Starting phenix.real_space_refine on Sat Jul 4 01:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.cif" model { file = "/net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp5_41467/07_2026/8tp5_41467.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.051 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 78 5.16 5 C 10986 2.51 5 N 2997 2.21 5 O 3447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17508 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "E" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "F" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 836 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "I" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain: "J" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 836 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 836 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.82, per 1000 atoms: 0.22 Number of scatterers: 17508 At special positions: 0 Unit cell: (140.3, 134.55, 167.9, 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 78 16.00 O 3447 8.00 N 2997 7.00 C 10986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.07 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.08 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.07 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.08 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS I 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.07 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.08 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.05 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 63 " " NAG A 404 " - " ASN A 129 " " NAG C 401 " - " ASN C 21 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 63 " " NAG C 404 " - " ASN C 129 " " NAG G 401 " - " ASN G 21 " " NAG G 402 " - " ASN G 33 " " NAG G 403 " - " ASN G 63 " " NAG G 404 " - " ASN G 129 " " NAG M 1 " - " ASN A 95 " " NAG N 1 " - " ASN C 95 " " NAG O 1 " - " ASN G 95 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 626.6 milliseconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4014 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 51 sheets defined 21.2% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP A 127 " --> pdb=" O LYS A 125A" (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP C 127 " --> pdb=" O LYS C 125A" (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 29 through 30C Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.933A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 125 through 127 removed outlier: 4.405A pdb=" N TRP G 127 " --> pdb=" O LYS G 125A" (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 145 through 154 Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 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 54 removed outlier: 7.749A pdb=" N LEU A 51 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA A 279 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU A 53 " --> pdb=" O ALA A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 87 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 144 through 146 removed outlier: 9.996A pdb=" N LYS A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 54 removed outlier: 7.749A pdb=" N LEU C 51 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA C 279 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU C 53 " --> pdb=" O ALA C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE C 87 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 144 through 146 removed outlier: 9.995A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AC8, first strand: chain 'F' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER F 2 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 98 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS F 88 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER F 2 " --> pdb=" O TYR F 96 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 98 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS F 88 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 18 through 24 Processing sheet with id=AD2, first strand: chain 'I' and resid 31 through 36 removed outlier: 3.935A pdb=" N CYS I 137 " --> pdb=" O ILE I 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AD5, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AD6, first strand: chain 'G' and resid 51 through 54 removed outlier: 7.748A pdb=" N LEU G 51 " --> pdb=" O CYS G 277 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA G 279 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU G 53 " --> pdb=" O ALA G 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.444A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE G 87 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.577A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 144 through 146 removed outlier: 9.995A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE3, first strand: chain 'G' and resid 286 through 288 removed outlier: 4.137A pdb=" N CYS G 281 " --> pdb=" O ILE G 288 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.751A pdb=" N ILE J 34 