Starting phenix.real_space_refine on Wed Jul 30 08:27:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5g_10696/07_2025/6y5g_10696.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5g_10696/07_2025/6y5g_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6y5g_10696/07_2025/6y5g_10696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5g_10696/07_2025/6y5g_10696.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5g_10696/07_2025/6y5g_10696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5g_10696/07_2025/6y5g_10696.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12036 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.11, per 1000 atoms: 0.67 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.42 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: 3.35 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3966 1.34 - 1.46: 2924 1.46 - 1.58: 5308 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 12276 Sorted by residual: bond pdb=" N ILE B 10 " pdb=" CA ILE B 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.13e+00 bond pdb=" N ILE F 10 " pdb=" CA ILE F 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N ILE D 10 " pdb=" CA ILE D 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N GLU D 11 " pdb=" CA GLU D 11 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.98e+00 bond pdb=" N GLU F 11 " pdb=" CA GLU F 11 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.96e+00 ... (remaining 12271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 15794 1.33 - 2.67: 717 2.67 - 4.00: 83 4.00 - 5.34: 32 5.34 - 6.67: 21 Bond angle restraints: 16647 Sorted by residual: angle pdb=" CA LYS D 39 " pdb=" CB LYS D 39 " pdb=" CG LYS D 39 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.28e+00 angle pdb=" CA LYS B 39 " pdb=" CB LYS B 39 " pdb=" CG LYS B 39 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 angle pdb=" CA LYS F 39 " pdb=" CB LYS F 39 " pdb=" CG LYS F 39 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.11e+00 angle pdb=" O GLU B 85 " pdb=" C GLU B 85 " pdb=" N ASP B 86 " ideal model delta sigma weight residual 122.07 124.70 -2.63 1.03e+00 9.43e-01 6.53e+00 angle pdb=" O GLU F 85 " pdb=" C GLU F 85 " pdb=" N ASP F 86 " ideal model delta sigma weight residual 122.07 124.66 -2.59 1.03e+00 9.43e-01 6.31e+00 ... (remaining 16642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 7287 22.13 - 44.27: 411 44.27 - 66.40: 72 66.40 - 88.53: 42 88.53 - 110.66: 15 Dihedral angle restraints: 7827 sinusoidal: 3609 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.60 -79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.61 -79.39 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.64 -79.36 1 1.00e+01 1.00e-02 7.83e+01 ... (remaining 7824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 1920 0.314 - 0.627: 6 0.627 - 0.941: 3 0.941 - 1.255: 3 1.255 - 1.568: 3 Chirality restraints: 1935 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.15e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 ... (remaining 1932 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 73 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 74 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO E 74 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 73 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO C 74 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.026 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 886 2.73 - 3.27: 10349 3.27 - 3.82: 18279 3.82 - 4.36: 22695 4.36 - 4.90: 40185 Nonbonded interactions: 92394 Sorted by model distance: nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.189 3.120 nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.189 3.120 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLU F 131 " pdb=" OH TYR F 141 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLU B 131 " pdb=" OH TYR B 141 " model vdw 2.280 3.040 ... (remaining 92389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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: 4.200 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.130 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 12330 Z= 0.278 Angle : 1.805 59.392 16791 Z= 0.658 Chirality : 0.101 1.568 1935 Planarity : 0.004 0.047 2130 Dihedral : 15.738 110.663 5067 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.94 % Allowed : 12.65 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP C 234 HIS 0.004 0.001 HIS C 75 PHE 0.013 0.001 PHE F 9 TYR 0.010 0.001 TYR E 161 ARG 0.002 0.000 ARG D 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 18) link_NAG-ASN : angle 2.07196 ( 54) link_ALPHA1-6 : bond 0.06532 ( 3) link_ALPHA1-6 : angle 19.34584 ( 9) link_BETA1-4 : bond 0.06544 ( 12) link_BETA1-4 : angle 31.34804 ( 36) link_ALPHA1-3 : bond 0.06558 ( 3) link_ALPHA1-3 : angle 30.53201 ( 9) hydrogen bonds : bond 0.16548 ( 414) hydrogen bonds : angle 6.16138 ( 1143) SS BOND : bond 0.03120 ( 18) SS BOND : angle 1.53718 ( 36) covalent geometry : bond 0.00522 (12276) covalent geometry : angle 0.66089 (16647) *********************** 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 : 1.297 Fit side-chains revert: symmetry clash REVERT: A 111 LEU cc_start: 0.8585 (tt) cc_final: 0.8270 (tp) REVERT: A 119 