Starting phenix.real_space_refine on Fri Sep 11 23:05:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y5g_10696/09_2026/6y5g_10696.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5g_10696/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6y5g_10696/09_2026/6y5g_10696.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y5g_10696/09_2026/6y5g_10696.cif" model { file = "/net/cci-nas-00/data/ceres_data/6y5g_10696/09_2026/6y5g_10696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5g_10696/09_2026/6y5g_10696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y5g_10696/09_2026/6y5g_10696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5g_10696/09_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 2.67, per 1000 atoms: 0.22 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: 1.19 Conformation dependent library (CDL) restraints added in 526.5 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: 0.29 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: 1.53 Time building geometry restraints manager: 1.46 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 - 17.87: 6427 17.87 - 35.73: 497 35.73 - 53.60: 126 53.60 - 71.47: 12 71.47 - 89.33: 27 Dihedral angle restraints: 7089 sinusoidal: 2871 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 7086 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: 0.04 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.930 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 14.323 89.331 4329 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/Z covalent geometry : bond 0.00522 / 0.24 (12276) covalent geometry : angle 0.66089 / 0.34 (16647) SS BOND : bond 0.03120 / 1.80 ( 18) SS BOND : angle 1.53718 / 1.08 ( 36) hydrogen bonds : bond 0.16548 / 11.94 ( 414) hydrogen bonds : angle 6.16138 / 4.25 ( 1143) link_ALPHA1-3 : bond 0.06558 / 3.29 ( 3) link_ALPHA1-3 : angle 30.53201 / 21.37 ( 9) link_ALPHA1-6 : bond 0.06532 / 3.28 ( 3) link_ALPHA1-6 : angle 19.34584 / 13.08 ( 9) link_BETA1-4 : bond 0.06544 / 4.04 ( 12) link_BETA1-4 : angle 31.34804 / 21.88 ( 36) link_NAG-ASN : bond 0.00313 / 0.19 ( 18) link_NAG-ASN : angle 2.07196 / 1.24 ( 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 : 0.426 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: 0.6085 time to fit residues: 154.9271 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 : 0.412 ------------------------------------------------------------------------------- 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... 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 = 0.3216 r_free = 0.3216 target = 0.117970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.100077 restraints weight = 14241.836| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.89 r_work: 0.2845 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12330 Z= 0.187 Angle : 0.646 6.782 16791 Z= 0.323 Chirality : 0.047 0.218 1935 Planarity : 0.005 0.046 2130 Dihedral : 4.695 22.428 1584 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.43 % Allowed : 14.91 % Favored : 81.65 % 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: -1.91 (0.19), residues: 1458 helix: 0.68 (0.28), residues: 375 sheet: -0.63 (0.35), residues: 204 loop : -2.47 (0.15), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.011 0.002 TYR C 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/Z covalent geometry : bond 0.00451 / 0.19 (12276) covalent geometry : angle 0.61955 / 0.32 (16647) SS BOND : bond 0.00706 / 0.47 ( 18) SS BOND : angle 2.16835 / 1.58 ( 36) hydrogen bonds : bond 0.06292 / 4.46 ( 414) hydrogen bonds : angle 4.75455 / 3.28 ( 1143) link_ALPHA1-3 : bond 0.00676 / 0.34 ( 3) link_ALPHA1-3 : angle 1.52333 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00436 / 0.22 ( 3) link_ALPHA1-6 : angle 2.10223 / 1.42 ( 9) link_BETA1-4 : bond 0.00347 / 0.20 ( 12) link_BETA1-4 : angle 1.97650 / 1.31 ( 36) link_NAG-ASN : bond 0.00358 / 0.22 ( 18) link_NAG-ASN : angle 2.09796 / 1.21 ( 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 224 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7065 (t0) REVERT: A 111 LEU cc_start: 0.8678 (tt) cc_final: 0.8412 (tp) REVERT: A 321 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8023 (ttt180) REVERT: B 54 ARG cc_start: 0.8024 (tpt90) cc_final: 0.5565 (tmt-80) REVERT: B 72 GLU cc_start: 0.7654 (mp0) cc_final: 0.7278 (mp0) REVERT: C 41 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 62 ILE cc_start: 0.8852 (mt) cc_final: 0.8584 (mp) REVERT: C 82 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8361 (mm-30) REVERT: C 321 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8074 (ttt180) REVERT: C 325 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7389 (mt-10) REVERT: E 27 LYS cc_start: 0.8545 (mttt) cc_final: 0.8125 (mtmm) REVERT: E 41 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: E 111 LEU cc_start: 0.8679 (tt) cc_final: 0.8383 (tt) REVERT: E 139 CYS cc_start: 0.8329 (t) cc_final: 0.7830 (t) REVERT: E 321 