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'K' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER K 2 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE K 98 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER K 2 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE K 98 " --> pdb=" O SER K 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS K 88 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 18 through 24 Processing sheet with id=AF4, first strand: chain 'L' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER L 2 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE L 98 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 2 through 4 removed outlier: 6.832A pdb=" N SER L 2 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N PHE L 98 " --> pdb=" O SER L 2 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS L 88 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 24 788 hydrogen bonds defined for protein. 2043 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: 3.22 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4751 1.33 - 1.47: 5836 1.47 - 1.61: 7221 1.61 - 1.75: 21 1.75 - 1.89: 99 Bond restraints: 17928 Sorted by residual: bond pdb=" CB HIS G 47 " pdb=" CG HIS G 47 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.30e+01 bond pdb=" CB HIS A 47 " pdb=" CG HIS A 47 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.24e+01 bond pdb=" CB HIS C 47 " pdb=" CG HIS C 47 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" NE1 TRP C 127 " pdb=" CE2 TRP C 127 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.10e-02 8.26e+03 3.11e+01 bond pdb=" NE1 TRP A 127 " pdb=" CE2 TRP A 127 " ideal model delta sigma weight residual 1.370 1.309 0.061 1.10e-02 8.26e+03 3.08e+01 ... (remaining 17923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.35: 24283 7.35 - 14.71: 32 14.71 - 22.06: 0 22.06 - 29.41: 0 29.41 - 36.77: 12 Bond angle restraints: 24327 Sorted by residual: angle pdb=" C2 NAG A 403 " pdb=" N2 NAG A 403 " pdb=" C7 NAG A 403 " ideal model delta sigma weight residual 124.56 161.33 -36.77 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG G 403 " pdb=" N2 NAG G 403 " pdb=" C7 NAG G 403 " ideal model delta sigma weight residual 124.56 161.27 -36.71 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG C 403 " pdb=" N2 NAG C 403 " pdb=" C7 NAG C 403 " ideal model delta sigma weight residual 124.56 161.26 -36.70 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG G 404 " pdb=" N2 NAG G 404 " pdb=" C7 NAG G 404 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG C 404 " pdb=" N2 NAG C 404 " pdb=" C7 NAG C 404 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 ... (remaining 24322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 10060 17.37 - 34.74: 266 34.74 - 52.11: 62 52.11 - 69.49: 46 69.49 - 86.86: 18 Dihedral angle restraints: 10452 sinusoidal: 4134 harmonic: 6318 Sorted by residual: dihedral pdb=" C ASN K 29 " pdb=" N ASN K 29 " pdb=" CA ASN K 29 " pdb=" CB ASN K 29 " ideal model delta harmonic sigma weight residual -122.60 -112.41 -10.19 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -117.95 31.95 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CB CYS G 64 " pdb=" SG CYS G 64 " pdb=" SG CYS G 76 " pdb=" CB CYS G 76 " ideal model delta sinusoidal sigma weight residual -86.00 -117.94 31.94 1 1.00e+01 1.00e-02 1.45e+01 ... (remaining 10449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1799 0.090 - 0.180: 629 0.180 - 0.270: 149 0.270 - 0.360: 54 0.360 - 0.449: 21 Chirality restraints: 2652 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 -2.59 0.19 2.00e-02 2.50e+03 9.01e+01 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 -2.59 0.19 2.00e-02 2.50e+03 8.95e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.87e+01 ... (remaining 2649 not shown) Planarity restraints: 3165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU I 171 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C GLU I 171 " -0.104 2.00e-02 2.50e+03 pdb=" O GLU I 171 " 0.037 2.00e-02 2.50e+03 pdb=" OXT GLU I 171 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 171 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C GLU D 171 " -0.104 2.00e-02 2.50e+03 pdb=" O GLU D 171 " 0.037 2.00e-02 2.50e+03 pdb=" OXT GLU D 171 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 171 " 0.030 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C GLU B 171 " -0.104 2.00e-02 2.50e+03 pdb=" O GLU B 171 " 0.037 2.00e-02 2.50e+03 pdb=" OXT GLU B 171 " 0.037 2.00e-02 2.50e+03 ... (remaining 3162 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5676 2.85 - 3.36: 15648 3.36 - 3.87: 30444 3.87 - 4.39: 36248 4.39 - 4.90: 59564 Nonbonded interactions: 147580 Sorted by model distance: nonbonded pdb=" OD1 ASN K 29 " pdb=" CB ASP K 92 " model vdw 2.336 3.440 nonbonded pdb=" NZ LYS B 83 " pdb=" OD1 ASP D 85 " model vdw 2.336 3.120 nonbonded pdb=" NZ LYS D 83 " pdb=" OD1 ASP I 85 " model vdw 2.337 3.120 nonbonded pdb=" OD1 ASP B 85 " pdb=" NZ LYS I 83 " model vdw 2.337 3.120 nonbonded pdb=" O SER L 26 " pdb=" O ASN L 29 " model vdw 2.396 3.040 ... (remaining 147575 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 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = 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: 2.880 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: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.021 0.133 17970 Z= 1.108 Angle : 1.864 36.768 24429 Z= 1.164 Chirality : 0.105 0.449 2652 Planarity : 0.009 0.060 3150 Dihedral : 10.477 86.858 6366 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.11 % Allowed : 0.21 % Favored : 99.68 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2181 helix: 0.69 (0.24), residues: 363 sheet: 0.96 (0.22), residues: 522 loop : 0.78 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 321 TYR 0.062 0.009 TYR I 24 PHE 0.043 0.007 PHE G 118 TRP 0.028 0.007 TRP I 21 HIS 0.020 0.004 HIS K 34 Details of bonding type rmsd/Z covalent geometry : bond 0.02096 / 1.10 (17928) covalent geometry : angle 1.85815 / 1.16 (24327) SS BOND : bond 0.02370 / 1.62 ( 24) SS BOND : angle 2.30850 / 1.46 ( 48) hydrogen bonds : bond 0.15716 / 10.41 ( 722) hydrogen bonds : angle 7.73041 / 5.42 ( 2043) link_BETA1-4 : bond 0.07581 / 3.80 ( 3) link_BETA1-4 : angle 4.35365 / 1.92 ( 9) link_NAG-ASN : bond 0.07961 / 4.66 ( 15) link_NAG-ASN : angle 3.21227 / 2.14 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LYS cc_start: 0.7629 (ptmm) cc_final: 0.7139 (mmmt) REVERT: C 144 LYS cc_start: 0.7605 (ptmm) cc_final: 0.7201 (mmmt) REVERT: D 132 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7124 (mt-10) REVERT: J 80 MET cc_start: 0.7417 (tmm) cc_final: 0.7045 (tmm) REVERT: L 30 THR cc_start: 0.7852 (p) cc_final: 0.7496 (p) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.5937 time to fit residues: 251.5036 Evaluate side-chains 185 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS A 322 ASN B 60 ASN C 18 HIS C 60 GLN C 298 HIS D 60 ASN F 34 HIS G 18 HIS G 60 GLN G 298 HIS G 322 ASN J 100AHIS K 34 HIS L 34 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.181236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128253 restraints weight = 20525.021| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.88 r_work: 0.3304 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17970 Z= 0.180 Angle : 0.634 6.716 24429 Z= 0.344 Chirality : 0.047 0.181 2652 Planarity : 0.005 0.035 3150 Dihedral : 6.515 84.216 2402 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.97 % Allowed : 7.74 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2181 helix: 1.86 (0.26), residues: 366 sheet: 0.76 (0.21), residues: 555 loop : 0.26 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 170 TYR 0.017 0.002 TYR B 22 PHE 0.040 0.003 PHE G 118 TRP 0.014 0.002 TRP B 21 HIS 0.006 0.002 HIS J 100A Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (17928) covalent geometry : angle 0.62220 / 0.34 (24327) SS BOND : bond 0.00326 / 0.21 ( 24) SS BOND : angle 0.97923 / 0.59 ( 48) hydrogen bonds : bond 0.05580 / 3.63 ( 722) hydrogen bonds : angle 5.90576 / 4.15 ( 2043) link_BETA1-4 : bond 0.00264 / 0.13 ( 3) link_BETA1-4 : angle 1.31895 / 0.94 ( 9) link_NAG-ASN : bond 0.00835 / 0.51 ( 15) link_NAG-ASN : angle 2.79579 / 1.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7430 (p0) cc_final: 0.6773 (p0) REVERT: B 24 TYR cc_start: 0.8876 (m-80) cc_final: 0.8632 (m-80) REVERT: B 77 MET cc_start: 0.8335 (mmm) cc_final: 0.8094 (mtp) REVERT: C 75 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7381 (mm-30) REVERT: C 144 LYS cc_start: 0.7842 (ptmm) cc_final: 0.7171 (mmmt) REVERT: C 238 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8310 (mm-30) REVERT: C 285 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7880 (mm-40) REVERT: C 323 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8338 (pt) REVERT: D 124 SER cc_start: 0.8889 (m) cc_final: 0.8657 (p) REVERT: G 21 ASN cc_start: 0.7819 (p0) cc_final: 0.7495 (p0) REVERT: G 32 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7661 (tppt) REVERT: G 45 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7536 (p0) REVERT: G 144 LYS cc_start: 0.7664 (ptmm) cc_final: 0.7047 (mmmt) REVERT: G 285 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7602 (mm-40) REVERT: G 323 ILE cc_start: 0.8505 (mt) cc_final: 0.8289 (pt) REVERT: I 43 ASN cc_start: 0.8390 (t0) cc_final: 0.8045 (m-40) REVERT: I 72 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7657 (ptmt) REVERT: I 123 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8097 (ttmt) REVERT: J 101 ASP cc_start: 0.7034 (t70) cc_final: 0.6804 (p0) REVERT: K 29 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7971 (m-40) outliers start: 56 outliers final: 23 residues processed: 237 average time/residue: 0.5254 time to fit residues: 140.7276 Evaluate side-chains 197 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 54 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 29 ASN Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 127 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 295 GLN B 26 HIS D 26 HIS G 190 ASN