Starting phenix.real_space_refine on Sat Aug 8 09:44:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mgb_48248/08_2026/9mgb_48248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mgb_48248/08_2026/9mgb_48248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2026/9mgb_48248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2026/9mgb_48248.map" model { file = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2026/9mgb_48248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mgb_48248/08_2026/9mgb_48248.cif" } resolution = 2.1 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= -0.002 sd= 0.098 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 150 5.16 5 C 16914 2.51 5 N 4464 2.21 5 O 5328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26856 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "B" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "C" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "D" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "F" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "G" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "I" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "J" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "L" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "M" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "O" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 157} Chain: "Q" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1279 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 172} Chain: "a" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "c" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "e" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "g" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "i" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "k" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1740 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'PEB': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'PEB': 2, 'PUB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.17, per 1000 atoms: 0.23 Number of scatterers: 26856 At special positions: 0 Unit cell: (173.9, 172.96, 93.06, 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 150 16.00 O 5328 8.00 N 4464 7.00 C 16914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 100 " distance=2.03 Simple disulfide: pdb=" SG CYS a 167 " - pdb=" SG CYS a 232 " distance=2.03 Simple disulfide: pdb=" SG CYS c 26 " - pdb=" SG CYS c 100 " distance=2.03 Simple disulfide: pdb=" SG CYS c 167 " - pdb=" SG CYS c 232 " distance=2.03 Simple disulfide: pdb=" SG CYS e 26 " - pdb=" SG CYS e 100 " distance=2.03 Simple disulfide: pdb=" SG CYS e 167 " - pdb=" SG CYS e 232 " distance=2.03 Simple disulfide: pdb=" SG CYS g 26 " - pdb=" SG CYS g 100 " distance=2.03 Simple disulfide: pdb=" SG CYS g 167 " - pdb=" SG CYS g 232 " distance=2.04 Simple disulfide: pdb=" SG CYS i 26 " - pdb=" SG CYS i 100 " distance=2.03 Simple disulfide: pdb=" SG CYS i 167 " - pdb=" SG CYS i 232 " distance=2.03 Simple disulfide: pdb=" SG CYS k 26 " - pdb=" SG CYS k 100 " distance=2.03 Simple disulfide: pdb=" SG CYS k 167 " - pdb=" SG CYS k 232 " 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6228 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 35 sheets defined 53.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 20 through 47 removed outlier: 4.444A pdb=" N ALA A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 75 through 100 Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 123 through 138 removed outlier: 4.002A pdb=" N TYR A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 20 through 33 Processing helix chain 'B' and resid 33 through 46 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 75 through 100 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 20 through 47 removed outlier: 4.407A pdb=" N ALA C 35 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 75 through 100 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 123 through 138 removed outlier: 3.930A pdb=" N TYR C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 164 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.055A