GLU cc_start: 0.8087 (tt0) cc_final: 0.7866 (tt0) REVERT: B 46 ASP cc_start: 0.7800 (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: 1.5144 time to fit residues: 384.7520 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 : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 125 GLN C 33 GLN C 216 ASN E 17 HIS E 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.116753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098734 restraints weight = 14199.219| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.90 r_work: 0.2830 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12330 Z= 0.223 Angle : 0.679 7.047 16791 Z= 0.339 Chirality : 0.049 0.218 1935 Planarity : 0.005 0.049 2130 Dihedral : 10.794 92.907 2322 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.19), residues: 1458 helix: 0.59 (0.28), residues: 375 sheet: -0.72 (0.33), residues: 234 loop : -2.54 (0.16), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS A 75 PHE 0.021 0.002 PHE D 9 TYR 0.013 0.002 TYR C 308 ARG 0.007 0.001 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 18) link_NAG-ASN : angle 2.20515 ( 54) link_ALPHA1-6 : bond 0.00407 ( 3) link_ALPHA1-6 : angle 2.68341 ( 9) link_BETA1-4 : bond 0.00238 ( 12) link_BETA1-4 : angle 2.46914 ( 36) link_ALPHA1-3 : bond 0.00991 ( 3) link_ALPHA1-3 : angle 2.39832 ( 9) hydrogen bonds : bond 0.06775 ( 414) hydrogen bonds : angle 4.77879 ( 1143) SS BOND : bond 0.01151 ( 18) SS BOND : angle 2.33021 ( 36) covalent geometry : bond 0.00546 (12276) covalent geometry : angle 0.64603 (16647) *********************** 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 228 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: A 77 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7100 (t0) REVERT: A 111 LEU cc_start: 0.8699 (tt) cc_final: 0.8425 (tp) REVERT: A 321 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8060 (ttt180) REVERT: A 325 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7090 (mt-10) REVERT: B 54 ARG cc_start: 0.8001 (tpt90) cc_final: 0.5520 (tmt-80) REVERT: B 72 GLU cc_start: 0.7684 (mp0) cc_final: 0.7278 (mp0) REVERT: C 41 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: C 62 ILE cc_start: 0.8871 (mt) cc_final: 0.8595 (mp) REVERT: C 82 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8394 (mm-30) REVERT: C 321 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8051 (ttt180) REVERT: C 325 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7401 (mt-10) REVERT: E 27 LYS cc_start: 0.8542 (mttt) cc_final: 0.8128 (mtmm) REVERT: E 41 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: E 70 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8470 (tp) REVERT: E 111 LEU cc_start: 0.8692 (tt) cc_final: 0.8392 (tt) REVERT: E 139 CYS cc_start: 0.8378 (t) cc_final: 0.7902 (t) REVERT: E 321 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7947 (ttt180) REVERT: D 49 ASN cc_start: 0.8123 (m-40) cc_final: 0.7861 (m-40) REVERT: D 62 LYS cc_start: 0.8400 (mttt) cc_final: 0.7989 (mmtt) REVERT: D 115 MET cc_start: 0.9016 (tpt) cc_final: 0.8744 (mmm) REVERT: D 121 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7733 (ttmm) REVERT: D 139 LYS cc_start: 0.8512 (tttp) cc_final: 0.8195 (tptm) REVERT: F 37 ASP cc_start: 0.8421 (t0) cc_final: 0.8078 (t70) REVERT: F 115 MET cc_start: 0.9094 (tpt) cc_final: 0.8719 (mmm) REVERT: F 150 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6793 (tt0) REVERT: F 160 ASP cc_start: 0.8252 (m-30) cc_final: 0.8030 (m-30) REVERT: F 168 ASN cc_start: 0.8331 (t0) cc_final: 0.7718 (m-40) outliers start: 44 outliers final: 17 residues processed: 206 average time/residue: 1.7320 time to fit residues: 384.2253 Evaluate side-chains 182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 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 70 LEU 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 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 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3212 r_free = 0.3212 target = 0.117771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.099888 restraints weight = 14560.173| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.92 r_work: 0.2853 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12330 Z= 0.149 Angle : 0.613 9.111 16791 Z= 0.313 Chirality : 0.046 0.241 1935 Planarity : 0.004 0.037 2130 Dihedral : 9.824 86.896 2322 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.90 % Allowed : 16.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1458 helix: 1.42 (0.29), residues: 357 sheet: 0.01 (0.40), residues: 174 loop : -2.18 (0.16), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 234 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE F 138 TYR 0.007 0.001 TYR C 308 ARG 0.007 0.000 ARG A 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 18) link_NAG-ASN : angle 1.98607 ( 54) link_ALPHA1-6 : bond 0.00694 ( 3) link_ALPHA1-6 : angle 2.03989 ( 9) link_BETA1-4 : bond 0.00309 ( 12) link_BETA1-4 : angle 2.02203 ( 36) link_ALPHA1-3 : bond 0.00736 ( 3) link_ALPHA1-3 : angle 1.46584 ( 9) hydrogen bonds : bond 0.05695 ( 414) hydrogen bonds : angle 4.53875 ( 1143) SS BOND : bond 0.00827 ( 18) SS BOND : angle 3.04600 ( 36) covalent geometry : bond 0.00352 (12276) covalent