Starting phenix.real_space_refine on Sun Aug 24 05:53:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp5_41467/08_2025/8tp5_41467.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp5_41467/08_2025/8tp5_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_41467/08_2025/8tp5_41467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp5_41467/08_2025/8tp5_41467.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp5_41467/08_2025/8tp5_41467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp5_41467/08_2025/8tp5_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.91, per 1000 atoms: 0.28 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: 1.71 Conformation dependent library (CDL) restraints added in 886.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.74 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: 3.69 Time building geometry restraints manager: 2.22 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: 10408 17.37 - 34.74: 281 34.74 - 52.11: 65 52.11 - 69.49: 58 69.49 - 86.86: 18 Dihedral angle restraints: 10830 sinusoidal: 4512 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 10827 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 10.607 86.858 6744 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 aren 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 covalent geometry : bond 0.02096 (17928) covalent geometry : angle 1.85815 (24327) SS BOND : bond 0.02370 ( 24) SS BOND : angle 2.30850 ( 48) hydrogen bonds : bond 0.15716 ( 722) hydrogen bonds : angle 7.73041 ( 2043) link_BETA1-4 : bond 0.07581 ( 3) link_BETA1-4 : angle 4.35365 ( 9) link_NAG-ASN : bond 0.07961 ( 15) link_NAG-ASN : angle 3.21227 ( 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 : 0.754 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: 0.6682 time to fit residues: 281.1854 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 : 0.613 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 298 HIS A 322 ASN B 60 ASN C 18 HIS C 60 GLN C 298 HIS 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 = 0.4099 r_free = 0.4099 target = 0.181376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133165 restraints weight = 20512.485| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.88 r_work: 0.3373 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17970 Z= 0.178 Angle : 0.628 6.620 24429 Z= 0.340 Chirality : 0.047 0.224 2652 Planarity : 0.005 0.034 3150 Dihedral : 6.929 84.301 2780 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.97 % Allowed : 7.79 % Favored : 89.24 % 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 aren not related in a simple way. whole: 0.92 (0.17), residues: 2181 helix: 1.85 (0.26), residues: 366 sheet: 0.75 (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 I 170 TYR 0.016 0.002 TYR B 22 PHE 0.039 0.003 PHE G 118 TRP 0.014 0.002 TRP B 21 HIS 0.006 0.002 HIS E 58 Details of bonding type rmsd covalent geometry : bond 0.00392 (17928) covalent geometry : angle 0.61738 (24327) SS BOND : bond 0.00329 ( 24) SS BOND : angle 0.92239 ( 48) hydrogen bonds : bond 0.05530 ( 722) hydrogen bonds : angle 5.88942 ( 2043) link_BETA1-4 : bond 0.00353 ( 3) link_BETA1-4 : angle 1.18942 ( 9) link_NAG-ASN : bond 0.00926 ( 15) link_NAG-ASN : angle 2.63347 ( 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 260 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASN cc_start: 0.7347 (p0) cc_final: 0.6709 (p0) REVERT: B 24 TYR cc_start: 0.8845 (m-80) cc_final: 0.8634 (m-80) REVERT: B 77 MET cc_start: 0.8199 (mmm) cc_final: 0.7945 (mtp) REVERT: C 46 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8336 (t) REVERT: C 75 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: C 144 LYS cc_start: 0.7779 (ptmm) cc_final: 0.7042 (mmmt) REVERT: C 238 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8217 (mm-30) REVERT: C 285 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (mm-40) REVERT: C 323 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8284 (pt) REVERT: D 124 SER cc_start: 0.8848 (m) cc_final: 0.8611 (p) REVERT: D 132 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8098 (tm-30) REVERT: G 21 ASN cc_start: 0.7747 (p0) cc_final: 0.7428 (p0) REVERT: G 32 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7569 (tppt) REVERT: G 45 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7584 (p0) REVERT: G 144 LYS cc_start: 0.7577 (ptmm) cc_final: 0.6902 (mmmt) REVERT: G 285 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7454 (mm-40) REVERT: G 323 ILE cc_start: 0.8463 (mt) cc_final: 0.8231 (pt) REVERT: I 43 ASN cc_start: 0.8340 (t0) cc_final: 0.7982 (m-40) REVERT: I 72 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7617 (ptmt) REVERT: I 123 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7964 (ttmt) REVERT: J 101 ASP cc_start: 0.6897 (t70) cc_final: 0.6675 (p0) REVERT: K 29 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7807 (m-40) outliers start: 56 outliers final: 23 residues processed: 239 average time/residue: 0.6137 time to fit residues: 164.5950 Evaluate side-chains 200 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 46 SER 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: 0.5980 chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 95 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 295 GLN B 26 HIS D 26 HIS G 190 ASN G 295 GLN I 26 HIS K 29 ASN L 29 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.181918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133864 restraints weight = 20491.997| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.73 r_work: 0.3203 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17970 Z= 0.148 Angle : 0.550 7.020 24429 Z= 0.297 Chirality : 0.044 0.188 2652 Planarity : 0.004 0.038 3150 Dihedral : 5.904 81.868 2780 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.18 % Allowed : 9.59 % 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 aren not related in a simple way. whole: 0.90 (0.17), residues: 2181 helix: 2.32 (0.26), residues: 360 sheet: 0.79 (0.21), residues: 564 loop : 0.05 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 95A TYR 0.013 0.001 TYR D 162 PHE 0.030 0.002 PHE A 118 TRP 0.010 0.001 TRP J 36 HIS 0.010 0.002 HIS I 26 Details of bonding type rmsd covalent geometry : bond 0.00337 (17928) covalent geometry : angle 0.54099 (24327) SS BOND : bond 0.00363 ( 24) SS BOND : angle 1.26573 ( 48) hydrogen bonds : bond 0.04878 ( 722) hydrogen bonds : angle 5.34639 ( 2043) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 1.30452 ( 9) link_NAG-ASN : bond 0.00368 ( 15) link_NAG-ASN : angle 2.01374 ( 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 265 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 205 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7285 (pp30) REVERT: B 24 TYR cc_start: 0.8935 (m-80) cc_final: 0.8509 (m-80) REVERT: B 39 LYS cc_start: 0.8762 (tttm) cc_final: 0.8153 (tppt) REVERT: B 77 MET cc_start: 0.8346 (mmm) cc_final: 0.7903 (mtp) REVERT: B 113 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.7993 (m) REVERT: B 116 LYS cc_start: 0.7991 (tttt) cc_final: 0.7755 (ttmm) REVERT: C 144 LYS cc_start: 0.7708 (ptmm) cc_final: 0.6903 (mmmt) REVERT: C 238 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8191 (mm-30) REVERT: C 246 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 285 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7833 (mm-40) REVERT: D 124 SER cc_start: 0.8654 (m) cc_final: 0.8403 (p) REVERT: G 21 ASN cc_start: 0.7656 (p0) cc_final: 0.7340 (p0) REVERT: G 31 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: G 32 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7436 (tppt) REVERT: G 144 LYS cc_start: 0.7537 (ptmm) cc_final: 0.6777 (mmmt) REVERT: I 72 LYS cc_start: 0.8354 (pttm) cc_final: 0.7656 (ptmt) REVERT: I 116 LYS cc_start: 0.8017 (tttt) cc_final: 0.7784 (ttmm) REVERT: I 123 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7990 (ttmt) REVERT: I 132 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8144 (tm-30) REVERT: J 100 PHE cc_start: 0.8106 (m-80) cc_final: 0.7893 (m-80) REVERT: J 101 ASP cc_start: 0.6775 (t70) cc_final: 0.6517 (p0) REVERT: K 29 ASN cc_start: 0.7973 (m110) cc_final: 0.7635 (m-40) outliers start: 60 outliers final: 25 residues processed: 240 average time/residue: 0.6214 time to fit residues: 167.3005 Evaluate side-chains 210 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 40 SER 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 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 D residue 131 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 31 GLU Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 295 GLN 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: 0.9990 chunk 123 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 295 GLN B 26 HIS C 141 HIS D 26 HIS D 60 ASN G 141 HIS G 199 ASN I 26 HIS I 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134311 restraints weight = 20325.751| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.61 r_work: 0.3156 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17970 Z= 0.224 