) REVERT: C 41 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: C 70 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 73 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7868 (t70) REVERT: C 82 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8358 (mm-30) REVERT: C 321 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8153 (ttt180) REVERT: C 325 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7272 (mt-10) REVERT: E 27 LYS cc_start: 0.8548 (mttt) cc_final: 0.8139 (mtmm) REVERT: E 41 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: E 70 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8554 (tp) REVERT: E 104 ASP cc_start: 0.8123 (m-30) cc_final: 0.7909 (m-30) REVERT: E 111 LEU cc_start: 0.8727 (tt) cc_final: 0.8459 (tt) REVERT: E 321 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7958 (ttt180) REVERT: D 38 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7583 (mt) REVERT: D 49 ASN cc_start: 0.7976 (m-40) cc_final: 0.7676 (m-40) REVERT: D 62 LYS cc_start: 0.8384 (mttt) cc_final: 0.7973 (mmtt) REVERT: D 139 LYS cc_start: 0.8546 (tttp) cc_final: 0.8222 (tptm) REVERT: D 168 ASN cc_start: 0.8382 (t0) cc_final: 0.7768 (t0) REVERT: F 37 ASP cc_start: 0.8433 (t0) cc_final: 0.8025 (t70) REVERT: F 115 MET cc_start: 0.9048 (tpt) cc_final: 0.8669 (mmm) REVERT: F 123 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7919 (ttp80) REVERT: F 139 LYS cc_start: 0.8682 (tttm) cc_final: 0.8419 (tptm) REVERT: F 150 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6754 (tt0) REVERT: F 160 ASP cc_start: 0.8315 (m-30) cc_final: 0.8097 (m-30) REVERT: F 168 ASN cc_start: 0.8391 (t0) cc_final: 0.7692 (m-40) outliers start: 53 outliers final: 25 residues processed: 190 average time/residue: 0.6393 time to fit residues: 130.8072 Evaluate side-chains 184 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 0.0470 chunk 51 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.100029 restraints weight = 14468.428| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.90 r_work: 0.2916 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12330 Z= 0.163 Angle : 0.672 16.518 16791 Z= 0.340 Chirality : 0.049 0.349 1935 Planarity : 0.004 0.045 2130 Dihedral : 7.612 63.041 2322 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.06 % Allowed : 17.33 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1458 helix: 1.83 (0.29), residues: 357 sheet: 0.11 (0.36), residues: 204 loop : -1.97 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.008 0.001 TYR A 195 PHE 0.016 0.001 PHE D 9 TRP 0.008 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00385 (12276) covalent geometry : angle 0.62934 (16647) SS BOND : bond 0.01027 ( 18) SS BOND : angle 4.13660 ( 36) hydrogen bonds : bond 0.05738 ( 414) hydrogen bonds : angle 4.39708 ( 1143) link_ALPHA1-3 : bond 0.00974 ( 3) link_ALPHA1-3 : angle 1.20240 ( 9) link_ALPHA1-6 : bond 0.00914 ( 3) link_ALPHA1-6 : angle 1.51063 ( 9) link_BETA1-4 : bond 0.00293 ( 12) link_BETA1-4 : angle 1.88253 ( 36) link_NAG-ASN : bond 0.00369 ( 18) link_NAG-ASN : angle 2.01986 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: A 77 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7142 (t0) REVERT: A 111 LEU cc_start: 0.8697 (tt) cc_final: 0.8474 (tp) REVERT: A 280 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: B 72 GLU cc_start: 0.7467 (mp0) cc_final: 0.7173 (mp0) REVERT: C 41 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: C 70 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8402 (tp) REVERT: C 73 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7886 (t70) REVERT: C 321 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8116 (ttt180) REVERT: C 325 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7257 (mt-10) REVERT: E 27 LYS cc_start: 0.8540 (mttt) cc_final: 0.8117 (mtmm) REVERT: E 31 ASP cc_start: 0.7411 (t0) cc_final: 0.7139 (t70) REVERT: E 41 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: E 70 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8588 (tp) REVERT: E 104 ASP cc_start: 0.8060 (m-30) cc_final: 0.7848 (m-30) REVERT: E 111 LEU cc_start: 0.8716 (tt) cc_final: 0.8455 (tt) REVERT: E 321 