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7916 (ttt180) REVERT: D 49 ASN cc_start: 0.8010 (m-40) cc_final: 0.7739 (m-40) REVERT: D 62 LYS cc_start: 0.8386 (mttt) cc_final: 0.7948 (mmtt) REVERT: D 115 MET cc_start: 0.9000 (tpt) cc_final: 0.8669 (mmm) REVERT: D 121 LYS cc_start: 0.8068 (ttpt) cc_final: 0.7704 (ttmm) REVERT: D 131 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: D 139 LYS cc_start: 0.8493 (tttp) cc_final: 0.8201 (tptm) REVERT: F 37 ASP cc_start: 0.8404 (t0) cc_final: 0.8064 (t70) REVERT: F 115 MET cc_start: 0.9107 (tpt) cc_final: 0.8703 (mmm) REVERT: F 150 GLU cc_start: 0.7065 (mt-10) cc_final: 0.6765 (tt0) REVERT: F 160 ASP cc_start: 0.8235 (m-30) cc_final: 0.8007 (m-30) REVERT: F 168 ASN cc_start: 0.8293 (t0) cc_final: 0.7703 (m-40) outliers start: 44 outliers final: 16 residues processed: 203 average time/residue: 0.6037 time to fit residues: 132.0590 Evaluate side-chains 184 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 0.6980 chunk 80 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 295 GLN C 216 ASN E 295 GLN ** 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 = 0.3204 r_free = 0.3204 target = 0.117081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.099061 restraints weight = 14514.728| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.92 r_work: 0.2855 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12330 Z= 0.214 Angle : 0.669 7.505 16791 Z= 0.341 Chirality : 0.048 0.249 1935 Planarity : 0.005 0.039 2130 Dihedral : 4.882 36.621 1584 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: -1.45 (0.20), residues: 1458 helix: 1.28 (0.28), residues: 357 sheet: -0.17 (0.36), residues: 204 loop : -2.26 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 57 TYR 0.011 0.002 TYR C 308 PHE 0.019 0.002 PHE D 9 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.21 (12276) covalent geometry : angle 0.63879 / 0.33 (16647) SS BOND : bond 0.00953 / 0.61 ( 18) SS BOND : angle 2.97746 / 2.23 ( 36) hydrogen bonds : bond 0.06589 / 4.65 ( 414) hydrogen bonds : angle 4.64077 / 3.21 ( 1143) link_ALPHA1-3 : bond 0.00324 / 0.16 ( 3) link_ALPHA1-3 : angle 1.65469 / 1.21 ( 9) link_ALPHA1-6 : bond 0.00369 / 0.19 ( 3) link_ALPHA1-6 : angle 1.79779 / 1.18 ( 9) link_BETA1-4 : bond 0.00317 / 0.21 ( 12) link_BETA1-4 : angle 1.86546 / 1.22 ( 36) link_NAG-ASN : bond 0.00338 / 0.21 ( 18) link_NAG-ASN : angle 2.05389 / 1.15 ( 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 : 0.491 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: A 77 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7113 (t0) REVERT: A 111 LEU cc_start: 0.8681 (tt) cc_final: 0.8420 (tp) REVERT: A 280 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: A 321 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8001 (ttt180) REVERT: A 325 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7020 (mt-10) REVERT: B 54 ARG cc_start: 0.7918 (tpt90) cc_final: 0.5418 (tmt-80) REVERT: B 72 GLU cc_start: 0.7557 (mp0) cc_final: 0.7160 (mp0) REVERT: C 70 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8440 (tp) REVERT: C 82 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8360 (mm-30) REVERT: C 321 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8089 (ttt180) REVERT: C 325 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7304 (mt-10) REVERT: E 27 LYS cc_start: 0.8503 (mttt) cc_final: 0.8067 (mtmm) REVERT: E 31 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6969 (t0) REVERT: E 41 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: E 70 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8421 (tp) REVERT: E 111 LEU cc_start: 0.8683 (tt) cc_final: 0.8396 (tt) REVERT: E 321 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7905 (ttt180) REVERT: D 38 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7610 (mt) REVERT: D 49 ASN cc_start: 0.8029 (m-40) cc_final: 0.7731 (m-40) REVERT: D 62 LYS cc_start: 0.8398 (mttt) cc_final: 0.7971 (mmtt) REVERT: D 120 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: D 139 LYS cc_start: 0.8591 (tttp) cc_final: 0.8180 (tptm) REVERT: F 37 ASP cc_start: 0.8384 (t0) cc_final: 0.8044 (t70) REVERT: F 115 MET cc_start: 0.9042 (tpt) cc_final: 0.8638 (mmm) REVERT: F 139 LYS cc_start: 0.8604 (tttm) cc_final: 0.8378 (tptm) REVERT: F 150 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6697 (tt0) REVERT: F 160 ASP cc_start: 0.8301 (m-30) cc_final: 0.8073 (m-30) REVERT: F 168 ASN cc_start: 0.8328 (t0) cc_final: 0.7643 (m-40) outliers start: 51 outliers final: 19 residues processed: 199 average time/residue: 0.5564 time to fit residues: 119.7526 Evaluate side-chains 187 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU 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 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: 0.5980 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN 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 = 0.3215 r_free = 0.3215 target = 