Angle : 0.629 11.317 24429 Z= 0.330 Chirality : 0.046 0.213 2652 Planarity : 0.005 0.039 3150 Dihedral : 5.731 79.559 2778 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.13 % Allowed : 11.23 % Favored : 85.64 % 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 aren not related in a simple way. whole: 0.69 (0.17), residues: 2181 helix: 2.44 (0.27), residues: 357 sheet: 0.75 (0.21), residues: 564 loop : -0.23 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 95A TYR 0.014 0.002 TYR C 209 PHE 0.032 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 covalent geometry : bond 0.00537 (17928) covalent geometry : angle 0.61615 (24327) SS BOND : bond 0.01198 ( 24) SS BOND : angle 1.94230 ( 48) hydrogen bonds : bond 0.04984 ( 722) hydrogen bonds : angle 5.41603 ( 2043) link_BETA1-4 : bond 0.00009 ( 3) link_BETA1-4 : angle 1.44425 ( 9) link_NAG-ASN : bond 0.00491 ( 15) link_NAG-ASN : angle 2.24624 ( 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 262 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.9014 (m-80) cc_final: 0.8580 (m-80) REVERT: B 113 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8209 (m) REVERT: B 171 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6468 (pm20) REVERT: C 21 ASN cc_start: 0.7625 (p0) cc_final: 0.7245 (p0) REVERT: C 144 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7019 (mmmt) REVERT: C 238 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8259 (mm-30) REVERT: C 246 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7686 (mt-10) REVERT: C 285 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: D 106 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7316 (mmp80) REVERT: D 124 SER cc_start: 0.8854 (m) cc_final: 0.8622 (p) REVERT: G 21 ASN cc_start: 0.7798 (p0) cc_final: 0.7420 (p0) REVERT: G 32 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7550 (tppt) REVERT: G 60 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7734 (tm-30) REVERT: G 144 LYS cc_start: 0.7684 (ptmm) cc_final: 0.6984 (mmmt) REVERT: I 72 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7656 (ptmt) REVERT: I 123 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8058 (ttmt) REVERT: J 89 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7542 (tpt) REVERT: J 91 TYR cc_start: 0.8802 (m-80) cc_final: 0.8591 (m-80) REVERT: K 29 ASN cc_start: 0.8552 (m110) cc_final: 0.8312 (m-40) outliers start: 59 outliers final: 36 residues processed: 238 average time/residue: 0.6176 time to fit residues: 165.7892 Evaluate side-chains 216 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 171 GLU 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 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 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 131 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 158 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 149 optimal weight: 0.0980 chunk 138 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS K 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131398 restraints weight = 20299.975| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.65 r_work: 0.3342 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17970 Z= 0.144 Angle : 0.553 10.227 24429 Z= 0.292 Chirality : 0.043 0.189 2652 Planarity : 0.004 0.043 3150 Dihedral : 5.458 77.620 2778 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.76 % Allowed : 12.72 % Favored : 84.53 % 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 aren not related in a simple way. whole: 0.72 (0.18), residues: 2181 helix: 2.57 (0.26), residues: 360 sheet: 0.74 (0.21), residues: 564 loop : -0.24 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 95A TYR 0.023 0.001 TYR B 162 PHE 0.024 0.002 PHE A 118 TRP 0.007 0.001 TRP H 36 HIS 0.009 0.001 HIS I 26 Details of bonding type rmsd covalent geometry : bond 0.00337 (17928) covalent geometry : angle 0.54200 (24327) SS BOND : bond 0.00539 ( 24) SS BOND : angle 1.89792 ( 48) hydrogen bonds : bond 0.04513 ( 722) hydrogen bonds : angle 5.20432 ( 2043) link_BETA1-4 : bond 0.00135 ( 3) link_BETA1-4 : angle 1.25364 ( 9) link_NAG-ASN : bond 0.00270 ( 15) link_NAG-ASN : angle 1.81161 ( 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 248 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.9009 (m-80) cc_final: 0.8603 (m-80) REVERT: B 43 ASN cc_start: 0.8356 (t0) cc_final: 0.8104 (m-40) REVERT: B 113 SER cc_start: 0.8754 (p) cc_final: 0.8445 (m) REVERT: B 171 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6336 (pm20) REVERT: C 21 ASN cc_start: 0.7680 (p0) cc_final: 0.7338 (p0) REVERT: C 144 LYS cc_start: 0.7904 (ptmm) cc_final: 0.7267 (mmmt) REVERT: C 246 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7610 (mt-10) REVERT: C 285 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8195 (mm-40) REVERT: D 106 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7550 (mmp80) REVERT: D 116 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8042 (ttmm) REVERT: D 124 SER cc_start: 0.8881 (m) cc_final: 0.8668 (p) REVERT: G 32 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7624 (tppt) REVERT: H 100 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8445 (mt-10) REVERT: I 72 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7680 (ptmt) REVERT: J 91 TYR cc_start: 0.8932 (m-80) cc_final: 0.8700 (m-80) REVERT: K 29 ASN cc_start: 0.8369 (m-40) cc_final: 0.8103 (m110) outliers start: 52 outliers final: 27 residues processed: 224 average time/residue: 0.5991 time to fit residues: 151.3859 Evaluate side-chains 211 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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 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 131 LYS Chi-restraints excluded: chain D residue 137 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 G residue 78 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain I residue 72 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 158 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 180 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.0040 chunk 1 optimal weight: 0.0970 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139935 restraints weight = 20189.387| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.56 r_work: 0.3208 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17970 Z= 0.117 Angle : 0.512 9.452 24429 Z= 0.271 Chirality : 0.042 0.171 2652 Planarity : 0.004 0.039 3150 Dihedral : 5.105 74.458 2778 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.49 % Allowed : 13.14 % Favored : 84.37 % 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 aren not related in a simple way. whole: 0.81 (0.18), residues: 2181 helix: 2.86 (0.27), residues: 357 sheet: 0.76 (0.21), residues: 594 loop : -0.26 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 95A TYR 0.024 0.001 TYR B 162 PHE 0.019 0.001 PHE B 110 TRP 0.007 0.001 TRP I 92 HIS 0.011 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00267 (17928) covalent geometry : angle 0.50340 (24327) SS BOND : bond 0.00503 ( 24) SS BOND : angle 1.59284 ( 48) hydrogen bonds : bond 0.04127 ( 722) hydrogen bonds : angle 5.03624 ( 2043) link_BETA1-4 : bond 0.00398 ( 3) link_BETA1-4 : angle 1.16217 ( 9) link_NAG-ASN : bond 0.00204 ( 15) link_NAG-ASN : angle 1.61104 ( 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 249 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8038 (ttmt) REVERT: B 24 TYR cc_start: 0.8935 (m-80) cc_final: 0.8623 (m-80) REVERT: B 103 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: B 113 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8246 (m) REVERT: B 171 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: C 21 ASN cc_start: 0.7735 (p0) cc_final: 0.7361 (p0) REVERT: C 144 LYS cc_start: 0.7781 (ptmm) cc_final: 0.7023 (mmmt) REVERT: C 246 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 285 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8032 (mm-40) REVERT: D 106 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7394 (mmp80) REVERT: D 124 SER cc_start: 0.8768 (m) cc_final: 0.8506 (p) REVERT: D 131 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8081 (tttp) REVERT: E 61 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7699 (tp40) REVERT: H 100 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8464 (mt-10) REVERT: H 100 PHE cc_start: 0.8319 (m-80) cc_final: 0.7941 (m-80) REVERT: I 72 LYS cc_start: 0.8312 (pttm) cc_final: 0.7672 (ptmt) REVERT: I 116 LYS cc_start: 0.8050 (mtpm) cc_final: 0.7510 (ttmm) REVERT: J 89 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7779 (tpt) REVERT: K 29 ASN cc_start: 0.8209 (m-40) cc_final: 0.7899 (m110) outliers start: 47 outliers final: 22 residues processed: 230 average time/residue: 0.5714 time to fit residues: 148.4145 Evaluate side-chains 206 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 103 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 171 GLU 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 F residue 3 VAL Chi-restraints excluded: chain F residue 29 ASN 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 89 MET 