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7938 (ttt180) REVERT: D 38 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7571 (mt) REVERT: D 49 ASN cc_start: 0.8015 (m-40) cc_final: 0.7699 (m-40) REVERT: D 62 LYS cc_start: 0.8390 (mttt) cc_final: 0.7999 (mmtt) REVERT: D 121 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7570 (ttpt) REVERT: D 139 LYS cc_start: 0.8511 (tttp) cc_final: 0.8186 (tptm) REVERT: D 168 ASN cc_start: 0.8433 (t0) cc_final: 0.7757 (t0) REVERT: F 37 ASP cc_start: 0.8437 (t0) cc_final: 0.8016 (t70) REVERT: F 115 MET cc_start: 0.9052 (tpt) cc_final: 0.8666 (mmm) REVERT: F 150 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6758 (tt0) REVERT: F 160 ASP cc_start: 0.8276 (m-30) cc_final: 0.8073 (m-30) REVERT: F 168 ASN cc_start: 0.8403 (t0) cc_final: 0.7704 (m-40) outliers start: 52 outliers final: 31 residues processed: 185 average time/residue: 0.6887 time to fit residues: 137.0171 Evaluate side-chains 191 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 83 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 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 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.100016 restraints weight = 14398.320| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.90 r_work: 0.2898 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12330 Z= 0.180 Angle : 0.687 19.538 16791 Z= 0.347 Chirality : 0.049 0.341 1935 Planarity : 0.004 0.047 2130 Dihedral : 7.326 57.953 2322 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.14 % Allowed : 17.33 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1458 helix: 1.81 (0.29), residues: 357 sheet: 0.10 (0.36), residues: 204 loop : -1.97 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 57 TYR 0.009 0.002 TYR C 308 PHE 0.017 0.002 PHE D 9 TRP 0.009 0.001 TRP C 234 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00432 (12276) covalent geometry : angle 0.64413 (16647) SS BOND : bond 0.01090 ( 18) SS BOND : angle 4.18183 ( 36) hydrogen bonds : bond 0.05945 ( 414) hydrogen bonds : angle 4.40860 ( 1143) link_ALPHA1-3 : bond 0.00985 ( 3) link_ALPHA1-3 : angle 1.19009 ( 9) link_ALPHA1-6 : bond 0.00970 ( 3) link_ALPHA1-6 : angle 1.46485 ( 9) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.89963 ( 36) link_NAG-ASN : bond 0.00367 ( 18) link_NAG-ASN : angle 2.04763 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: A 77 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7095 (t0) REVERT: A 111 LEU cc_start: 0.8685 (tt) cc_final: 0.8473 (tp) REVERT: A 280 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: B 72 GLU cc_start: 0.7396 (mp0) cc_final: 0.7095 (mp0) REVERT: C 41 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7685 (tm-30) REVERT: C 70 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8367 (tp) REVERT: C 73 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7900 (t70) REVERT: C 321 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8095 (ttt180) REVERT: C 325 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7207 (mt-10) REVERT: E 27 LYS cc_start: 0.8514 (mttt) cc_final: 0.8077 (mtmm) REVERT: E 41 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: E 70 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8538 (tp) REVERT: E 104 ASP cc_start: 0.8049 (m-30) cc_final: 0.7838 (m-30) REVERT: E 111 LEU cc_start: 0.8699 (tt) cc_final: 0.8446 (tt) REVERT: E 321 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7916 (ttt180) REVERT: D 38 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7536 (mt) REVERT: D 49 ASN cc_start: 0.7980 (m-40) cc_final: 0.7679 (m-40) REVERT: D 62 LYS cc_start: 0.8376 (mttt) cc_final: 0.7970 (mmtt) REVERT: D 121 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7507 (ttpt) REVERT: D 139 LYS cc_start: 0.8509 (tttp) cc_final: 0.8240 (tptm) REVERT: D 168 ASN cc_start: 0.8339 (t0) cc_final: 0.7651 (t0) REVERT: F 37 ASP cc_start: 0.8422 (t0) cc_final: 0.7867 (t70) REVERT: F 115 MET cc_start: 0.9029 (tpt) cc_final: 0.8624 (mmm) REVERT: F 139 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8479 (tptm) REVERT: F 150 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6664 (tt0) REVERT: F 