pdb=" N LYS D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 33 Processing helix chain 'D' and resid 33 through 46 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 64 through 67 Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 102 through 110 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 123 through 143 Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'F' and resid 3 through 15 Processing helix chain 'F' and resid 20 through 47 removed outlier: 4.362A pdb=" N ALA F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N SER F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 75 through 100 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 112 through 120 Processing helix chain 'F' and resid 123 through 138 removed outlier: 4.007A pdb=" N TYR F 127 " --> pdb=" O PRO F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 164 Processing helix chain 'G' and resid 3 through 14 Processing helix chain 'G' and resid 20 through 33 Processing helix chain 'G' and resid 33 through 47 removed outlier: 3.515A pdb=" N ASN G 47 " --> pdb=" O SER G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 64 through 67 Processing helix chain 'G' and resid 75 through 100 Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 123 through 143 Processing helix chain 'G' and resid 158 through 176 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 20 through 47 removed outlier: 4.415A pdb=" N ALA I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER I 36 " --> pdb=" O GLN I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 75 through 100 Processing helix chain 'I' and resid 102 through 109 Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'I' and resid 123 through 138 removed outlier: 3.975A pdb=" N TYR I 127 " --> pdb=" O PRO I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 Processing helix chain 'J' and resid 3 through 14 Processing helix chain 'J' and resid 20 through 33 Processing helix chain 'J' and resid 33 through 46 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 64 through 67 Processing helix chain 'J' and resid 75 through 100 Processing helix chain 'J' and resid 102 through 110 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 123 through 143 Processing helix chain 'J' and resid 158 through 176 Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 20 through 47 removed outlier: 4.413A pdb=" N ALA L 35 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER L 36 " --> pdb=" O GLN L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 75 through 100 Processing helix chain 'L' and resid 102 through 109 Processing helix chain 'L' and resid 112 through 120 Processing helix chain 'L' and resid 123 through 138 removed outlier: 3.927A pdb=" N TYR L 127 " --> pdb=" O PRO L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 164 Processing helix chain 'M' and resid 3 through 15 removed outlier: 4.043A pdb=" N LYS M 15 " --> pdb=" O ASN M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 Processing helix chain 'M' and resid 33 through 46 Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 75 through 100 Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 112 through 121 Processing helix chain 'M' and resid 123 through 143 Processing helix chain 'M' and resid 158 through 176 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 20 through 47 removed outlier: 4.396A pdb=" N ALA O 35 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER O 36 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 75 through 100 Processing helix chain 'O' and resid 102 through 109 Processing helix chain 'O' and resid 112 through 120 Processing helix chain 'O' and resid 123 through 138 removed outlier: 3.939A pdb=" N TYR O 127 " --> pdb=" O PRO O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 164 Processing helix chain 'Q' and resid 3 through 14 Processing helix chain 'Q' and resid 20 through 33 Processing helix chain 'Q' and resid 33 through 46 Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 64 through 68 Processing helix chain 'Q' and resid 75 through 100 Processing helix chain 'Q' and resid 102 