geometry : angle 0.57772 (16647) *********************** 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 217 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: A 77 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7120 (t0) REVERT: A 111 LEU cc_start: 0.8673 (tt) cc_final: 0.8406 (tp) REVERT: A 280 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: A 321 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8063 (ttt180) REVERT: B 54 ARG cc_start: 0.7965 (tpt90) cc_final: 0.5550 (tmt-80) REVERT: B 72 GLU cc_start: 0.7525 (mp0) cc_final: 0.7211 (mp0) REVERT: C 62 ILE cc_start: 0.8739 (mt) cc_final: 0.8441 (mp) REVERT: C 82 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8308 (mm-30) REVERT: C 321 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8156 (ttt180) REVERT: E 27 LYS cc_start: 0.8525 (mttt) cc_final: 0.8105 (mtmm) REVERT: E 31 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6991 (t0) REVERT: E 41 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: E 111 LEU cc_start: 0.8681 (tt) cc_final: 0.8399 (tt) REVERT: E 139 CYS cc_start: 0.8498 (t) cc_final: 0.7968 (t) REVERT: E 321 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7949 (ttt180) REVERT: D 38 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7548 (mt) REVERT: D 49 ASN cc_start: 0.8050 (m-40) cc_final: 0.7754 (m-40) REVERT: D 62 LYS cc_start: 0.8398 (mttt) cc_final: 0.7960 (mmtt) REVERT: D 120 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: D 139 LYS cc_start: 0.8587 (tttp) cc_final: 0.8189 (tptm) REVERT: F 37 ASP cc_start: 0.8411 (t0) cc_final: 0.8107 (t70) REVERT: F 115 MET cc_start: 0.9075 (tpt) cc_final: 0.8727 (mmm) REVERT: F 121 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7641 (tttp) REVERT: F 139 LYS cc_start: 0.8642 (tttm) cc_final: 0.8296 (tptm) REVERT: F 150 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6725 (tt0) REVERT: F 160 ASP cc_start: 0.8262 (m-30) cc_final: 0.8041 (m-30) REVERT: F 168 ASN cc_start: 0.8300 (t0) cc_final: 0.7659 (m-40) outliers start: 50 outliers final: 17 residues processed: 197 average time/residue: 1.3330 time to fit residues: 282.9308 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 195 TYR 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 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: 0.9980 chunk 59 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 111 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN E 54 ASN E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.116910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.099151 restraints weight = 14301.923| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.89 r_work: 0.2877 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1989 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= 0.183 Angle : 0.673 21.016 16791 Z= 0.339 Chirality : 0.049 0.315 1935 Planarity : 0.004 0.042 2130 Dihedral : 8.732 76.341 2322 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.98 % Allowed : 16.63 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1458 helix: 1.53 (0.28), residues: 357 sheet: 0.02 (0.36), residues: 204 loop : -2.11 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 75 PHE 0.019 0.002 PHE D 9 TYR 0.012 0.002 TYR A 195 ARG 0.009 0.001 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 18) link_NAG-ASN : angle 2.11112 ( 54) link_ALPHA1-6 : bond 0.00828 ( 3) link_ALPHA1-6 : angle 1.75356 ( 9) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 2.01851 ( 36) link_ALPHA1-3 : bond 0.00914 ( 3) link_ALPHA1-3 : angle 1.53939 ( 9) hydrogen bonds : bond 0.06164 ( 414) hydrogen bonds : angle 4.48710 ( 1143) SS BOND : bond 0.01021 ( 18) SS BOND : angle 3.51881 ( 36) covalent geometry : bond 0.00443 (12276) covalent geometry : angle 0.63565 (16647) *********************** 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 206 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: A 77 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7080 (t0) REVERT: A 111 LEU cc_start: 0.8669 (tt) cc_final: 0.8416 (tp) REVERT: A 280 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: A 325 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7076 (mt-10) REVERT: B 72 GLU cc_start: 0.7482 (mp0) cc_final: 0.7172 (mp0) REVERT: C 41 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: C 70 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8397 (tp) REVERT: C 73 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7957 (t70) REVERT: C 82 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8305 (mm-30) REVERT: C 321 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8083 (ttt180) REVERT: C 325 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7283 (mt-10) REVERT: E 27 LYS cc_start: 0.8536 (mttt) cc_final: 0.8113 (mtmm) REVERT: E 31 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.7074 (t0) REVERT: E 41 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: E 70 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8416 (tp) REVERT: E 111 LEU cc_start: 0.8721 (tt) cc_final: 0.8451 (tt) REVERT: E 321 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7899 (ttt180) REVERT: E 325 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6933 (mt-10) REVERT: D 38 