I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.182269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132477 restraints weight = 20523.375| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.76 r_work: 0.3302 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17970 Z= 0.142 Angle : 0.545 6.617 24429 Z= 0.295 Chirality : 0.044 0.196 2652 Planarity : 0.004 0.038 3150 Dihedral : 5.799 81.802 2402 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.91 % Allowed : 9.86 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2181 helix: 2.31 (0.26), residues: 360 sheet: 0.77 (0.21), residues: 564 loop : 0.03 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 95A TYR 0.015 0.001 TYR B 162 PHE 0.028 0.002 PHE A 118 TRP 0.010 0.001 TRP J 36 HIS 0.011 0.001 HIS I 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17928) covalent geometry : angle 0.53675 / 0.29 (24327) SS BOND : bond 0.00693 / 0.35 ( 24) SS BOND : angle 1.23341 / 0.84 ( 48) hydrogen bonds : bond 0.04828 / 3.13 ( 722) hydrogen bonds : angle 5.32617 / 3.72 ( 2043) link_BETA1-4 : bond 0.00817 / 0.41 ( 3) link_BETA1-4 : angle 1.39792 / 0.83 ( 9) link_NAG-ASN : bond 0.00387 / 0.24 ( 15) link_NAG-ASN : angle 1.89458 / 1.14 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7328 (pp30) REVERT: B 24 TYR cc_start: 0.8966 (m-80) cc_final: 0.8540 (m-80) REVERT: B 39 LYS cc_start: 0.8816 (tttm) cc_final: 0.8267 (tppt) REVERT: B 77 MET cc_start: 0.8440 (mmm) cc_final: 0.8041 (mtp) REVERT: B 103 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: B 113 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8166 (m) REVERT: C 144 LYS cc_start: 0.7781 (ptmm) cc_final: 0.7068 (mmmt) REVERT: C 238 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8241 (mm-30) REVERT: C 246 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7346 (mt-10) REVERT: C 285 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7859 (mm-40) REVERT: D 123 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8127 (ttmt) REVERT: G 21 ASN cc_start: 0.7668 (p0) cc_final: 0.7299 (p0) REVERT: G 32 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7543 (tppt) REVERT: G 144 LYS cc_start: 0.7655 (ptmm) cc_final: 0.6969 (mmmt) REVERT: H 100 PHE cc_start: 0.8368 (m-80) cc_final: 0.8045 (m-80) REVERT: I 72 LYS cc_start: 0.8309 (pttm) cc_final: 0.7686 (ptmt) REVERT: I 116 LYS cc_start: 0.8172 (tttt) cc_final: 0.7966 (ttmm) REVERT: I 123 LYS cc_start: 0.8456 (ttmt) cc_final: 0.8172 (ttmt) REVERT: I 132 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8189 (tm-30) REVERT: J 100 PHE cc_start: 0.8218 (m-80) cc_final: 0.7989 (m-80) REVERT: J 101 ASP cc_start: 0.6900 (t70) cc_final: 0.6676 (p0) REVERT: K 29 ASN cc_start: 0.8117 (m110) cc_final: 0.7730 (m-40) outliers start: 55 outliers final: 20 residues processed: 237 average time/residue: 0.4995 time to fit residues: 133.9980 Evaluate side-chains 205 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 31 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS B 26 HIS C 141 HIS D 26 HIS G 141 HIS G 199 ASN G 295 GLN I 26 HIS I 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.177247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 136)---------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129743 restraints weight = 20316.632| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.62 r_work: 0.3141 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17970 Z= 0.219 Angle : 0.632 11.824 24429 Z= 0.332 Chirality : 0.046 0.196 2652 Planarity : 0.005 0.039 3150 Dihedral : 5.578 79.197 2400 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.39 % Allowed : 11.23 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.17), residues: 2181 helix: 2.46 (0.27), residues: 357 sheet: 0.78 (0.22), residues: 549 loop : -0.23 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 95A TYR 0.022 0.002 TYR D 162 PHE 0.033 0.003 PHE A 118 TRP 0.010 0.002 TRP J 36 HIS 0.010 0.002 HIS I 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (17928) covalent geometry : angle 0.61928 / 0.33 (24327) SS BOND : bond 0.00739 / 0.41 ( 24) SS BOND : angle 2.01849 / 1.41 ( 48) hydrogen bonds : bond 0.05017 / 3.25 ( 722) hydrogen bonds : angle 5.37813 / 3.76 ( 2043) link_BETA1-4 : bond 0.00139 / 0.07 ( 3) link_BETA1-4 : angle 1.59085 / 1.04 ( 9) link_NAG-ASN : bond 0.00487 / 0.31 ( 15) link_NAG-ASN : angle 2.20986 / 1.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8095 (tppt) REVERT: B 24 TYR cc_start: 0.8976 (m-80) cc_final: 0.8543 (m-80) REVERT: B 103 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: B 113 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8257 (m) REVERT: B 171 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6541 (pm20) REVERT: C 21 ASN cc_start: 0.7577 (p0) cc_final: 0.7173 (p0) REVERT: C 32 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7479 (tppt) REVERT: C 144 LYS cc_start: 0.7857 (ptmm) cc_final: 0.7003 (mmmt) REVERT: C 238 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 246 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7637 (mt-10) REVERT: C 285 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: D 106 