through 110 Processing helix chain 'Q' and resid 112 through 121 Processing helix chain 'Q' and resid 123 through 143 Processing helix chain 'Q' and resid 158 through 176 Processing helix chain 'a' and resid 32 through 36 removed outlier: 3.539A pdb=" N TYR a 36 " --> pdb=" O PHE a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 69 Processing helix chain 'a' and resid 91 through 95 Processing helix chain 'a' and resid 223 through 227 Processing helix chain 'c' and resid 32 through 36 removed outlier: 3.504A pdb=" N TYR c 36 " --> pdb=" O PHE c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 223 through 227 Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 223 through 227 Processing helix chain 'g' and resid 32 through 36 removed outlier: 3.521A pdb=" N TYR g 36 " --> pdb=" O PHE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 223 through 227 Processing helix chain 'i' and resid 32 through 36 Processing helix chain 'i' and resid 91 through 95 Processing helix chain 'i' and resid 223 through 227 Processing helix chain 'k' and resid 32 through 36 Processing helix chain 'k' and resid 91 through 95 Processing helix chain 'k' and resid 223 through 227 Processing sheet with id=AA1, first strand: chain 'a' and resid 9 through 10 Processing sheet with id=AA2, first strand: chain 'a' and resid 14 through 15 removed outlier: 6.670A pdb=" N GLU a 14 " --> pdb=" O THR a 121 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE a 38 " --> pdb=" O GLU a 54 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU a 54 " --> pdb=" O ILE a 38 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP a 40 " --> pdb=" O ILE a 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 14 through 15 removed outlier: 6.670A pdb=" N GLU a 14 " --> pdb=" O THR a 121 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR a 113 " --> pdb=" O ARG a 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 148 through 149 Processing sheet with id=AA5, first strand: chain 'a' and resid 154 through 156 removed outlier: 6.175A pdb=" N GLN a 181 " --> pdb=" O LEU a 190 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU a 190 " --> pdb=" O GLN a 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 154 through 156 removed outlier: 3.776A pdb=" N THR a 241 " --> pdb=" O GLN a 234 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 9 through 10 Processing sheet with id=AA8, first strand: chain 'c' and resid 62 through 64 removed outlier: 6.682A pdb=" N TRP c 40 " --> pdb=" O ILE c 52 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU c 54 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE c 38 " --> pdb=" O GLU c 54 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR c 113 " --> pdb=" O ARG c 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 62 through 64 removed outlier: 6.682A pdb=" N TRP c 40 " --> pdb=" O ILE c 52 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU c 54 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE c 38 " --> pdb=" O GLU c 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'c' and resid 154 through 156 removed outlier: 6.884A pdb=" N LEU c 155 " --> pdb=" O GLU c 249 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN c 181 " --> pdb=" O LEU c 190 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU c 190 " --> pdb=" O GLN c 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 154 through 156 removed outlier: 6.884A pdb=" N LEU c 155 " --> pdb=" O GLU c 249 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR c 241 " --> pdb=" O GLN c 234 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'e' and resid 9 through 10 Processing sheet with id=AB5, first strand: chain 'e' and resid 14 through 15 removed outlier: 6.888A pdb=" N GLU e 14 " --> pdb=" O THR e 121 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE e 38 " --> pdb=" O GLU e 54 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU e 54 " --> pdb=" O ILE e 38 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP e 40 " --> pdb=" O ILE e 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'e' and resid 14 through 15 removed outlier: 6.888A pdb=" N GLU e 14 " --> pdb=" O THR e 121 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR e 113 " --> pdb=" O ARG e 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'e' and resid 197 through 198 removed outlier: 6.368A pdb=" N TRP e 179 " --> pdb=" O LEU e 191 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR e 193 " --> pdb=" O LEU e 177 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU e 177 " --> pdb=" O TYR e 193 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR e 241 " --> pdb=" O GLN e 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 197 through 198 removed outlier: 6.368A pdb=" N TRP e 179 " --> pdb=" O LEU e 191 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR e 193 " --> pdb=" O LEU e 177 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU e 177 " --> pdb=" O TYR e 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC2, first strand: chain 'g' and resid 14 through 15 removed outlier: 7.215A pdb=" N GLU g 14 " --> pdb=" O THR g 121 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE g 38 " --> pdb=" O GLU g 54 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU g 54 " --> pdb=" O ILE g 38 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP g 40 " --> pdb=" O ILE g 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 14 through 15 removed outlier: 7.215A pdb=" N GLU g 14 " --> pdb=" O THR g 121 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR g 113 " --> pdb=" O ARG g 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 148 through 149 Processing sheet with id=AC5, first strand: chain 'g' and resid 154 through 156 removed outlier: 5.961A pdb=" N GLN g 181 " --> pdb=" O LEU g 190 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU g 190 " --> pdb=" O GLN g 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 154 through 156 removed outlier: 3.793A pdb=" N THR g 241 " --> pdb=" O GLN g 234 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'i' and resid 9 through 10 Processing sheet with id=AC8, first strand: chain 'i' and resid 14 through 15 removed outlier: 3.730A pdb=" N THR i 121 " --> pdb=" O GLU i 14 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE i 38 " --> pdb=" O GLU i 54 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU i 54 " --> pdb=" O ILE i 38 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP i 40 " --> pdb=" O ILE i 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'i' and resid 14 through 15 removed outlier: 3.730A pdb=" N THR i 121 " --> pdb=" O GLU i 14 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR i 113 " --> pdb=" O ARG i 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'i' and resid 148 through 149 Processing sheet with id=AD2, first strand: chain 'i' and resid 154 through 156 removed outlier: 3.518A pdb=" N GLU i 249 " --> pdb=" O LEU i 155 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN i 181 " --> pdb=" O LEU i 190 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU i 190 " --> pdb=" O GLN i 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'i' and resid 154 through 156 removed outlier: 3.518A pdb=" N GLU i 249 " --> pdb=" O LEU i 155 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR i 241 " --> pdb=" O GLN i 234 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'k' and resid 9 through 10 Processing sheet with id=AD5, first strand: chain 'k' and resid 62 through 64 removed outlier: 6.593A pdb=" N TRP k 40 " --> pdb=" O ILE k 52 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU k 54 " --> pdb=" O ILE k 38 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE k 38 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR k 113 " --> pdb=" O ARG k 102 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 148 through 150 Processing sheet with id=AD7, first strand: chain 'k' and resid 154 through 156 removed outlier: 6.192A pdb=" N GLN k 181 " --> pdb=" O LEU k 190 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU k 190 " --> pdb=" O GLN k 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'k' and resid 154 through 156 removed outlier: 3.805A pdb=" N THR k 241 " --> pdb=" O GLN k 234 " (cutoff:3.500A) 1704 hydrogen bonds defined for protein. 