160 ASP cc_start: 0.8286 (m-30) cc_final: 0.8075 (m-30) REVERT: F 168 ASN cc_start: 0.8352 (t0) cc_final: 0.7642 (m-40) outliers start: 53 outliers final: 29 residues processed: 187 average time/residue: 0.6941 time to fit residues: 139.4649 Evaluate side-chains 193 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 16 optimal weight: 0.0470 chunk 115 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN E 295 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.118729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.100970 restraints weight = 14414.994| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.90 r_work: 0.2934 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12330 Z= 0.143 Angle : 0.669 18.218 16791 Z= 0.338 Chirality : 0.048 0.363 1935 Planarity : 0.004 0.044 2130 Dihedral : 7.089 53.830 2322 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.67 % Allowed : 18.11 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1458 helix: 1.93 (0.29), residues: 357 sheet: 0.17 (0.36), residues: 204 loop : -1.90 (0.17), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 57 TYR 0.007 0.001 TYR E 195 PHE 0.014 0.001 PHE D 9 TRP 0.008 0.001 TRP E 234 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00330 (12276) covalent geometry : angle 0.62500 (16647) SS BOND : bond 0.00993 ( 18) SS BOND : angle 4.25045 ( 36) hydrogen bonds : bond 0.05501 ( 414) hydrogen bonds : angle 4.37386 ( 1143) link_ALPHA1-3 : bond 0.00977 ( 3) link_ALPHA1-3 : angle 1.14424 ( 9) link_ALPHA1-6 : bond 0.01003 ( 3) link_ALPHA1-6 : angle 1.34900 ( 9) link_BETA1-4 : bond 0.00322 ( 12) link_BETA1-4 : angle 1.82527 ( 36) link_NAG-ASN : bond 0.00368 ( 18) link_NAG-ASN : angle 1.96820 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: A 77 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7092 (t0) REVERT: A 111 LEU cc_start: 0.8605 (tt) cc_final: 0.8384 (tp) REVERT: A 280 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: B 72 GLU cc_start: 0.7385 (mp0) cc_final: 0.7041 (mp0) REVERT: C 31 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: C 41 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: C 70 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8334 (tp) REVERT: C 73 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7833 (t70) REVERT: C 321 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8037 (ttt180) REVERT: C 325 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7246 (mt-10) REVERT: E 27 LYS cc_start: 0.8509 (mttt) cc_final: 0.8064 (mtmm) REVERT: E 41 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: E 70 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8546 (tp) REVERT: E 104 ASP cc_start: 0.8017 (m-30) cc_final: 0.7805 (m-30) REVERT: E 111 LEU cc_start: 0.8691 (tt) cc_final: 0.8447 (tt) REVERT: E 321 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7910 (ttt180) REVERT: D 38 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7456 (mt) REVERT: D 49 ASN cc_start: 0.7921 (m-40) cc_final: 0.7605 (m-40) REVERT: D 62 LYS cc_start: 0.8364 (mttt) cc_final: 0.7942 (mmtt) REVERT: D 72 GLU cc_start: 0.7653 (mp0) cc_final: 0.7033 (mp0) REVERT: D 123 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.7809 (ttp-170) REVERT: D 139 LYS cc_start: 0.8428 (tttp) cc_final: 0.8053 (tptm) REVERT: D 168 ASN cc_start: 0.8318 (t0) cc_final: 0.7634 (t0) REVERT: F 37 ASP cc_start: 0.8429 (t0) cc_final: 0.7988 (t70) REVERT: F 57 GLU cc_start: 0.7388 (tm-30) cc_final: 0.6902 (pt0) REVERT: F 115 MET cc_start: 0.9065 (tpt) cc_final: 0.8623 (mmm) REVERT: F 121 LYS cc_start: 0.7908 (tttt) cc_final: 0.7429 (tttp) REVERT: F 139 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8369 (tptm) REVERT: F 150 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6636 (tt0) REVERT: F 160 ASP cc_start: 0.8262 (m-30) cc_final: 0.8039 (m-30) REVERT: F 168 ASN cc_start: 0.8354 (t0) cc_final: 0.7643 (m-40) outliers start: 47 outliers final: 25 residues processed: 182 average time/residue: 0.7073 time to fit residues: 138.2648 Evaluate side-chains 187 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 97 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.117925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.100171 