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7271 (mmp80) REVERT: G 32 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7453 (tppt) REVERT: G 60 GLN cc_start: 0.7993 (tp-100) cc_final: 0.7754 (tm-30) REVERT: G 144 LYS cc_start: 0.7680 (ptmm) cc_final: 0.6947 (mmmt) REVERT: I 72 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7630 (ptmt) REVERT: I 123 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7957 (ttmt) REVERT: J 91 TYR cc_start: 0.8719 (m-80) cc_final: 0.8511 (m-80) REVERT: K 29 ASN cc_start: 0.8496 (m110) cc_final: 0.8241 (m-40) outliers start: 64 outliers final: 33 residues processed: 240 average time/residue: 0.4799 time to fit residues: 130.4551 Evaluate side-chains 216 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 295 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 158 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS B 26 HIS B 62 GLN D 26 HIS D 62 GLN F 29 ASN I 26 HIS I 62 GLN K 29 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.170880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 148)---------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122437 restraints weight = 20322.767| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.54 r_work: 0.3045 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 17970 Z= 0.383 Angle : 0.783 11.357 24429 Z= 0.403 Chirality : 0.052 0.194 2652 Planarity : 0.006 0.049 3150 Dihedral : 5.870 77.051 2400 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.87 % Allowed : 12.29 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.17), residues: 2181 helix: 2.25 (0.27), residues: 351 sheet: 0.57 (0.21), residues: 549 loop : -0.65 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 229 TYR 0.026 0.003 TYR B 162 PHE 0.042 0.003 PHE A 118 TRP 0.014 0.002 TRP C 84 HIS 0.009 0.002 HIS I 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.38 (17928) covalent geometry : angle 0.76956 / 0.40 (24327) SS BOND : bond 0.00775 / 0.48 ( 24) SS BOND : angle 2.13338 / 1.42 ( 48) hydrogen bonds : bond 0.05710 / 3.71 ( 722) hydrogen bonds : angle 5.60921 / 3.93 ( 2043) link_BETA1-4 : bond 0.00332 / 0.16 ( 3) link_BETA1-4 : angle 2.03044 / 1.23 ( 9) link_NAG-ASN : bond 0.00751 / 0.47 ( 15) link_NAG-ASN : angle 2.66757 / 1.63 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 196 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7923 (tppt) REVERT: B 17 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8163 (ttp) REVERT: B 24 TYR cc_start: 0.8935 (m-80) cc_final: 0.8602 (m-80) REVERT: B 43 ASN cc_start: 0.8402 (t0) cc_final: 0.8097 (m-40) REVERT: B 113 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8128 (m) REVERT: B 116 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7844 (ttmm) REVERT: B 171 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6485 (pm20) REVERT: C 21 ASN cc_start: 0.7680 (p0) cc_final: 0.7315 (p0) REVERT: C 144 LYS cc_start: 0.7857 (ptmm) cc_final: 0.6848 (mmmt) REVERT: C 246 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 310 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7679 (ttm170) REVERT: D 72 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7593 (pttt) REVERT: D 106 ARG cc_start: 0.7636 (mtp180) cc_final: 0.7082 (mmp80) REVERT: E 100 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8637 (mt-10) REVERT: G 60 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7864 (tm-30) REVERT: G 144 LYS cc_start: 0.7672 (ptmm) cc_final: 0.6875 (mmmt) REVERT: H 100 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8600 (mt-10) REVERT: I 123 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7909 (ttmt) REVERT: J 63 PHE cc_start: 0.7841 (m-80) cc_final: 0.7365 (m-80) REVERT: J 89 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7591 (tpt) REVERT: J 91 TYR cc_start: 0.8643 (m-80) cc_final: 0.8427 (m-80) REVERT: K 29 ASN cc_start: 0.8465 (m-40) cc_final: 0.8188 (m-40) outliers start: 73 outliers final: 50 residues processed: 236 average time/residue: 0.5206 time to fit residues: 138.9567 Evaluate side-chains 238 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 MET Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 309 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 158 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS D 26 HIS F 29 ASN I 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123155 restraints weight = 20172.175| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.83 r_work: 0.3205 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17970 Z= 0.150 Angle : 0.576 11.454 24429 Z= 0.302 Chirality : 0.043 0.175 2652 Planarity : 0.004 0.062 3150 Dihedral : 5.393 74.901 2400 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.38 % Allowed : 14.41 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 2181 helix: 2.48 (0.27), residues: 357 sheet: 0.58 (0.20), residues: 603 loop : -0.53 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 95A TYR 0.025 0.001 TYR B 162 PHE 0.021 0.002 PHE A 118 TRP 0.008 0.001 TRP I 92 HIS 0.009 0.001 HIS D 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (17928) covalent geometry : angle 0.56403 / 0.30 (24327) SS BOND : bond 0.00528 / 0.28 ( 24) SS BOND : angle 2.00271 / 1.32 ( 48) hydrogen bonds : bond 0.04596 / 2.98 ( 722) hydrogen bonds : angle 5.28695 / 3.70 ( 2043) link_BETA1-4 : bond 0.00104 / 0.05 ( 3) link_BETA1-4 : angle 1.61160 / 1.05 ( 9) link_NAG-ASN : bond 0.00249 / 0.15 ( 15) link_NAG-ASN : angle 1.80595 / 1.09 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.9005 (m-80) cc_final: 0.8628 (m-80) REVERT: B 43 ASN cc_start: 0.8401 (t0) cc_final: 0.8175 (m-40) REVERT: B 113 SER cc_start: 0.8895 (p) cc_final: 0.8589 (m) REVERT: B 116 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8460 (ttmm) REVERT: B 171 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6441 (pm20) REVERT: C 144 LYS cc_start: 0.7962 (ptmm) cc_final: 0.7329 (mmmt) REVERT: C 246 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7824 (mt-10) REVERT: D 106 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7789 (mmp80) REVERT: G 32 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7758 (tppt) REVERT: G 60 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7790 (tm-30) REVERT: I 43 ASN cc_start: 0.8424 (t0) cc_final: 0.8153 (m-40) REVERT: I 72 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7815 (ptmt) REVERT: I 116 LYS cc_start: 0.8556 (mtpm) cc_final: 0.8123 (ttmm) REVERT: J 63 PHE cc_start: 0.8126 (m-80) cc_final: 0.7687 (m-80) REVERT: J 91 TYR cc_start: 0.8994 (m-80) cc_final: 0.8762 (m-80) outliers start: 45 outliers final: 22 residues processed: 227 average time/residue: 0.5108 time to fit residues: 129.9893 Evaluate side-chains 210 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain L residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS D 26 HIS F 29 ASN I 26 HIS K 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.177612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132631 restraints weight = 20274.891| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.50 r_work: 0.3241 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 17970 Z= 0.380 Angle : 0.768 11.412 24429 Z= 0.394 Chirality : 0.051 0.179 2652 Planarity : 0.006 0.067 3150 Dihedral : 5.664 72.996 2400 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.66 % Allowed : 13.94 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2181 helix: 2.20 (0.27), residues: 357 sheet: 0.51 (0.21), residues: 549 loop : -0.75 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 95A TYR 0.027 0.003 TYR B 162 PHE 0.037 0.003 PHE A 118 TRP 0.013 0.002 TRP C 127 HIS 0.010 0.002 HIS H 100E Details of bonding type rmsd/Z covalent geometry : bond 0.00932 / 0.38 (17928) covalent geometry : angle 0.75532 / 0.39 (24327) SS BOND : bond 0.00820 / 0.50 ( 24) SS BOND : angle 2.06899 / 1.34 ( 48) hydrogen bonds : bond 0.05560 / 3.63 ( 722) hydrogen bonds : angle 5.60794 / 3.93 ( 2043) link_BETA1-4 : bond 0.00212 / 0.10 ( 3) link_BETA1-4 : angle 1.96863 / 1.17 ( 9) link_NAG-ASN : bond 0.00724 / 0.46 ( 15) link_NAG-ASN : angle 2.56868 / 1.57 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 199 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8987 (m-80) cc_final: 0.8629 (m-80) REVERT: B 43 ASN cc_start: 0.8391 (t0) cc_final: 0.8156 (m-40) REVERT: B 106 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7523 (mmp80) REVERT: B 113 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8329 (m) REVERT: B 116 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8004 (ttmm) REVERT: B 171 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6349 (pm20) REVERT: C 144 LYS cc_start: 0.7941 (ptmm) cc_final: 0.7077 (mmmt) REVERT: C 246 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7819 (mt-10) REVERT: D 72 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7505 (pttt) REVERT: E 100 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8892 (mt-10) REVERT: G 60 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7876 (tm-30) REVERT: G 310 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7922 (ptp90) REVERT: H 50 ARG cc_start: 0.8774 (ptt90) cc_final: 0.8075 (ptt180) REVERT: I 116 LYS cc_start: 0.8236 (mtpm) cc_final: 0.7675 (ttmm) REVERT: J 63 PHE cc_start: 0.8042 (m-80) cc_final: 0.7641 (m-80) REVERT: J 91 TYR cc_start: 0.8806 (m-80) cc_final: 0.8586 (m-80) outliers start: 69 outliers final: 47 residues processed: 238 average time/residue: 0.4933 time to fit residues: 132.0136 Evaluate side-chains 238 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 285 GLN Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 61 optimal weight: 0.7980 chunk 147 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS D 26 HIS F 29 ASN I 26 HIS K 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.173701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 144)---------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126316 restraints weight = 20243.088| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.58 r_work: 0.3109 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17970 Z= 0.145 Angle : 0.572 10.648 24429 Z= 0.301 Chirality : 0.043 0.154 2652 Planarity : 0.005 0.076 3150 Dihedral : 5.237 70.363 2400 