4731 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: 5.51 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4501 1.30 - 1.43: 7291 1.43 - 1.56: 15376 1.56 - 1.69: 0 1.69 - 1.82: 210 Bond restraints: 27378 Sorted by residual: bond pdb=" C1B PEB F 202 " pdb=" CHA PEB F 202 " ideal model delta sigma weight residual 1.441 1.362 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1B PEB I 202 " pdb=" CHA PEB I 202 " ideal model delta sigma weight residual 1.441 1.363 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1B PEB O 202 " pdb=" CHA PEB O 202 " ideal model delta sigma weight residual 1.441 1.366 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C3C PUB G 201 " pdb=" C4C PUB G 201 " ideal model delta sigma weight residual 1.450 1.376 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C3C PUB B 201 " pdb=" C4C PUB B 201 " ideal model delta sigma weight residual 1.450 1.376 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 27373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 36343 2.06 - 4.13: 802 4.13 - 6.19: 73 6.19 - 8.26: 11 8.26 - 10.32: 1 Bond angle restraints: 37230 Sorted by residual: angle pdb=" C2A PEB A 202 " pdb=" C3A PEB A 202 " pdb=" CAA PEB A 202 " ideal model delta sigma weight residual 114.07 103.75 10.32 3.00e+00 1.11e-01 1.18e+01 angle pdb=" N ASN C 80 " pdb=" CA ASN C 80 " pdb=" C ASN C 80 " ideal model delta sigma weight residual 111.28 107.95 3.33 1.09e+00 8.42e-01 9.35e+00 angle pdb=" CA LEU k 119 " pdb=" C LEU k 119 " pdb=" O LEU k 119 " ideal model delta sigma weight residual 120.51 116.21 4.30 1.43e+00 4.89e-01 9.03e+00 angle pdb=" CA THR k 118 " pdb=" CB THR k 118 " pdb=" OG1 THR k 118 " ideal model delta sigma weight residual 109.60 105.24 4.36 1.50e+00 4.44e-01 8.46e+00 angle pdb=" N ASN A 80 " pdb=" CA ASN A 80 " pdb=" C ASN A 80 " ideal model delta sigma weight residual 111.28 108.15 3.13 1.09e+00 8.42e-01 8.23e+00 ... (remaining 37225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14866 17.94 - 35.89: 1819 35.89 - 53.83: 419 53.83 - 71.77: 103 71.77 - 89.72: 61 Dihedral angle restraints: 17268 sinusoidal: 7482 harmonic: 9786 Sorted by residual: dihedral pdb=" CB CYS k 26 " pdb=" SG CYS k 26 " pdb=" SG CYS k 100 " pdb=" CB CYS k 100 " ideal model delta sinusoidal sigma weight residual 93.00 57.00 36.00 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS i 26 " pdb=" SG CYS i 26 " pdb=" SG CYS i 100 " pdb=" CB CYS i 100 " ideal model delta sinusoidal sigma weight residual 93.00 58.43 34.57 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CB CYS c 26 " pdb=" SG CYS c 26 " pdb=" SG CYS c 100 " pdb=" CB CYS c 100 " ideal model delta sinusoidal sigma weight residual 93.00 59.40 33.60 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 17265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3393 0.051 - 0.102: 530 0.102 - 0.153: 108 0.153 - 0.203: 15 0.203 - 0.254: 16 Chirality restraints: 4062 Sorted by residual: chirality pdb=" C1D PEB G 203 " pdb=" ND PEB G 203 " pdb=" C2D PEB G 203 " pdb=" CHC PEB G 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.82 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1D PEB J 203 " pdb=" ND PEB J 203 " pdb=" C2D PEB J 203 " pdb=" CHC PEB J 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.81 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C1D PEB D 203 " pdb=" ND PEB D 203 " pdb=" C2D PEB D 203 " pdb=" CHC PEB D 203 " both_signs ideal model delta sigma weight residual False -2.56 -2.81 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 4059 not shown) Planarity restraints: 4728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PEB I 202 " 0.376 2.00e-02 2.50e+03 2.81e-01 1.78e+03 pdb=" C1B PEB I 202 " -0.013 2.00e-02 2.50e+03 pdb=" C2B PEB I 202 " 0.110 2.00e-02 2.50e+03 pdb=" C3B PEB I 202 " -0.045 2.00e-02 2.50e+03 pdb=" C4B PEB I 202 " 0.123 2.00e-02 2.50e+03 pdb=" CAB PEB I 202 " -0.380 2.00e-02 2.50e+03 pdb=" CHA PEB I 202 " -0.518 2.00e-02 2.50e+03 pdb=" CHB PEB I 202 " -0.010 2.00e-02 2.50e+03 pdb=" CMB PEB I 202 " 0.358 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PEB D 202 " -0.365 