restraints weight = 14379.769| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.89 r_work: 0.2859 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12330 Z= 0.169 Angle : 0.682 17.092 16791 Z= 0.346 Chirality : 0.049 0.332 1935 Planarity : 0.004 0.043 2130 Dihedral : 6.955 50.949 2322 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.51 % Allowed : 18.35 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1458 helix: 1.98 (0.29), residues: 354 sheet: 0.14 (0.36), residues: 204 loop : -1.90 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 57 TYR 0.008 0.001 TYR C 308 PHE 0.016 0.002 PHE D 9 TRP 0.009 0.001 TRP C 234 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00402 (12276) covalent geometry : angle 0.63967 (16647) SS BOND : bond 0.00915 ( 18) SS BOND : angle 4.19740 ( 36) hydrogen bonds : bond 0.05804 ( 414) hydrogen bonds : angle 4.40611 ( 1143) link_ALPHA1-3 : bond 0.00954 ( 3) link_ALPHA1-3 : angle 1.16312 ( 9) link_ALPHA1-6 : bond 0.01002 ( 3) link_ALPHA1-6 : angle 1.28937 ( 9) link_BETA1-4 : bond 0.00314 ( 12) link_BETA1-4 : angle 1.88270 ( 36) link_NAG-ASN : bond 0.00365 ( 18) link_NAG-ASN : angle 2.00729 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: A 77 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7139 (t0) REVERT: A 111 LEU cc_start: 0.8656 (tt) cc_final: 0.8435 (tp) REVERT: A 280 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: B 72 GLU cc_start: 0.7448 (mp0) cc_final: 0.7103 (mp0) REVERT: B 97 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8402 (tp30) REVERT: C 31 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: C 70 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 73 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7921 (t70) REVERT: C 321 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8115 (ttt180) REVERT: C 325 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7297 (mt-10) REVERT: E 27 LYS cc_start: 0.8505 (mttt) cc_final: 0.8080 (mtmm) REVERT: E 41 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: E 70 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8593 (tp) REVERT: E 111 LEU cc_start: 0.8735 (tt) cc_final: 0.8478 (tt) REVERT: E 321 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7986 (ttt180) REVERT: D 38 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7517 (mt) REVERT: D 49 ASN cc_start: 0.8018 (m-40) cc_final: 0.7732 (m-40) REVERT: D 62 LYS cc_start: 0.8386 (mttt) cc_final: 0.8006 (mmtt) REVERT: D 72 GLU cc_start: 0.7699 (mp0) cc_final: 0.7081 (mp0) REVERT: D 139 LYS cc_start: 0.8513 (tttp) cc_final: 0.8238 (tptm) REVERT: D 168 ASN cc_start: 0.8341 (t0) cc_final: 0.7675 (t0) REVERT: F 57 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6977 (pt0) REVERT: F 115 MET cc_start: 0.9037 (tpt) cc_final: 0.8615 (mmm) REVERT: F 121 LYS cc_start: 0.8086 (tttt) cc_final: 0.7609 (tttp) REVERT: F 139 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8508 (tptm) REVERT: F 150 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6704 (tt0) REVERT: F 160 ASP cc_start: 0.8271 (m-30) cc_final: 0.8049 (m-30) REVERT: F 168 ASN cc_start: 0.8389 (t0) cc_final: 0.7680 (m-40) outliers start: 45 outliers final: 27 residues processed: 185 average time/residue: 0.6709 time to fit residues: 133.3876 Evaluate side-chains 190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 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 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.118225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.100499 restraints weight = 14482.847| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.89 r_work: 0.2863 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 : 0.004 0.037 12330 Z= 0.159 Angle : 0.676 16.173 16791 Z= 0.343 Chirality : 0.048 0.357 1935 Planarity : 0.004 0.040 2130 Dihedral : 6.791 48.440 2322 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.51 % Allowed : 18.27 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1458 helix: 2.01 (0.29), residues: 354 sheet: 0.19 (0.32), residues: 261 loop : -1.98 (0.17), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.008 0.001 TYR C 308 