0.117929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.100087 restraints weight = 14282.236| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.87 r_work: 0.2910 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12330 Z= 0.167 Angle : 0.618 8.351 16791 Z= 0.315 Chirality : 0.046 0.257 1935 Planarity : 0.004 0.045 2130 Dihedral : 4.861 37.082 1584 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.90 % Allowed : 16.94 % Favored : 79.16 % 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: -1.19 (0.20), residues: 1458 helix: 1.53 (0.29), residues: 357 sheet: 0.00 (0.36), residues: 204 loop : -2.11 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 57 TYR 0.008 0.001 TYR C 308 PHE 0.018 0.002 PHE D 9 TRP 0.009 0.001 TRP E 234 HIS 0.003 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (12276) covalent geometry : angle 0.58743 / 0.31 (16647) SS BOND : bond 0.00887 / 0.55 ( 18) SS BOND : angle 2.92014 / 2.19 ( 36) hydrogen bonds : bond 0.05864 / 4.12 ( 414) hydrogen bonds : angle 4.47378 / 3.10 ( 1143) link_ALPHA1-3 : bond 0.00447 / 0.22 ( 3) link_ALPHA1-3 : angle 1.42461 / 1.01 ( 9) link_ALPHA1-6 : bond 0.00577 / 0.29 ( 3) link_ALPHA1-6 : angle 1.65000 / 1.10 ( 9) link_BETA1-4 : bond 0.00350 / 0.23 ( 12) link_BETA1-4 : angle 1.72675 / 1.13 ( 36) link_NAG-ASN : bond 0.00335 / 0.20 ( 18) link_NAG-ASN : angle 1.94511 / 1.07 ( 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 211 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: A 77 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7074 (t0) REVERT: A 111 LEU cc_start: 0.8669 (tt) cc_final: 0.8415 (tp) REVERT: A 280 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: B 72 GLU cc_start: 0.7542 (mp0) cc_final: 0.7195 (mp0) REVERT: C 41 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: C 70 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8388 (tp) REVERT: C 73 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7873 (t70) REVERT: C 82 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8344 (mm-30) REVERT: C 321 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8086 (ttt180) REVERT: C 325 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7228 (mt-10) REVERT: E 27 LYS cc_start: 0.8542 (mttt) cc_final: 0.8127 (mtmm) REVERT: E 31 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.7033 (t0) REVERT: E 41 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: E 70 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8445 (tp) REVERT: E 111 LEU cc_start: 0.8689 (tt) cc_final: 0.8415 (tt) REVERT: E 321 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7930 (ttt180) REVERT: E 325 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6916 (mt-10) REVERT: D 38 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7582 (mt) REVERT: D 49 ASN cc_start: 0.8064 (m-40) cc_final: 0.7772 (m-40) REVERT: D 62 LYS cc_start: 0.8379 (mttt) cc_final: 0.7974 (mmtt) REVERT: D 139 LYS cc_start: 0.8609 (tttp) cc_final: 0.8190 (tptm) REVERT: F 37 ASP cc_start: 0.8392 (t0) cc_final: 0.7999 (t70) REVERT: F 115 MET cc_start: 0.9083 (tpt) cc_final: 0.8715 (mmm) REVERT: F 139 LYS cc_start: 0.8661 (tttm) cc_final: 0.8406 (tptm) REVERT: F 150 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6687 (tt0) REVERT: F 160 ASP cc_start: 0.8268 (m-30) cc_final: 0.8047 (m-30) REVERT: F 168 ASN cc_start: 0.8385 (t0) cc_final: 0.7666 (m-40) outliers start: 50 outliers final: 18 residues processed: 193 average time/residue: 0.6110 time to fit residues: 126.9773 Evaluate side-chains 180 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 277 CYS Chi-restraints excluded: chain A residue 280 GLU 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 101 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 31 ASP 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 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 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: 0.0770 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3216 r_free = 0.3216 target = 0.118009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.100035 restraints weight = 14475.313| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.92 r_work: 0.2890 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2050 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= 0.163 Angle : 0.669 19.502 16791 Z= 0.339 Chirality : 0.048 0.370 1935 Planarity : 0.004 0.044 2130 Dihedral : 4.769 37.794 1584 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.45 % Allowed : 16.78 % Favored : 78.77 % 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: -1.01 (0.20), residues: 1458 helix: 1.74 (0.29), residues: 354 sheet: 0.21 (0.39), residues: 174 loop : -1.97 (0.16), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.009 0.001 TYR A 195 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/Z covalent geometry : bond 0.00386 / 0.16 (12276) covalent geometry : angle 0.62810 / 0.32 (16647) SS BOND : bond 0.01063 / 0.63 ( 18) SS BOND : angle 4.10364 / 2.66 ( 36) hydrogen bonds : bond 0.05774 / 4.06 ( 414) hydrogen bonds : angle 4.44049 / 3.08 ( 1143) link_ALPHA1-3 : bond 0.00425 / 0.21 ( 3) link_ALPHA1-3 : angle 1.45450 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00500 / 0.25 ( 3) link_ALPHA1-6 : angle 1.54513 / 1.03 ( 9) link_BETA1-4 : bond 0.00325 / 0.21 ( 12) link_BETA1-4 : angle 1.72202 / 1.13 ( 36) link_NAG-ASN : bond 0.00335 / 0.20 ( 18) link_NAG-ASN : angle 1.92375 / 1.06 ( 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 210 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 77 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7110 (t0) REVERT: A 111 LEU cc_start: 0.8697 (tt) cc_final: 0.8469 (tp) REVERT: A 280 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: B 72 GLU cc_start: 0.7466 (mp0) cc_final: 0.7197 (mp0) REVERT: C 41 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: C 70 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8434 (tp) REVERT: C 73 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7902 (t70) REVERT: C 82 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8371 (mm-30) REVERT: C 321 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8137 (ttt180) REVERT: E 27 LYS cc_start: 0.8548 (mttt) cc_final: 0.8143 (mtmm) REVERT: E 41 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: E 70 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8554 (tp) REVERT: E 111 LEU cc_start: 0.8689 (tt) cc_final: 0.8421 (tt) REVERT: E 321 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: E 325 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6972 (mt-10) REVERT: D 38 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7621 (mt) REVERT: D 49 ASN cc_start: 0.8029 (m-40) cc_final: 0.7732 (m-40) REVERT: D 62 LYS cc_start: 0.8389 (mttt) cc_final: 0.7992 (mmtt) REVERT: D 123 ARG cc_start: 0.8283 (ttp-170) cc_final: 0.7971 (ttp-170) REVERT: D 139 LYS cc_start: 0.8591 (tttp) cc_final: 0.8229 (tptm) REVERT: F 37 ASP cc_start: 0.8447 (t0) cc_final: 0.8057 (t70) REVERT: F 115 MET cc_start: 0.9101 (tpt) cc_final: 0.8711 (mmm) REVERT: F 139 LYS cc_start: 0.8654 (tttm) cc_final: 0.8403 (tptm) REVERT: F 150 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6732 (tt0) REVERT: F 160 ASP cc_start: 0.8304 (m-30) cc_final: 0.8086 (m-30) REVERT: F 168 ASN cc_start: 0.8404 (t0) cc_final: 0.7709 (m-40) outliers start: 57 outliers final: 23 residues processed: 191 average time/residue: 0.5714 time to fit residues: 117.6060 Evaluate side-chains 183 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 216 ASN Chi-restraints excluded: chain A residue 242 VAL 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 143 LYS 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 101 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 195 TYR Chi-restraints excluded: chain E residue 206 THR 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 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 0.0470 chunk 51 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3236 r_free = 0.3236 target = 0.119547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.101474 restraints weight = 14349.862| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.92 r_work: 0.2939 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12330 Z= 0.131 Angle : 0.629 15.394 16791 Z= 0.320 Chirality : 0.046 0.336 1935 Planarity : 0.004 0.047 2130 Dihedral : 4.677 35.533 1584 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.28 % Allowed : 17.80 % Favored : 78.92 % 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: -0.86 (0.20), residues: 1458 helix: 1.89 (0.29), residues: 360 sheet: 0.33 (0.39), residues: 174 loop : -1.91 (0.16), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 57 TYR 0.007 0.001 TYR A 195 PHE 0.013 0.001 PHE D 9 TRP 0.007 0.001 TRP E 234 HIS 0.003 0.001 HIS F 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12276) covalent geometry : angle 0.58972 / 0.31 (16647) SS BOND : bond 0.00869 / 0.52 ( 18) SS BOND : angle 3.85494 / 2.47 ( 36) hydrogen bonds : bond 0.05237 / 3.66 ( 414) hydrogen bonds : angle 4.31823 / 3.00 ( 1143) link_ALPHA1-3 : bond 0.00468 / 0.24 ( 3) link_ALPHA1-3 : angle 1.44765 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00488 / 0.25 ( 3) link_ALPHA1-6 : angle 1.46681 / 0.98 ( 9) link_BETA1-4 : bond 0.00308 / 0.19 ( 12) link_BETA1-4 : angle 1.67346 / 1.09 ( 36) link_NAG-ASN : bond 0.00344 / 0.21 ( 18) link_NAG-ASN : angle 1.82200 / 1.00 ( 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 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: A 77 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7038 (t0) REVERT: A 111 LEU cc_start: 0.8592 (tt) cc_final: 0.8377 (tp) REVERT: A 280 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: B 72 GLU cc_start: 0.7365 (mp0) cc_final: 0.7012 (mp0) REVERT: B 74 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8003 (mp0) REVERT: B 123 ARG cc_start: 0.8230 (ttp80) cc_final: 0.8017 (ttp80) REVERT: C 41 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: C 70 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 73 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7804 (t70) REVERT: C 82 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8315 (mm-30) REVERT: C 321 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8094 (ttt180) REVERT: C 325 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7243 (mt-10) REVERT: E 27 LYS cc_start: 0.8521 (mttt) cc_final: 0.8156 (mtmm) REVERT: E 41 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: E 70 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8562 (tp) REVERT: E 111 LEU cc_start: 0.8699 (tt) cc_final: 0.8452 (tt) REVERT: E 321 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7933 (ttt180) REVERT: E 325 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6923 (mt-10) REVERT: D 38 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7432 (mt) REVERT: D 49 ASN cc_start: 0.7917 (m-40) cc_final: 0.7602 (m-40) REVERT: D 62 LYS cc_start: 0.8362 (mttt) cc_final: 0.7945 (mmtt) REVERT: D 139 LYS cc_start: 0.8469 (tttp) cc_final: 0.8143 (tptm) REVERT: D 168 ASN cc_start: 0.8385 (t0) cc_final: 0.7708 (t0) REVERT: F 115 MET cc_start: 0.9054 (tpt) cc_final: 0.8696 (mmm) REVERT: F 150 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6643 (tt0) REVERT: F 160 ASP cc_start: 0.8214 (m-30) cc_final: 0.8006 (m-30) REVERT: F 168 ASN cc_start: 0.8357 (t0) cc_final: 0.7661 (m-40) outliers start: 42 outliers final: 22 residues processed: 181 average time/residue: 0.6167 time to fit residues: 120.1911 Evaluate side-chains 176 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 119 GLU 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 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 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 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 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: 0.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3215 r_free = 0.3215 target = 0.117950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.100073 restraints weight = 14368.072| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.89 r_work: 0.2912 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12330 Z= 0.189 Angle : 0.691 17.832 16791 Z= 0.350 Chirality : 0.048 0.365 1935 Planarity : 0.004 0.043 2130 Dihedral : 4.802 35.027 1584 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.67 % Allowed : 17.72 % 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: -0.91 (0.20), residues: 1458 helix: 1.82 (0.28), residues: 360 sheet: 0.13 (0.36), residues: 204 loop : -1.96 (0.17), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.010 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/Z covalent geometry : bond 0.00455 / 0.19 (12276) covalent geometry : angle 0.65035 / 0.34 (16647) SS BOND : bond 0.01021 / 0.61 ( 18) SS BOND : angle 4.19986 / 2.73 ( 36) hydrogen bonds : bond 0.05977 / 4.20 ( 414) hydrogen bonds : angle 4.39376 / 3.05 ( 1143) link_ALPHA1-3 : bond 0.00418 / 0.21 ( 3) link_ALPHA1-3 : angle 1.44756 / 1.03 ( 9) link_ALPHA1-6 : bond 0.00454 / 0.23 ( 3) link_ALPHA1-6 : angle 1.53946 / 1.02 ( 9) link_BETA1-4 : bond 0.00281 / 0.18 ( 12) link_BETA1-4 : angle 1.76400 / 1.15 ( 36) link_NAG-ASN : bond 0.00322 / 0.20 ( 18) link_NAG-ASN : angle 1.92480 / 1.07 ( 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 201 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 77 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7114 (t0) REVERT: A 111 LEU cc_start: 0.8711 (tt) cc_final: 0.8503 (tp) REVERT: A 280 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: B 72 GLU cc_start: 0.7432 (mp0) cc_final: 0.7077 (mp0) REVERT: B 97 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8357 (tp30) REVERT: C 31 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: C 41 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: C 70 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8411 (tp) REVERT: C 73 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7900 (t70) REVERT: C 82 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8342 (mm-30) REVERT: C 321 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8085 (ttt180) REVERT: C 325 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7246 (mt-10) REVERT: E 27 LYS cc_start: 0.8525 (mttt) cc_final: 0.8091 (mtmm) REVERT: E 41 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: E 70 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8434 (tp) REVERT: E 111 LEU cc_start: 0.8727 (tt) cc_final: 0.8466 (tt) REVERT: E 321 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7928 (ttt180) REVERT: D 38 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7555 (mt) REVERT: D 49 ASN cc_start: 0.8015 (m-40) cc_final: 0.7713 (m-40) REVERT: D 62 LYS cc_start: 0.8390 (mttt) cc_final: 0.7996 (mmtt) REVERT: D 139 LYS cc_start: 0.8465 (tttp) cc_final: 0.8109 (tptm) REVERT: D 168 ASN cc_start: 0.8360 (t0) cc_final: 0.7689 (t0) REVERT: F 37 ASP cc_start: 0.8437 (t0) cc_final: 