2.00e-02 2.50e+03 2.62e-01 1.55e+03 pdb=" C1B PEB D 202 " -0.117 2.00e-02 2.50e+03 pdb=" C2B PEB D 202 " 0.037 2.00e-02 2.50e+03 pdb=" C3B PEB D 202 " -0.105 2.00e-02 2.50e+03 pdb=" C4B PEB D 202 " 0.010 2.00e-02 2.50e+03 pdb=" CAB PEB D 202 " -0.327 2.00e-02 2.50e+03 pdb=" CHA PEB D 202 " 0.040 2.00e-02 2.50e+03 pdb=" CHB PEB D 202 " 0.484 2.00e-02 2.50e+03 pdb=" CMB PEB D 202 " 0.342 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PEB L 202 " -0.249 2.00e-02 2.50e+03 2.60e-01 1.52e+03 pdb=" C1B PEB L 202 " -0.106 2.00e-02 2.50e+03 pdb=" C2B PEB L 202 " 0.063 2.00e-02 2.50e+03 pdb=" C3B PEB L 202 " -0.103 2.00e-02 2.50e+03 pdb=" C4B PEB L 202 " 0.044 2.00e-02 2.50e+03 pdb=" CAB PEB L 202 " -0.403 2.00e-02 2.50e+03 pdb=" CHA PEB L 202 " -0.081 2.00e-02 2.50e+03 pdb=" CHB PEB L 202 " 0.436 2.00e-02 2.50e+03 pdb=" CMB PEB L 202 " 0.399 2.00e-02 2.50e+03 ... (remaining 4725 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 338 2.62 - 3.19: 24080 3.19 - 3.76: 49962 3.76 - 4.33: 67093 4.33 - 4.90: 106533 Nonbonded interactions: 248006 Sorted by model distance: nonbonded pdb=" OD2 ASP I 87 " pdb=" OH TYR g 106 " model vdw 2.045 3.040 nonbonded pdb=" OD2 ASP F 87 " pdb=" OH TYR a 106 " model vdw 2.061 3.040 nonbonded pdb=" OH TYR J 95 " pdb=" O ARG L 17 " model vdw 2.168 3.040 nonbonded pdb=" O TYR i 194 " pdb=" OG1 THR i 195 " model vdw 2.171 3.040 nonbonded pdb=" O ARG C 17 " pdb=" OH TYR G 95 " model vdw 2.173 3.040 ... (remaining 248001 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.600 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 27400 Z= 0.301 Angle : 0.653 10.324 37254 Z= 0.317 Chirality : 0.042 0.254 4062 Planarity : 0.018 0.281 4728 Dihedral : 16.961 89.715 11004 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 0.47 % Allowed : 16.45 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3342 helix: 1.74 (0.12), residues: 1626 sheet: 0.20 (0.19), residues: 678 loop : 0.29 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 58 TYR 0.011 0.001 TYR e 235 PHE 0.009 0.002 PHE a 99 TRP 0.007 0.001 TRP k 240 HIS 0.006 0.001 HIS I 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.27 (27378) covalent geometry : angle 0.65305 / 0.32 (37230) SS BOND : bond 0.00219 / 0.12 ( 12) SS BOND : angle 0.53961 / 0.31 ( 24) hydrogen bonds : bond 0.13502 / 9.30 ( 1644) hydrogen bonds : angle 5.61642 / 4.18 ( 4731) Misc. bond : bond 0.06860 / 3.86 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 685 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.8042 (ptp) cc_final: 0.7772 (ptp) REVERT: c 22 VAL cc_start: 0.9018 (t) cc_final: 0.8714 (p) REVERT: c 221 ASN cc_start: 0.8351 (p0) cc_final: 0.7892 (p0) REVERT: g 155 LEU cc_start: 0.8668 (mt) cc_final: 0.8350 (tp) REVERT: k 221 ASN cc_start: 0.7999 (t0) cc_final: 0.7646 (p0) outliers start: 13 outliers final: 6 residues processed: 695 average time/residue: 0.7307 time to fit residues: 578.4408 Evaluate side-chains 618 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 612 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain G residue 50 CYS Chi-restraints excluded: chain I residue 139 CYS Chi-restraints excluded: chain M residue 50 CYS Chi-restraints excluded: chain Q residue 50 CYS Chi-restraints excluded: chain k residue 108 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 6.9990 chunk 20 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.6533 > 50:) chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 121 ASN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 108 ASN e 171 GLN g 182 GLN k 247 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.060233 restraints weight = 45033.712| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.03 r_work: 0.2590 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27400 Z= 0.198 Angle : 0.574 10.773 37254 Z= 0.290 Chirality : 0.039 0.192 4062 Planarity : 0.004 0.046 4728 Dihedral : 9.865 89.336 5413 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.00 % Allowed : 19.10 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.14), residues: 3342 helix: 1.99 (0.12), residues: 1632 sheet: 0.35 (0.19), residues: 678 loop : 