PHE 0.015 0.001 PHE D 9 TRP 0.008 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00374 (12276) covalent geometry : angle 0.63272 (16647) SS BOND : bond 0.00878 ( 18) SS BOND : angle 4.27965 ( 36) hydrogen bonds : bond 0.05696 ( 414) hydrogen bonds : angle 4.40030 ( 1143) link_ALPHA1-3 : bond 0.00974 ( 3) link_ALPHA1-3 : angle 1.13976 ( 9) link_ALPHA1-6 : bond 0.01057 ( 3) link_ALPHA1-6 : angle 1.21791 ( 9) link_BETA1-4 : bond 0.00308 ( 12) link_BETA1-4 : angle 1.83541 ( 36) link_NAG-ASN : bond 0.00364 ( 18) link_NAG-ASN : angle 1.97221 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: A 77 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7142 (t0) REVERT: A 111 LEU cc_start: 0.8652 (tt) cc_final: 0.8430 (tp) REVERT: A 280 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: B 72 GLU cc_start: 0.7413 (mp0) cc_final: 0.7088 (mp0) REVERT: B 97 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: C 31 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7372 (t0) REVERT: C 41 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: C 70 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8377 (tp) REVERT: C 73 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7911 (t70) REVERT: C 321 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8132 (ttt180) REVERT: E 27 LYS cc_start: 0.8504 (mttt) cc_final: 0.8073 (mtmm) REVERT: E 41 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: E 70 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8586 (tp) REVERT: E 111 LEU cc_start: 0.8729 (tt) cc_final: 0.8467 (tt) REVERT: E 321 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: D 38 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7555 (mt) REVERT: D 49 ASN cc_start: 0.8014 (m-40) cc_final: 0.7735 (m-40) REVERT: D 62 LYS cc_start: 0.8376 (mttt) cc_final: 0.7972 (mmtt) REVERT: D 121 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7548 (ttpt) REVERT: D 139 LYS cc_start: 0.8512 (tttp) cc_final: 0.8230 (tptm) REVERT: D 168 ASN cc_start: 0.8342 (t0) cc_final: 0.7674 (t0) REVERT: F 57 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6971 (pt0) REVERT: F 115 MET cc_start: 0.9039 (tpt) cc_final: 0.8619 (mmm) REVERT: F 121 LYS cc_start: 0.8095 (tttt) cc_final: 0.7599 (tttp) REVERT: F 139 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8413 (tptm) REVERT: F 150 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6691 (tt0) REVERT: F 160 ASP cc_start: 0.8261 (m-30) cc_final: 0.8052 (m-30) REVERT: F 168 ASN cc_start: 0.8386 (t0) cc_final: 0.7665 (m-40) outliers start: 45 outliers final: 25 residues processed: 180 average time/residue: 0.6631 time to fit residues: 128.1964 Evaluate side-chains 189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 chunk 101 optimal weight: 0.9980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN D 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.102246 restraints weight = 14391.360| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.89 r_work: 0.2937 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12330 Z= 0.126 Angle : 0.636 15.219 16791 Z= 0.323 Chirality : 0.046 0.308 1935 Planarity : 0.004 0.037 2130 Dihedral : 6.558 46.457 2322 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.36 % Allowed : 18.35 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1458 helix: 2.12 (0.29), residues: 357 sheet: 0.38 (0.35), residues: 231 loop : -1.90 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 57 TYR 0.007 0.001 TYR C 195 PHE 0.013 0.001 PHE E 120 TRP 0.007 0.001 TRP E 234 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00287 (12276) covalent geometry : angle 0.59467 (16647) SS BOND : bond 0.00700 ( 18) SS BOND : angle 4.04468 ( 36) hydrogen bonds : bond 0.05117 ( 414) hydrogen bonds : angle 4.32149 ( 1143) link_ALPHA1-3 : bond 0.00992 ( 3) link_ALPHA1-3 : angle 1.13214 ( 9) link_ALPHA1-6 : bond 0.01103 ( 3) link_ALPHA1-6 : angle 1.16854 ( 9) link_BETA1-4 : bond 0.00327 ( 12) link_BETA1-4 : angle 1.75688 ( 36) link_NAG-ASN : bond 0.00367 ( 18) link_NAG-ASN : angle 1.86494 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4178.27 seconds wall clock time: 72 minutes 1.94 seconds (4321.94 seconds total)