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 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 93 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 32 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 126 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS I 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.176776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129234 restraints weight = 20254.677| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.63 r_work: 0.3131 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17970 Z= 0.163 Angle : 0.561 9.629 24429 Z= 0.294 Chirality : 0.043 0.157 2652 Planarity : 0.004 0.039 3150 Dihedral : 5.203 71.354 2778 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.54 % Allowed : 13.94 % Favored : 83.52 % 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 aren not related in a simple way. whole: 0.77 (0.18), residues: 2181 helix: 2.89 (0.27), residues: 357 sheet: 0.72 (0.21), residues: 594 loop : -0.30 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 95A TYR 0.024 0.001 TYR B 162 PHE 0.024 0.002 PHE C 118 TRP 0.008 0.001 TRP E 36 HIS 0.010 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00391 (17928) covalent geometry : angle 0.55105 (24327) SS BOND : bond 0.00543 ( 24) SS BOND : angle 1.62183 ( 48) hydrogen bonds : bond 0.04375 ( 722) hydrogen bonds : angle 5.10291 ( 2043) link_BETA1-4 : bond 0.00218 ( 3) link_BETA1-4 : angle 1.25866 ( 9) link_NAG-ASN : bond 0.00284 ( 15) link_NAG-ASN : angle 1.85097 ( 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 234 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8843 (m-80) cc_final: 0.8493 (m-80) REVERT: B 103 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: B 113 SER cc_start: 0.8546 (OUTLIER) cc_final: 0.8179 (m) REVERT: C 21 ASN cc_start: 0.7746 (p0) cc_final: 0.7387 (p0) REVERT: C 144 LYS cc_start: 0.7779 (ptmm) cc_final: 0.6920 (mmmt) REVERT: C 246 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7682 (mt-10) REVERT: C 285 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8083 (mm-40) REVERT: D 106 ARG cc_start: 0.7576 (mtp180) cc_final: 0.7252 (mmp80) REVERT: D 124 SER cc_start: 0.8705 (m) cc_final: 0.8441 (p) REVERT: D 131 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8015 (tttp) REVERT: E 61 GLN cc_start: 0.8030 (tp-100) cc_final: 0.7734 (tp40) REVERT: G 310 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7842 (ptp90) REVERT: H 100 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8499 (mt-10) REVERT: I 72 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7694 (ptmt) REVERT: I 116 LYS cc_start: 0.7934 (mtpm) cc_final: 0.7345 (ttmm) REVERT: J 63 PHE cc_start: 0.7849 (m-80) cc_final: 0.7446 (m-80) REVERT: K 29 ASN cc_start: 0.8374 (m-40) cc_final: 0.8047 (m110) outliers start: 48 outliers final: 28 residues processed: 211 average time/residue: 0.6286 time to fit residues: 148.1688 Evaluate side-chains 207 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 295 GLN 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 103 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 171 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 D residue 113 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 G residue 78 LEU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 61 optimal weight: 0.0770 chunk 147 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS D 26 HIS I 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.178231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131370 restraints weight = 20168.809| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.72 r_work: 0.3326 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17970 Z= 0.130 Angle : 0.528 9.595 24429 Z= 0.278 Chirality : 0.042 0.149 2652 Planarity : 0.004 0.048 3150 Dihedral : 5.021 69.060 2778 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.54 % Allowed : 14.26 % 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 aren not related in a simple way. whole: 0.79 (0.18), residues: 2181 helix: 2.91 (0.27), residues: 357 sheet: 0.73 (0.21), residues: 594 loop : -0.28 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 95A TYR 0.024 0.001 TYR B 162 PHE 0.020 0.002 PHE C 118 TRP 0.005 0.001 TRP H 36 HIS 0.010 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00303 (17928) covalent geometry : angle 0.51940 (24327) SS BOND : bond 0.00506 ( 24) SS BOND : angle 1.52520 ( 48) hydrogen bonds : bond 0.04150 ( 722) hydrogen bonds : angle 5.03597 ( 2043) link_BETA1-4 : bond 0.00231 ( 3) link_BETA1-4 : angle 1.19874 ( 9) link_NAG-ASN : bond 0.00213 ( 15) link_NAG-ASN : angle 1.65980 ( 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 234 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.7917 (pp30) cc_final: 0.7673 (pm20) REVERT: B 24 TYR cc_start: 0.8923 (m-80) cc_final: 0.8600 (m-80) REVERT: B 113 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8576 (m) REVERT: C 144 LYS cc_start: 0.7909 (ptmm) cc_final: 0.7337 (mmmt) REVERT: C 246 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7631 (mt-10) REVERT: D 113 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8455 (m) REVERT: D 124 SER cc_start: 0.8805 (m) cc_final: 0.8594 (p) REVERT: D 131 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8216 (tttp) REVERT: G 310 ARG cc_start: 0.8272 (mtm180) cc_final: 0.8066 (ptp90) REVERT: I 72 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7699 (ptmt) REVERT: I 116 LYS cc_start: 0.8353 (mtpm) cc_final: 0.7962 (ttmm) REVERT: J 63 PHE cc_start: 0.8078 (m-80) cc_final: 0.7668 (m-80) REVERT: J 89 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8250 (tpt) REVERT: K 29 ASN cc_start: 0.8563 (m-40) cc_final: 0.8259 (m110) outliers start: 48 outliers final: 29 residues processed: 215 average time/residue: 0.5899 time to fit residues: 142.0927 Evaluate side-chains 212 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 113 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 81 SER 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 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 G residue 78 LEU 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 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 47 LEU 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: 0.5980 chunk 175 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS I 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128927 restraints weight = 20278.765| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.83 r_work: 0.3343 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17970 Z= 0.136 Angle : 0.534 8.634 24429 Z= 0.280 Chirality : 0.042 0.148 2652 Planarity : 0.004 0.045 3150 Dihedral : 4.936 65.789 2778 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.49 % Allowed : 14.68 % Favored : 82.83 % 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 aren not related in a simple way. whole: 0.80 (0.18), residues: 2181 helix: 2.98 (0.27), residues: 357 sheet: 0.74 (0.21), residues: 594 loop : -0.30 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 95A TYR 0.024 0.001 TYR B 162 PHE 0.020 0.002 PHE C 118 TRP 0.006 0.001 TRP I 14 HIS 0.010 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00321 (17928) covalent geometry : angle 0.52602 (24327) SS BOND : bond 0.00491 ( 24) SS BOND : angle 1.36762 ( 48) hydrogen bonds : bond 0.04144 ( 722) hydrogen bonds : angle 5.03706 ( 2043) link_BETA1-4 : bond 0.00255 ( 3) link_BETA1-4 : angle 1.20675 ( 9) link_NAG-ASN : bond 0.00228 ( 15) link_NAG-ASN : angle 1.68860 ( 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 239 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: B 24 TYR cc_start: 0.8901 (m-80) cc_final: 0.8564 (m-80) REVERT: B 113 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8388 (m) REVERT: C 144 LYS cc_start: 0.7872 (ptmm) cc_final: 0.7204 (mmmt) REVERT: C 246 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7540 (mt-10) REVERT: D 113 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8252 (m) REVERT: D 124 SER cc_start: 0.8736 (m) cc_final: 0.8476 (p) REVERT: D 131 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8173 (tttp) REVERT: G 310 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7930 (ptp90) REVERT: I 72 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7683 (ptmt) REVERT: J 63 PHE cc_start: 0.8073 (m-80) cc_final: 0.7628 (m-80) REVERT: J 89 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7927 (tpt) REVERT: K 29 ASN cc_start: 0.8511 (m-40) cc_final: 0.8209 (m110) outliers start: 47 outliers final: 30 residues processed: 217 average time/residue: 0.5523 time to fit residues: 134.9841 Evaluate side-chains 216 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 295 GLN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 SER 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 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 G residue 78 LEU 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 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 47 LEU 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: 3.9990 chunk 133 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 