0.8045 (t70) REVERT: F 57 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6887 (pt0) REVERT: F 115 MET cc_start: 0.9037 (tpt) cc_final: 0.8614 (mmm) REVERT: F 121 LYS cc_start: 0.8040 (tttt) cc_final: 0.7562 (tttp) REVERT: F 139 LYS cc_start: 0.8690 (tttm) cc_final: 0.8340 (tptm) REVERT: F 150 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6695 (tt0) REVERT: F 160 ASP cc_start: 0.8279 (m-30) cc_final: 0.8074 (m-30) REVERT: F 168 ASN cc_start: 0.8380 (t0) cc_final: 0.7675 (m-40) outliers start: 47 outliers final: 24 residues processed: 186 average time/residue: 0.5824 time to fit residues: 117.0073 Evaluate side-chains 189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 101 ASP 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 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: 1.9990 chunk 133 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN 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 = 0.3230 r_free = 0.3230 target = 0.119208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.101162 restraints weight = 14300.107| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.91 r_work: 0.2910 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12330 Z= 0.143 Angle : 0.649 15.635 16791 Z= 0.330 Chirality : 0.046 0.333 1935 Planarity : 0.004 0.040 2130 Dihedral : 4.701 33.668 1584 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.75 % Allowed : 17.88 % Favored : 78.38 % 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: -0.79 (0.20), residues: 1458 helix: 1.95 (0.29), residues: 360 sheet: 0.20 (0.36), residues: 204 loop : -1.90 (0.17), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 57 TYR 0.007 0.001 TYR C 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/Z covalent geometry : bond 0.00333 / 0.14 (12276) covalent geometry : angle 0.60887 / 0.32 (16647) SS BOND : bond 0.00857 / 0.52 ( 18) SS BOND : angle 4.02423 / 2.59 ( 36) hydrogen bonds : bond 0.05466 / 3.83 ( 414) hydrogen bonds : angle 4.35583 / 3.02 ( 1143) link_ALPHA1-3 : bond 0.00463 / 0.23 ( 3) link_ALPHA1-3 : angle 1.45794 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00472 / 0.24 ( 3) link_ALPHA1-6 : angle 1.50248 / 1.01 ( 9) link_BETA1-4 : bond 0.00296 / 0.19 ( 12) link_BETA1-4 : angle 1.68907 / 1.10 ( 36) link_NAG-ASN : bond 0.00315 / 0.19 ( 18) link_NAG-ASN : angle 1.85155 / 1.02 ( 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: 48 poor density : 150 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: A 77 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7070 (t0) REVERT: A 111 LEU cc_start: 0.8603 (tt) cc_final: 0.8382 (tp) REVERT: A 280 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8083 (mm-30) REVERT: B 72 GLU cc_start: 0.7359 (mp0) cc_final: 0.7058 (mp0) REVERT: B 97 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8296 (tp30) REVERT: B 123 ARG cc_start: 0.8239 (ttp80) cc_final: 0.8035 (ttp80) REVERT: C 31 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7309 (t0) REVERT: C 41 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: C 70 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8361 (tp) REVERT: C 73 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7841 (t70) REVERT: C 82 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8291 (mm-30) REVERT: C 321 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8043 (ttt180) REVERT: C 325 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7221 (mt-10) REVERT: E 27 LYS cc_start: 0.8497 (mttt) cc_final: 0.8122 (mtmm) REVERT: E 41 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: E 70 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8554 (tp) REVERT: E 111 LEU cc_start: 0.8703 (tt) cc_final: 0.8460 (tt) REVERT: E 321 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7921 (ttt180) REVERT: D 38 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7456 (mt) REVERT: D 49 ASN cc_start: 0.7967 (m-40) cc_final: 0.7668 (m-40) REVERT: D 62 LYS cc_start: 0.8368 (mttt) cc_final: 0.7951 (mmtt) REVERT: D 72 GLU cc_start: 0.7614 (mp0) cc_final: 0.6994 (mp0) REVERT: D 139 LYS cc_start: 0.8427 (tttp) cc_final: 0.8079 (tptm) REVERT: D 168 ASN cc_start: 0.8327 (t0) cc_final: 0.7644 (t0) REVERT: F 37 ASP cc_start: 0.8448 (t0) cc_final: 0.8030 (t70) REVERT: F 57 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6850 (pt0) REVERT: F 115 MET cc_start: 0.9061 (tpt) cc_final: 0.8610 (mmm) REVERT: F 121 LYS cc_start: 0.8017 (tttt) cc_final: 0.7535 (tttp) REVERT: F 139 LYS cc_start: 0.8630 (tttm) cc_final: 0.8265 (tptm) REVERT: F 150 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6640 (tt0) REVERT: F 160 ASP cc_start: 0.8238 (m-30) cc_final: 0.8017 (m-30) REVERT: F 168 ASN cc_start: 0.8365 (t0) cc_final: 0.7618 (m-40) outliers start: 48 outliers final: 26 residues processed: 183 average time/residue: 0.5924 time to fit residues: 116.9212 Evaluate side-chains 185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR 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 