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7562 (mt) REVERT: D 49 ASN cc_start: 0.8036 (m-40) cc_final: 0.7744 (m-40) REVERT: D 62 LYS cc_start: 0.8372 (mttt) cc_final: 0.7948 (mmtt) REVERT: D 120 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: D 139 LYS cc_start: 0.8612 (tttp) cc_final: 0.8191 (tptm) REVERT: F 37 ASP cc_start: 0.8386 (t0) cc_final: 0.8008 (t70) REVERT: F 115 MET cc_start: 0.9031 (tpt) cc_final: 0.8658 (mmm) REVERT: F 150 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6685 (tt0) REVERT: F 160 ASP cc_start: 0.8277 (m-30) cc_final: 0.8057 (m-30) REVERT: F 168 ASN cc_start: 0.8383 (t0) cc_final: 0.7644 (m-40) outliers start: 51 outliers final: 18 residues processed: 185 average time/residue: 1.5766 time to fit residues: 314.6867 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.779 ------------------------------------------------------------------------------- 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 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 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 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.117538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.099660 restraints weight = 14267.606| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.90 r_work: 0.2885 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12330 Z= 0.173 Angle : 0.687 20.343 16791 Z= 0.347 Chirality : 0.049 0.369 1935 Planarity : 0.004 0.034 2130 Dihedral : 7.975 67.571 2322 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.14 % Allowed : 17.33 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1458 helix: 1.74 (0.28), residues: 354 sheet: 0.07 (0.36), residues: 204 loop : -2.04 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.003 0.001 HIS A 75 PHE 0.017 0.002 PHE D 9 TYR 0.009 0.001 TYR A 195 ARG 0.008 0.000 ARG A 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 18) link_NAG-ASN : angle 2.05910 ( 54) link_ALPHA1-6 : bond 0.00973 ( 3) link_ALPHA1-6 : angle 1.65237 ( 9) link_BETA1-4 : bond 0.00298 ( 12) link_BETA1-4 : angle 1.93335 ( 36) link_ALPHA1-3 : bond 0.00935 ( 3) link_ALPHA1-3 : angle 1.27857 ( 9) hydrogen bonds : bond 0.05935 ( 414) hydrogen bonds : angle 4.44907 ( 1143) SS BOND : bond 0.01086 ( 18) SS BOND : angle 4.15044 ( 36) covalent geometry : bond 0.00411 (12276) covalent geometry : angle 0.64361 (16647) *********************** 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: 53 poor density : 157 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: A 77 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7118 (t0) REVERT: A 111 LEU cc_start: 0.8699 (tt) cc_final: 0.8470 (tp) REVERT: A 280 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: B 72 GLU cc_start: 0.7487 (mp0) cc_final: 0.7120 (mp0) REVERT: C 70 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8425 (tp) REVERT: C 73 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7913 (t70) REVERT: C 82 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8350 (mm-30) REVERT: C 321 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8128 (ttt180) REVERT: E 27 LYS cc_start: 0.8556 (mttt) cc_final: 0.8146 (mtmm) REVERT: E 31 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7069 (t0) REVERT: E 41 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: E 70 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8562 (tp) REVERT: E 111 LEU cc_start: 0.8726 (tt) cc_final: 0.8458 (tt) REVERT: E 321 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7960 (ttt180) REVERT: E 325 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6987 (mt-10) REVERT: D 38 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7581 (mt) REVERT: D 49 ASN cc_start: 0.8032 (m-40) cc_final: 0.7735 (m-40) REVERT: D 62 LYS cc_start: 0.8400 (mttt) cc_final: 0.8001 (mmtt) REVERT: D 121 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7648 (ttpt) REVERT: D 139 LYS cc_start: 0.8573 (tttp) cc_final: 0.8209 (tptm) REVERT: D 168 ASN cc_start: 0.8344 (t0) cc_final: 0.7725 (t0) REVERT: F 37 ASP cc_start: 0.8441 (t0) cc_final: 0.8023 (t70) REVERT: F 115 MET cc_start: 0.9048 (tpt) cc_final: 0.8677 (mmm) REVERT: F 123 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7927 (ttp80) REVERT: F 139 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8495 (tptm) REVERT: F 150 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6749 (tt0) REVERT: F 160 ASP cc_start: 0.8296 (m-30) cc_final: 0.8084 (m-30) REVERT: F 168 ASN cc_start: 0.8423 (t0) cc_final: 0.7703 (m-40) outliers start: 53 outliers final: 23 residues processed: 188 average time/residue: 1.5141 time to fit residues: 305.8245 Evaluate side-chains 186 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 C residue 31 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 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 277 CYS 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 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS 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 99 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 111 optimal weight: 0.0470 chunk 134 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.117904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.100075 restraints weight = 