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.97 % Allowed : 14.84 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2181 helix: 2.51 (0.28), residues: 357 sheet: 0.67 (0.21), residues: 561 loop : -0.65 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 95A TYR 0.026 0.001 TYR B 162 PHE 0.020 0.002 PHE A 118 TRP 0.008 0.001 TRP I 92 HIS 0.010 0.001 HIS I 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (17928) covalent geometry : angle 0.56298 / 0.30 (24327) SS BOND : bond 0.00409 / 0.22 ( 24) SS BOND : angle 1.65679 / 1.08 ( 48) hydrogen bonds : bond 0.04449 / 2.88 ( 722) hydrogen bonds : angle 5.29613 / 3.70 ( 2043) link_BETA1-4 : bond 0.00380 / 0.19 ( 3) link_BETA1-4 : angle 1.77888 / 1.15 ( 9) link_NAG-ASN : bond 0.00224 / 0.13 ( 15) link_NAG-ASN : angle 1.71964 / 1.03 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8874 (m-80) cc_final: 0.8511 (m-80) REVERT: B 43 ASN cc_start: 0.8381 (t0) cc_final: 0.8078 (m-40) REVERT: B 106 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7388 (mmp80) REVERT: B 113 SER cc_start: 0.8537 (p) cc_final: 0.8141 (m) REVERT: B 116 LYS cc_start: 0.8100 (mtpp) cc_final: 0.7713 (ttmm) REVERT: B 171 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6419 (pm20) REVERT: C 144 LYS cc_start: 0.7784 (ptmm) cc_final: 0.6918 (mmmt) REVERT: C 246 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7692 (mt-10) REVERT: D 106 ARG cc_start: 0.7905 (mtm110) cc_final: 0.7301 (mmp80) REVERT: D 149 MET cc_start: 0.6677 (mmt) cc_final: 0.6476 (mmt) REVERT: G 32 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7574 (tppt) REVERT: G 60 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7880 (tm-30) REVERT: G 310 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7980 (ptp90) REVERT: H 50 ARG cc_start: 0.8672 (ptt90) cc_final: 0.7970 (ptt180) REVERT: I 43 ASN cc_start: 0.8340 (t0) cc_final: 0.8005 (m-40) REVERT: I 72 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7711 (ptmt) REVERT: I 116 LYS cc_start: 0.7996 (mtpm) cc_final: 0.7423 (ttmm) REVERT: J 63 PHE cc_start: 0.7920 (m-80) cc_final: 0.7381 (m-80) REVERT: J 89 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7799 (tpt) REVERT: J 91 TYR cc_start: 0.8661 (m-80) cc_final: 0.8448 (m-80) REVERT: K 29 ASN cc_start: 0.8692 (m110) cc_final: 0.8238 (m-40) outliers start: 56 outliers final: 37 residues processed: 232 average time/residue: 0.4794 time to fit residues: 126.2203 Evaluate side-chains 227 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 137 CYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 122 optimal weight: 6.9990 chunk 148 optimal weight: 0.0040 chunk 175 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS D 26 HIS ** E 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140712 restraints weight = 20331.382| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.55 r_work: 0.3340 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17970 Z= 0.135 Angle : 0.551 10.073 24429 Z= 0.290 Chirality : 0.043 0.152 2652 Planarity : 0.005 0.077 3150 Dihedral : 5.013 66.900 2400 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.81 % Allowed : 15.53 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2181 helix: 2.63 (0.28), residues: 360 sheet: 0.60 (0.21), residues: 591 loop : -0.53 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG L 95A TYR 0.024 0.001 TYR D 162 PHE 0.019 0.002 PHE I 110 TRP 0.007 0.001 TRP I 92 HIS 0.011 0.001 HIS I 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (17928) covalent geometry : angle 0.54282 / 0.29 (24327) SS BOND : bond 0.00523 / 0.28 ( 24) SS BOND : angle 1.46471 / 0.95 ( 48) hydrogen bonds : bond 0.04247 / 2.75 ( 722) hydrogen bonds : angle 5.17540 / 3.62 ( 2043) link_BETA1-4 : bond 0.00353 / 0.18 ( 3) link_BETA1-4 : angle 1.57153 / 1.02 ( 9) link_NAG-ASN : bond 0.00208 / 0.13 ( 15) link_NAG-ASN : angle 1.64278 / 0.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8968 (m-80) cc_final: 0.8660 (m-80) REVERT: B 43 ASN cc_start: 0.8375 (t0) cc_final: 0.8094 (m-40) REVERT: B 106 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7692 (mmp80) REVERT: B 113 SER cc_start: 0.8716 (p) cc_final: 0.8385 (m) REVERT: B 116 LYS cc_start: 0.8375 (mtpp) cc_final: 0.8063 (ttmm) REVERT: B 127 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8027 (ttmm) REVERT: C 144 LYS cc_start: 0.7873 (ptmm) cc_final: 0.7158 (mmmt) REVERT: C 246 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7687 (mt-10) REVERT: D 106 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7642 (mmp80) REVERT: E 61 GLN cc_start: 0.7866 (tp-100) cc_final: 0.7576 (tp40) REVERT: G 32 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7563 (tppt) REVERT: G 60 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7903 (tm-30) REVERT: H 50 ARG cc_start: 0.8752 (ptt90) cc_final: 0.8072 (ptt180) REVERT: I 11 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7005 (pp20) REVERT: I 72 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7748 (ptmt) REVERT: J 63 PHE cc_start: 0.8087 (m-80) cc_final: 0.7626 (m-80) REVERT: J 89 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8155 (tpt) REVERT: J 91 TYR cc_start: 0.8835 (m-80) cc_final: 0.8610 (m-80) REVERT: K 29 ASN cc_start: 0.8897 (m110) cc_final: 0.8485 (m-40) REVERT: L 54 ARG cc_start: 0.8929 (mtm110) cc_final: 0.8722 (mtm110) outliers start: 53 outliers final: 35 residues processed: 227 average time/residue: 0.4735 time to fit residues: 122.0471 Evaluate side-chains 223 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 124 SER Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 140 optimal weight: 1.9990 chunk 75 optimal weight: 0.0040 chunk 133 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS D 26 HIS ** E 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 148)---------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131648 restraints weight = 20279.378| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.48 r_work: 0.3358 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17970 Z= 0.166 Angle : 0.571 9.434 24429 Z= 0.299 Chirality : 0.043 0.155 2652 Planarity : 0.005 0.050 3150 Dihedral : 4.971 64.109 2400 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.54 % Allowed : 16.11 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2181 helix: 2.71 (0.28), residues: 360 sheet: 0.75 (0.21), residues: 561 loop : -0.51 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 106 TYR 0.026 0.001 TYR B 162 PHE 0.021 0.002 PHE A 118 TRP 0.010 0.001 TRP I 14 HIS 0.010 0.001 HIS I 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (17928) covalent geometry : angle 0.56332 / 0.30 (24327) SS BOND : bond 0.00520 / 0.29 ( 24) SS BOND : angle 1.42257 / 0.90 ( 48) hydrogen bonds : bond 0.04339 / 2.80 ( 722) hydrogen bonds : angle 5.21423 / 3.65 ( 2043) link_BETA1-4 : bond 0.00286 / 0.14 ( 3) link_BETA1-4 : angle 1.58373 / 1.03 ( 9) link_NAG-ASN : bond 0.00262 / 0.16 ( 15) link_NAG-ASN : angle 1.74118 / 1.05 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8960 (m-80) cc_final: 0.8652 (m-80) REVERT: B 106 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7642 (mmp80) REVERT: B 113 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8355 (m) REVERT: B 116 LYS cc_start: 0.8248 (mtpp) cc_final: 0.7883 (ttmm) REVERT: C 144 LYS cc_start: 0.7884 (ptmm) cc_final: 0.7170 (mmmt) REVERT: C 246 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7651 (mt-10) REVERT: D 106 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7614 (mmp80) REVERT: E 61 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7567 (tp40) REVERT: G 32 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7564 (tppt) REVERT: G 60 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7840 (tm-30) REVERT: H 50 ARG cc_start: 0.8744 (ptt90) cc_final: 0.8051 (ptt180) REVERT: I 11 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6938 (pp20) REVERT: I 72 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7717 (ptmt) REVERT: J 63 PHE cc_start: 0.8069 (m-80) cc_final: 0.7595 (m-80) REVERT: J 89 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7745 (tpt) REVERT: J 91 TYR cc_start: 0.8819 (m-80) cc_final: 0.8569 (m-80) REVERT: K 29 ASN cc_start: 0.8883 (m110) cc_final: 0.8441 (m-40) REVERT: L 54 ARG cc_start: 0.8939 (mtm110) cc_final: 0.8725 (mtm110) outliers start: 48 outliers final: 36 residues processed: 221 average time/residue: 0.4785 time to fit residues: 119.9620 Evaluate side-chains 226 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 72 LYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 72 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 148 CYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 19 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 173 optimal weight: 0.0020 chunk 8 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 HIS D 26 HIS ** E 100JGLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.182607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141280 restraints weight = 20347.448| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.46 r_work: 0.3328 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17970 Z= 0.137 Angle : 0.545 8.846 24429 Z= 0.285 Chirality : 0.043 0.164 2652 Planarity : 0.004 0.046 3150 Dihedral : 4.813 60.183 2400 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.65 % Allowed : 16.06 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2181 helix: 2.79 (0.28), residues: 360 sheet: 0.66 (0.21), residues: 591 loop : -0.48 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 106 TYR 0.024 0.001 TYR B 162 PHE 0.018 0.002 PHE E 63 TRP 0.009 0.001 TRP I 14 HIS 0.011 0.001 HIS I 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (17928) covalent geometry : angle 0.53765 / 0.28 (24327) SS BOND : bond 0.00474 / 0.26 ( 24) SS BOND : angle 1.36587 / 0.87 ( 48) hydrogen bonds : bond 0.04112 / 2.66 ( 722) hydrogen bonds : angle 5.14910 / 3.60 ( 2043) link_BETA1-4 : bond 0.00305 / 0.15 ( 3) link_BETA1-4 : angle 1.53222 / 0.98 ( 9) link_NAG-ASN : bond 0.00197 / 0.12 ( 15) link_NAG-ASN : angle 1.57284 / 0.94 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6611.53 seconds wall clock time: 113 minutes 15.59 seconds (6795.59 seconds total)