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 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 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: 0.6980 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 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 = 0.3210 r_free = 0.3210 target = 0.117614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099858 restraints weight = 14311.355| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.87 r_work: 0.2855 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12330 Z= 0.194 Angle : 0.718 19.158 16791 Z= 0.363 Chirality : 0.049 0.384 1935 Planarity : 0.004 0.044 2130 Dihedral : 4.908 33.898 1584 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.28 % Allowed : 18.27 % Favored : 78.45 % 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: -0.82 (0.21), residues: 1458 helix: 1.92 (0.28), residues: 354 sheet: 0.03 (0.32), residues: 255 loop : -1.94 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 57 TYR 0.010 0.002 TYR C 308 PHE 0.018 0.002 PHE D 9 TRP 0.010 0.001 TRP C 234 HIS 0.004 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 (12276) covalent geometry : angle 0.67436 / 0.35 (16647) SS BOND : bond 0.01007 / 0.61 ( 18) SS BOND : angle 4.50248 / 2.90 ( 36) hydrogen bonds : bond 0.06162 / 4.32 ( 414) hydrogen bonds : angle 4.47593 / 3.10 ( 1143) link_ALPHA1-3 : bond 0.00409 / 0.20 ( 3) link_ALPHA1-3 : angle 1.45255 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00415 / 0.21 ( 3) link_ALPHA1-6 : angle 1.53389 / 1.01 ( 9) link_BETA1-4 : bond 0.00270 / 0.17 ( 12) link_BETA1-4 : angle 1.77377 / 1.15 ( 36) link_NAG-ASN : bond 0.00309 / 0.19 ( 18) link_NAG-ASN : angle 1.95773 / 1.10 ( 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 195 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: A 77 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7118 (t0) REVERT: A 111 LEU cc_start: 0.8703 (tt) cc_final: 0.8492 (tp) REVERT: A 280 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8103 (mm-30) REVERT: B 72 GLU cc_start: 0.7393 (mp0) cc_final: 0.7036 (mp0) REVERT: C 31 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7356 (t0) REVERT: C 41 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: C 70 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8431 (tp) REVERT: C 73 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7993 (t70) REVERT: C 82 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8310 (mm-30) REVERT: C 321 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8077 (ttt180) REVERT: C 325 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7268 (mt-10) REVERT: E 27 LYS cc_start: 0.8501 (mttt) cc_final: 0.8061 (mtmm) REVERT: E 41 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: E 70 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8425 (tp) REVERT: E 111 LEU cc_start: 0.8725 (tt) cc_final: 0.8471 (tt) REVERT: E 321 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7945 (ttt180) REVERT: D 38 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7570 (mt) REVERT: D 49 ASN cc_start: 0.7978 (m-40) cc_final: 0.7691 (m-40) REVERT: D 62 LYS cc_start: 0.8380 (mttt) cc_final: 0.7980 (mmtt) REVERT: D 72 GLU cc_start: 0.7649 (mp0) cc_final: 0.7027 (mp0) REVERT: D 139 LYS cc_start: 0.8496 (tttp) cc_final: 0.8182 (tptm) REVERT: D 168 ASN cc_start: 0.8344 (t0) cc_final: 0.7660 (t0) REVERT: F 57 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6908 (pt0) REVERT: F 115 MET cc_start: 0.9022 (tpt) cc_final: 0.8591 (mmm) REVERT: F 121 LYS cc_start: 0.8039 (tttt) cc_final: 0.7540 (tttp) REVERT: F 139 LYS cc_start: 0.8677 (tttm) cc_final: 0.8312 (tptm) REVERT: F 150 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6644 (tt0) REVERT: F 160 ASP cc_start: 0.8219 (m-30) cc_final: 0.7994 (m-30) REVERT: F 168 ASN cc_start: 0.8382 (t0) cc_final: 0.7621 (m-40) outliers start: 42 outliers final: 27 residues processed: 182 average time/residue: 0.6118 time to fit residues: 119.8640 Evaluate side-chains 189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 216 ASN 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 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 165 GLU Chi-restraints excluded: chain F residue 10 ILE 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: 0.9980 chunk 104 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN E 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.119198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.101444 restraints weight = 14351.267| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.86 r_work: 0.2935 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12330 Z= 0.148 Angle : 0.662 16.859 16791 Z= 0.337 Chirality : 0.046 0.342 1935 Planarity : 0.004 0.039 2130 Dihedral : 4.793 33.299 1584 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.20 % Allowed : 18.58 % 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: -0.70 (0.21), residues: 1458 helix: 2.07 (0.29), residues: 354 sheet: 0.23 (0.32), residues: 261 loop : -1.95 (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 0.014 0.001 PHE D 9 TRP 0.008 0.001 TRP C 234 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (12276) covalent geometry : angle 0.61962 / 0.32 (16647) SS BOND : bond 0.00799 / 0.49 ( 18) SS BOND : angle 4.24068 / 2.69 ( 36) hydrogen bonds : bond 0.05543 / 3.88 ( 414) hydrogen bonds : angle 4.41750 / 3.06 ( 1143) link_ALPHA1-3 : bond 0.00458 / 0.23 ( 3) link_ALPHA1-3 : angle 1.46066 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00451 / 0.23 ( 3) link_ALPHA1-6 : angle 1.49616 / 1.00 ( 9) link_BETA1-4 : bond 0.00281 / 0.18 ( 12) link_BETA1-4 : angle 1.69845 / 1.10 ( 36) link_NAG-ASN : bond 0.00306 / 0.18 ( 18) link_NAG-ASN : angle 1.85150 / 1.03 ( 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: 41 poor density : 154 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: A 77 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7127 (t0) REVERT: A 111 LEU cc_start: 0.8618 (tt) cc_final: 0.8397 (tp) REVERT: A 280 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: B 72 GLU cc_start: 0.7331 (mp0) cc_final: 0.6973 (mp0) REVERT: C 31 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7337 (t0) REVERT: C 41 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: C 70 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8383 (tp) REVERT: C 73 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7898 (t70) REVERT: C 82 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8312 (mm-30) REVERT: C 321 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8071 (ttt180) REVERT: E 27 LYS cc_start: 0.8502 (mttt) cc_final: 0.8062 (mtmm) REVERT: E 41 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: E 70 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8587 (tp) REVERT: E 111 LEU cc_start: 0.8713 (tt) cc_final: 0.8466 (tt) REVERT: E 321 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7937 (ttt180) REVERT: D 38 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7550 (mt) REVERT: D 49 ASN cc_start: 0.8011 (m-40) cc_final: 0.7713 (m-40) REVERT: D 62 LYS cc_start: 0.8386 (mttt) cc_final: 0.7997 (mmtt) REVERT: D 72 GLU cc_start: 0.7605 (mp0) cc_final: 0.6969 (mp0) REVERT: D 123 ARG cc_start: 0.8370 (ttp-170) cc_final: 0.8126 (ttp-170) REVERT: D 139 LYS cc_start: 0.8509 (tttp) cc_final: 0.8211 (tptm) REVERT: D 168 ASN cc_start: 0.8320 (t0) cc_final: 0.7641 (t0) REVERT: F 57 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6924 (pt0) REVERT: F 115 MET cc_start: 0.9030 (tpt) cc_final: 0.8597 (mmm) REVERT: F 121 LYS cc_start: 0.8048 (tttt) cc_final: 0.7563 (tttp) REVERT: F 139 LYS cc_start: 0.8641 (tttm) cc_final: 0.8267 (tptm) REVERT: F 150 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6679 (tt0) REVERT: F 160 ASP cc_start: 0.8199 (m-30) cc_final: 0.7967 (m-30) outliers start: 41 outliers final: 26 residues processed: 182 average time/residue: 0.6017 time to fit residues: 117.9904 Evaluate side-chains 190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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 34 GLN 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 165 GLU Chi-restraints excluded: chain F residue 10 ILE 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: 0.6980 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 101 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN E 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.119034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.101170 restraints weight = 14333.137| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.89 r_work: 0.2934 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12330 Z= 0.159 Angle : 0.874 58.997 16791 Z= 0.491 Chirality : 0.050 0.829 1935 Planarity : 0.004 0.081 2130 Dihedral : 4.810 33.260 1584 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.12 % Allowed : 18.89 % Favored : 77.99 % Cbeta Deviations : 0.07 % 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: -0.69 (0.21), residues: 1458 helix: 2.09 (0.29), residues: 354 sheet: 0.22 (0.32), residues: 261 loop : -1.95 (0.17), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 57 TYR 0.007 0.001 TYR C 195 PHE 0.014 0.001 PHE D 9 TRP 0.008 0.001 TRP C 234 HIS 0.003 0.001 HIS C 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (12276) covalent geometry : angle 0.84421 / 0.48 (16647) SS BOND : bond 0.00762 / 0.47 ( 18) SS BOND : angle 4.17030 / 2.64 ( 36) hydrogen bonds : bond 0.05516 / 3.87 ( 414) hydrogen bonds : angle 4.41689 / 3.06 ( 1143) link_ALPHA1-3 : bond 0.00519 / 0.26 ( 3) link_ALPHA1-3 : angle 1.48578 / 1.05 ( 9) link_ALPHA1-6 : bond 0.00435 / 0.22 ( 3) link_ALPHA1-6 : angle 1.48686 / 0.99 ( 9) link_BETA1-4 : bond 0.00439 / 0.27 ( 12) link_BETA1-4 : angle 1.73148 / 1.11 ( 36) link_NAG-ASN : bond 0.00307 / 0.18 ( 18) link_NAG-ASN : angle 1.85192 / 1.03 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3660.72 seconds wall clock time: 63 minutes 22.35 seconds (3802.35 seconds total)