14580.550| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.91 r_work: 0.2886 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12330 Z= 0.155 Angle : 0.656 14.012 16791 Z= 0.333 Chirality : 0.048 0.332 1935 Planarity : 0.004 0.050 2130 Dihedral : 7.328 58.808 2322 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.06 % Allowed : 17.33 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1458 helix: 1.82 (0.29), residues: 357 sheet: 0.18 (0.36), residues: 204 loop : -1.96 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 234 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE D 9 TYR 0.008 0.001 TYR A 195 ARG 0.011 0.000 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 18) link_NAG-ASN : angle 1.99528 ( 54) link_ALPHA1-6 : bond 0.01013 ( 3) link_ALPHA1-6 : angle 1.43569 ( 9) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 1.85331 ( 36) link_ALPHA1-3 : bond 0.01020 ( 3) link_ALPHA1-3 : angle 1.14129 ( 9) hydrogen bonds : bond 0.05655 ( 414) hydrogen bonds : angle 4.38473 ( 1143) SS BOND : bond 0.00930 ( 18) SS BOND : angle 3.95285 ( 36) covalent geometry : bond 0.00366 (12276) covalent geometry : angle 0.61444 (16647) *********************** 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 204 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7129 (t0) REVERT: A 111 LEU cc_start: 0.8700 (tt) cc_final: 0.8478 (tp) REVERT: A 280 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: B 72 GLU cc_start: 0.7439 (mp0) cc_final: 0.7107 (mp0) REVERT: C 41 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: C 70 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8406 (tp) REVERT: C 73 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7881 (t70) REVERT: C 321 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8143 (ttt180) REVERT: C 325 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7236 (mt-10) REVERT: E 27 LYS cc_start: 0.8561 (mttt) cc_final: 0.8138 (mtmm) REVERT: E 31 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7113 (t0) REVERT: E 41 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: E 70 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8559 (tp) REVERT: E 111 LEU cc_start: 0.8737 (tt) cc_final: 0.8475 (tt) REVERT: E 321 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7961 (ttt180) REVERT: D 38 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7565 (mt) REVERT: D 49 ASN cc_start: 0.8024 (m-40) cc_final: 0.7735 (m-40) REVERT: D 62 LYS cc_start: 0.8378 (mttt) cc_final: 0.7962 (mmtt) REVERT: D 139 LYS cc_start: 0.8502 (tttp) cc_final: 0.8234 (tptm) REVERT: D 168 ASN cc_start: 0.8358 (t0) cc_final: 0.7682 (t0) REVERT: F 37 ASP cc_start: 0.8447 (t0) cc_final: 0.8123 (t70) REVERT: F 57 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7006 (pt0) REVERT: F 115 MET cc_start: 0.9090 (tpt) cc_final: 0.8687 (mmm) REVERT: F 123 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7942 (ttp80) REVERT: F 139 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8489 (tptm) REVERT: F 150 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6732 (tt0) REVERT: F 160 ASP cc_start: 0.8288 (m-30) cc_final: 0.8082 (m-30) REVERT: F 168 ASN cc_start: 0.8395 (t0) cc_final: 0.7693 (m-40) outliers start: 52 outliers final: 24 residues processed: 188 average time/residue: 1.3459 time to fit residues: 272.8105 Evaluate side-chains 185 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 B residue 145 ASP Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS 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 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 28 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 111 optimal weight: 0.0170 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3217 r_free = 0.3217 target = 0.118096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.100250 restraints weight = 14490.414| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.90 r_work: 0.2899 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12330 Z= 0.157 Angle : 0.668 19.238 16791 Z= 0.337 Chirality : 0.048 0.317 1935 Planarity : 0.004 0.046 2130 Dihedral : 7.068 53.218 2322 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.83 % Allowed : 17.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1458 helix: 1.94 (0.29), residues: 354 sheet: 0.18 (0.36), residues: 204 loop : -1.94 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE D 9 TYR 0.008 0.001 TYR A 195 ARG 0.010 0.000 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 18) link_NAG-ASN : angle 1.98801 ( 54) link_ALPHA1-6 : bond 0.01000 ( 3) link_ALPHA1-6 : angle 1.35833 ( 9) link_BETA1-4 : bond 0.00319 ( 12) link_BETA1-4 : angle 1.86787 ( 36) link_ALPHA1-3 : bond 0.00960 ( 3) link_ALPHA1-3 : angle 1.16992 ( 9) hydrogen bonds : bond 0.05639 ( 414) hydrogen bonds : angle 4.38685 ( 1143) SS BOND : bond 0.00898 ( 18) SS BOND : angle 4.09401 ( 36) covalent geometry : bond 0.00371 (12276) covalent geometry : angle 0.62542 (16647) *********************** 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: 49 poor density : 152 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: A 77 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7101 (t0) REVERT: A 111 LEU cc_start: 0.8631 (tt) cc_final: 0.8413 (tp) REVERT: A 280 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: B 72 GLU cc_start: 0.7388 (mp0) cc_final: 0.7054 (mp0) REVERT: C 31 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: C 41 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: C 70 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8363 (tp) REVERT: C 73 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (t70) REVERT: C 321 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8058 (ttt180) REVERT: E 27 LYS cc_start: 0.8523 (mttt) cc_final: 0.8155 (mtmm) REVERT: E 31 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7129 (t0) REVERT: E 41 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: E 70 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8526 (tp) REVERT: E 111 LEU cc_start: 0.8712 (tt) cc_final: 0.8454 (tt) REVERT: E 321 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7906 (ttt180) REVERT: D 38 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7513 (mt) REVERT: D 49 ASN cc_start: 0.7967 (m-40) cc_final: 0.7668 (m-40) REVERT: D 62 LYS cc_start: 0.8379 (mttt) cc_final: 0.7966 (mmtt) REVERT: D 121 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7517 (ttpt) REVERT: D 123 ARG cc_start: 0.8086 (ttp-110) cc_final: 0.7824 (ttp-170) REVERT: D 139 LYS cc_start: 0.8457 (tttp) cc_final: 0.8181 (tptm) REVERT: D 168 ASN cc_start: 0.8316 (t0) cc_final: 0.7629 (t0) REVERT: F 37 ASP cc_start: 0.8431 (t0) cc_final: 0.8018 (t70) REVERT: F 57 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6898 (pt0) REVERT: F 115 MET cc_start: 0.9017 (tpt) cc_final: 0.8611 (mmm) REVERT: F 121 LYS cc_start: 0.7918 (tttt) cc_final: 0.7410 (tttp) REVERT: F 123 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7871 (ttp80) REVERT: F 139 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8460 (tptm) REVERT: F 150 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6649 (tt0) REVERT: F 160 ASP cc_start: 0.8266 (m-30) cc_final: 0.8053 (m-30) REVERT: F 168 ASN cc_start: 0.8366 (t0) cc_final: 0.7643 (m-40) outliers start: 49 outliers final: 25 residues processed: 183 average time/residue: 1.5735 time to fit residues: 310.0021 Evaluate side-chains 190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 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 228 SER Chi-restraints excluded: chain C residue 277 CYS 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 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 0.0050 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3217 r_free = 0.3217 target = 0.118050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.100302 restraints weight = 14725.219| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.91 r_work: 0.2893 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12330 Z= 0.159 Angle : 0.675 16.957 16791 Z= 0.341 Chirality : 0.048 0.349 1935 Planarity : 0.004 0.047 2130 Dihedral : 6.916 50.265 2322 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.83 % Allowed : 17.88 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1458 helix: 1.92 (0.29), residues: 357 sheet: 0.18 (0.36), residues: 204 loop : -1.91 (0.17), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE D 9 TYR 0.008 0.001 TYR C 308 ARG 0.010 0.000 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 18) link_NAG-ASN : angle 1.97600 ( 54) link_ALPHA1-6 : bond 0.01027 ( 3) link_ALPHA1-6 : angle 1.26814 ( 9) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 1.86151 ( 36) link_ALPHA1-3 : bond 0.00965 ( 3) link_ALPHA1-3 : angle 1.14904 ( 9) hydrogen bonds : bond 0.05694 ( 414) hydrogen bonds : angle 4.39351 ( 1143) SS BOND : bond 0.00895 ( 18) SS BOND : angle 4.27552 ( 36) covalent geometry : bond 0.00376 (12276) covalent geometry : angle 0.63120 (16647) *********************** 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 203 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: A 77 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7138 (t0) REVERT: A 111 LEU cc_start: 0.8631 (tt) cc_final: 0.8410 (tp) REVERT: A 280 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: B 72 GLU cc_start: 0.7410 (mp0) cc_final: 0.7069 (mp0) REVERT: C 31 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7384 (t0) REVERT: C 41 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: C 70 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8383 (tp) REVERT: C 73 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7898 (t70) REVERT: C 321 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8093 (ttt180) REVERT: C 325 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7283 (mt-10) REVERT: E 27 LYS cc_start: 0.8538 (mttt) cc_final: 0.8188 (mtmm) REVERT: E 41 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: E 70 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8565 (tp) REVERT: E 111 LEU cc_start: 0.8738 (tt) cc_final: 0.8482 (tt) REVERT: E 321 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: D 38 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7570 (mt) REVERT: D 49 ASN cc_start: 0.8038 (m-40) cc_final: 0.7743 (m-40) REVERT: D 62 LYS cc_start: 0.8397 (mttt) cc_final: 0.8024 (mmtt) REVERT: D 72 GLU cc_start: 0.7673 (mp0) cc_final: 0.7058 (mp0) REVERT: D 121 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7597 (ttpt) REVERT: D 139 LYS cc_start: 0.8509 (tttp) cc_final: 0.8258 (tptm) REVERT: D 168 ASN cc_start: 0.8364 (t0) cc_final: 0.7696 (t0) REVERT: F 57 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6967 (pt0) REVERT: F 115 MET cc_start: 0.9045 (tpt) cc_final: 0.8638 (mmm) REVERT: F 121 LYS cc_start: 0.8084 (tttt) cc_final: 0.7605 (tttp) REVERT: F 123 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7974 (ttp80) REVERT: F 139 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8449 (tptm) REVERT: F 150 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6719 (tt0) REVERT: F 160 ASP cc_start: 0.8255 (m-30) cc_final: 0.8045 (m-30) REVERT: F 168 ASN cc_start: 0.8396 (t0) cc_final: 0.7689 (m-40) outliers start: 49 outliers final: 27 residues processed: 185 average time/residue: 1.4492 time to fit residues: 288.2870 Evaluate side-chains 189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 206 THR 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 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 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 140 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 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 = 0.3217 r_free = 0.3217 target = 0.118065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.100283 restraints weight = 14503.539| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.90 r_work: 0.2905 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12330 Z= 0.163 Angle : 0.678 17.430 16791 Z= 0.343 Chirality : 0.048 0.355 1935 Planarity : 0.004 0.045 2130 Dihedral : 6.785 47.940 2322 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.75 % Allowed : 18.27 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1458 helix: 1.96 (0.29), residues: 354 sheet: 0.05 (0.33), residues: 255 loop : -1.95 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.003 0.001 HIS C 75 PHE 0.016 0.002 PHE D 9 TYR 0.008 0.001 TYR C 308 ARG 0.010 0.001 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 18) link_NAG-ASN : angle 1.97232 ( 54) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 1.21983 ( 9) link_BETA1-4 : bond 0.00305 ( 12) link_BETA1-4 : angle 1.84667 ( 36) link_ALPHA1-3 : bond 0.00971 ( 3) link_ALPHA1-3 : angle 1.14589 ( 9) hydrogen bonds : bond 0.05723 ( 414) hydrogen bonds : angle 4.42376 ( 1143) SS BOND : bond 0.00837 ( 18) SS BOND : angle 4.33688 ( 36) covalent geometry : bond 0.00385 (12276) covalent geometry : angle 0.63313 (16647) *********************** 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 199 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: A 77 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7099 (t0) REVERT: A 111 LEU cc_start: 0.8612 (tt) cc_final: 0.8397 (tp) REVERT: A 280 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8089 (mm-30) REVERT: B 72 GLU cc_start: 0.7356 (mp0) cc_final: 0.7028 (mp0) REVERT: C 31 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7327 (t0) REVERT: C 41 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: C 70 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8347 (tp) REVERT: C 73 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7880 (t70) REVERT: C 321 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8038 (ttt180) REVERT: E 27 LYS cc_start: 0.8516 (mttt) cc_final: 0.8142 (mtmm) REVERT: E 41 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: E 70 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 111 LEU cc_start: 0.8709 (tt) cc_final: 0.8452 (tt) REVERT: E 321 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7896 (ttt180) REVERT: D 38 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7506 (mt) REVERT: D 49 ASN cc_start: 0.7982 (m-40) cc_final: 0.7686 (m-40) REVERT: D 62 LYS cc_start: 0.8384 (mttt) cc_final: 0.7974 (mmtt) REVERT: D 72 GLU cc_start: 0.7618 (mp0) cc_final: 0.6989 (mp0) REVERT: D 139 LYS cc_start: 0.8502 (tttp) cc_final: 0.8209 (tptm) REVERT: D 168 ASN cc_start: 0.8299 (t0) cc_final: 0.7630 (t0) REVERT: F 57 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6913 (pt0) REVERT: F 115 MET cc_start: 0.9010 (tpt) cc_final: 0.8592 (mmm) REVERT: F 121 LYS cc_start: 0.8007 (tttt) cc_final: 0.7501 (tttp) REVERT: F 123 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7907 (ttp80) REVERT: F 139 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8467 (tptm) REVERT: F 150 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6647 (tt0) REVERT: F 160 ASP cc_start: 0.8200 (m-30) cc_final: 0.7984 (m-30) REVERT: F 168 ASN cc_start: 0.8358 (t0) cc_final: 0.7630 (m-40) outliers start: 48 outliers final: 26 residues processed: 183 average time/residue: 1.7598 time to fit residues: 349.7024 Evaluate side-chains 187 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 206 THR 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 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 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 91 optimal weight: 0.0770 chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 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 = 0.3217 r_free = 0.3217 target = 0.118038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.100427 restraints weight = 14481.559| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.88 