218 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS I 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 146)---------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128820 restraints weight = 20114.559| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.62 r_work: 0.3345 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17970 Z= 0.148 Angle : 0.541 7.975 24429 Z= 0.284 Chirality : 0.043 0.148 2652 Planarity : 0.004 0.043 3150 Dihedral : 4.907 63.525 2778 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.28 % Allowed : 15.16 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.18), residues: 2181 helix: 2.85 (0.27), residues: 363 sheet: 0.76 (0.20), residues: 606 loop : -0.31 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 95A TYR 0.025 0.001 TYR B 162 PHE 0.021 0.002 PHE E 63 TRP 0.007 0.001 TRP I 14 HIS 0.009 0.001 HIS D 26 Details of bonding type rmsd covalent geometry : bond 0.00354 (17928) covalent geometry : angle 0.53358 (24327) SS BOND : bond 0.00494 ( 24) SS BOND : angle 1.32026 ( 48) hydrogen bonds : bond 0.04179 ( 722) hydrogen bonds : angle 5.06695 ( 2043) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 1.21855 ( 9) link_NAG-ASN : bond 0.00257 ( 15) link_NAG-ASN : angle 1.73864 ( 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 225 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8904 (m-80) cc_final: 0.8582 (m-80) REVERT: B 105 GLU cc_start: 0.8044 (tt0) cc_final: 0.7687 (tp30) REVERT: B 113 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8419 (m) REVERT: C 144 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7226 (mmmt) REVERT: C 149 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8160 (mtp180) REVERT: C 246 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7503 (mt-10) REVERT: D 113 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8301 (m) REVERT: D 124 SER cc_start: 0.8760 (m) cc_final: 0.8511 (p) REVERT: D 131 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8199 (tttp) REVERT: E 61 GLN cc_start: 0.7882 (tp-100) cc_final: 0.7611 (tp40) REVERT: H 50 ARG cc_start: 0.8744 (ptt90) cc_final: 0.8167 (ptt180) REVERT: I 72 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7675 (ptmt) REVERT: J 63 PHE cc_start: 0.8108 (m-80) cc_final: 0.7664 (m-80) REVERT: J 89 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8094 (tpt) REVERT: K 29 ASN cc_start: 0.8492 (m-40) cc_final: 0.8204 (m110) outliers start: 43 outliers final: 30 residues processed: 205 average time/residue: 0.5758 time to fit residues: 132.2024 Evaluate side-chains 211 residues out of total 1887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 295 GLN Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 SER 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 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 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 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 47 LEU 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: 0.3980 chunk 166 optimal weight: 7.9990 chunk 2 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 116 optimal weight: 0.0070 chunk 33 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 26 HIS D 26 HIS I 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129446 restraints weight = 20298.333| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.65 r_work: 0.3141 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17970 Z= 0.136 Angle : 0.537 7.551 24429 Z= 0.282 Chirality : 0.042 0.149 2652 Planarity : 0.004 0.081 3150 Dihedral : 4.850 61.083 2778 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.23 % Allowed : 15.42 % Favored : 82.35 % 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 aren not related in a simple way. whole: 0.81 (0.18), residues: 2181 helix: 2.87 (0.27), residues: 363 sheet: 0.79 (0.21), residues: 606 loop : -0.30 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG L 95A TYR 0.024 0.001 TYR B 162 PHE 0.021 0.002 PHE E 63 TRP 0.006 0.001 TRP I 14 HIS 0.010 0.001 HIS I 26 Details of bonding type rmsd covalent geometry : bond 0.00322 (17928) covalent geometry : angle 0.52992 (24327) SS BOND : bond 0.00469 ( 24) SS BOND : angle 1.26198 ( 48) hydrogen bonds : bond 0.04100 ( 722) hydrogen bonds : angle 5.05192 ( 2043) link_BETA1-4 : bond 0.00239 ( 3) link_BETA1-4 : angle 1.21649 ( 9) link_NAG-ASN : bond 0.00231 ( 15) link_NAG-ASN : angle 1.67907 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7441.58 seconds wall clock time: 127 minutes 27.24 seconds (7647.24 seconds total)