r_work: 0.2857 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12330 Z= 0.165 Angle : 0.677 16.209 16791 Z= 0.343 Chirality : 0.048 0.338 1935 Planarity : 0.004 0.044 2130 Dihedral : 6.706 47.121 2322 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.12 % Allowed : 18.89 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1458 helix: 1.95 (0.29), residues: 354 sheet: 0.05 (0.33), residues: 255 loop : -1.94 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 PHE 0.016 0.002 PHE D 9 TYR 0.008 0.001 TYR C 308 ARG 0.010 0.001 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 18) link_NAG-ASN : angle 1.96938 ( 54) link_ALPHA1-6 : bond 0.01070 ( 3) link_ALPHA1-6 : angle 1.19516 ( 9) link_BETA1-4 : bond 0.00298 ( 12) link_BETA1-4 : angle 1.84633 ( 36) link_ALPHA1-3 : bond 0.00951 ( 3) link_ALPHA1-3 : angle 1.14847 ( 9) hydrogen bonds : bond 0.05753 ( 414) hydrogen bonds : angle 4.43373 ( 1143) SS BOND : bond 0.00803 ( 18) SS BOND : angle 4.24761 ( 36) covalent geometry : bond 0.00392 (12276) covalent geometry : angle 0.63374 (16647) ********************** 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 193 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: A 77 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7149 (t0) REVERT: A 111 LEU cc_start: 0.8644 (tt) cc_final: 0.8422 (tp) REVERT: A 280 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: B 72 GLU cc_start: 0.7364 (mp0) cc_final: 0.7018 (mp0) REVERT: C 31 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7398 (t0) REVERT: C 41 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: C 70 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8386 (tp) REVERT: C 73 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7887 (t70) REVERT: C 77 ASP cc_start: 0.7684 (m-30) cc_final: 0.7168 (t0) REVERT: C 321 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8112 (ttt180) REVERT: C 325 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7255 (mt-10) REVERT: E 27 LYS cc_start: 0.8528 (mttt) cc_final: 0.8170 (mtmm) REVERT: E 41 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: E 70 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8564 (tp) REVERT: E 111 LEU cc_start: 0.8750 (tt) cc_final: 0.8485 (tt) REVERT: E 321 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7961 (ttt180) REVERT: D 38 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7554 (mt) REVERT: D 49 ASN cc_start: 0.8024 (m-40) cc_final: 0.7742 (m-40) REVERT: D 62 LYS cc_start: 0.8386 (mttt) cc_final: 0.7998 (mmtt) REVERT: D 72 GLU cc_start: 0.7682 (mp0) cc_final: 0.7086 (mp0) REVERT: D 139 LYS cc_start: 0.8509 (tttp) cc_final: 0.8206 (tptm) REVERT: D 168 ASN cc_start: 0.8352 (t0) cc_final: 0.7662 (t0) REVERT: F 57 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6967 (pt0) REVERT: F 115 MET cc_start: 0.9042 (tpt) cc_final: 0.8620 (mmm) REVERT: F 121 LYS cc_start: 0.8075 (tttt) cc_final: 0.7587 (tttp) REVERT: F 123 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7982 (ttp80) REVERT: F 139 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8496 (tptm) REVERT: F 150 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6701 (tt0) REVERT: F 160 ASP cc_start: 0.8224 (m-30) cc_final: 0.7998 (m-30) REVERT: F 168 ASN cc_start: 0.8455 (t0) cc_final: 0.7652 (m-40) outliers start: 40 outliers final: 25 residues processed: 180 average time/residue: 1.3963 time to fit residues: 271.9920 Evaluate side-chains 187 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 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 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 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 91 optimal weight: 0.0170 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 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 = 0.3220 r_free = 0.3220 target = 0.118284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.100576 restraints weight = 14529.083| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.90 r_work: 0.2896 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12330 Z= 0.156 Angle : 0.660 15.462 16791 Z= 0.334 Chirality : 0.047 0.320 1935 Planarity : 0.004 0.043 2130 Dihedral : 6.608 46.905 2322 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.20 % Allowed : 18.81 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.21), residues: 1458 helix: 1.95 (0.29), residues: 357 sheet: 0.05 (0.33), residues: 255 loop : -1.96 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 234 HIS 0.003 0.001 HIS C 75 PHE 0.015 0.001 PHE D 9 TYR 0.008 0.001 TYR C 308 ARG 0.010 0.001 ARG E 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 18) link_NAG-ASN : angle 1.93102 ( 54) link_ALPHA1-6 : bond 0.01082 ( 3) link_ALPHA1-6 : angle 1.17942 ( 9) link_BETA1-4 : bond 0.00301 ( 12) link_BETA1-4 : angle 1.82109 ( 36) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 1.13973 ( 9) hydrogen bonds : bond 0.05599 ( 414) hydrogen bonds : angle 4.41019 ( 1143) SS BOND : bond 0.00725 ( 18) SS BOND : angle 4.15971 ( 36) covalent geometry : bond 0.00368 (12276) covalent geometry : angle 0.61734 (16647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9096.87 seconds wall clock time: 162 minutes 18.38 seconds (9738.38 seconds total)