0.25 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 88 TYR 0.013 0.001 TYR i 193 PHE 0.013 0.002 PHE c 99 TRP 0.007 0.001 TRP i 40 HIS 0.006 0.002 HIS I 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (27378) covalent geometry : angle 0.57382 / 0.29 (37230) SS BOND : bond 0.00253 / 0.14 ( 12) SS BOND : angle 0.55979 / 0.32 ( 24) hydrogen bonds : bond 0.04361 / 2.99 ( 1644) hydrogen bonds : angle 4.75200 / 3.54 ( 4731) Misc. bond : bond 0.00079 / 0.05 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 610 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9142 (mtmt) cc_final: 0.8909 (pttm) REVERT: B 102 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9043 (p) REVERT: F 1 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7808 (mmp) REVERT: G 84 ARG cc_start: 0.8800 (ttp-110) cc_final: 0.8535 (ttp-110) REVERT: L 137 ARG cc_start: 0.8872 (tpt170) cc_final: 0.8668 (tpt170) REVERT: O 74 ASP cc_start: 0.8872 (p0) cc_final: 0.8650 (p0) REVERT: Q 102 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.8957 (p) REVERT: a 14 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8477 (mt-10) REVERT: a 71 LYS cc_start: 0.9052 (tppt) cc_final: 0.8610 (tppt) REVERT: a 77 ASP cc_start: 0.8256 (t70) cc_final: 0.7849 (t70) REVERT: a 88 ARG cc_start: 0.7958 (ptt-90) cc_final: 0.7278 (ptt-90) REVERT: a 155 LEU cc_start: 0.8248 (tp) cc_final: 0.7245 (tp) REVERT: a 249 GLU cc_start: 0.8158 (pm20) cc_final: 0.7856 (pm20) REVERT: c 14 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8432 (mt-10) REVERT: c 77 ASP cc_start: 0.8321 (t70) cc_final: 0.7746 (t70) REVERT: c 86 GLU cc_start: 0.8669 (tt0) cc_final: 0.8457 (tt0) REVERT: c 88 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7120 (ptt-90) REVERT: c 162 ARG cc_start: 0.9028 (mtp-110) cc_final: 0.8804 (ttm110) REVERT: c 205 ARG cc_start: 0.8704 (ptp90) cc_final: 0.8284 (ptt-90) REVERT: e 14 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8529 (mt-10) REVERT: e 44 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7896 (mmm160) REVERT: e 77 ASP cc_start: 0.8244 (t70) cc_final: 0.7722 (t70) REVERT: e 86 GLU cc_start: 0.8734 (tt0) cc_final: 0.8477 (tt0) REVERT: e 88 ARG cc_start: 0.8646 (mtm110) cc_final: 0.7905 (ptt-90) REVERT: e 147 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8414 (mm110) REVERT: g 15 LEU cc_start: 0.9071 (mp) cc_final: 0.8843 (tt) REVERT: g 71 LYS cc_start: 0.8524 (tppt) cc_final: 0.8127 (tppt) REVERT: g 77 ASP cc_start: 0.8247 (t70) cc_final: 0.7774 (t70) REVERT: g 88 ARG cc_start: 0.8440 (mtm110) cc_final: 0.8185 (mtm110) REVERT: g 155 LEU cc_start: 0.8322 (mt) cc_final: 0.7925 (mm) REVERT: g 205 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8022 (ttp-110) REVERT: g 237 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8757 (mtpm) REVERT: i 44 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7731 (mmm160) REVERT: i 71 LYS cc_start: 0.8726 (tppt) cc_final: 0.8468 (tppt) REVERT: i 77 ASP cc_start: 0.8323 (t70) cc_final: 0.7773 (t70) REVERT: i 88 ARG cc_start: 0.8387 (mtp-110) cc_final: 0.8108 (mtm110) REVERT: i 155 LEU cc_start: 0.8904 (pp) cc_final: 0.8393 (pp) REVERT: i 202 VAL cc_start: 0.8953 (t) cc_final: 0.8741 (t) REVERT: i 221 ASN cc_start: 0.8583 (m-40) cc_final: 0.7430 (p0) REVERT: i 223 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7270 (mm-30) REVERT: k 14 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8062 (mt-10) REVERT: k 77 ASP cc_start: 0.8342 (t70) cc_final: 0.7802 (t70) REVERT: k 221 ASN cc_start: 0.8238 (t0) cc_final: 0.8030 (p0) REVERT: k 249 GLU cc_start: 0.7828 (mp0) cc_final: 0.7608 (pm20) outliers start: 55 outliers final: 17 residues processed: 641 average time/residue: 0.7594 time to fit residues: 552.0652 Evaluate side-chains 591 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 570 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 71 LYS Chi-restraints excluded: chain c residue 92 SER Chi-restraints excluded: chain c residue 204 SER Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain g residue 205 ARG Chi-restraints excluded: chain i residue 108 ASN Chi-restraints excluded: chain i residue 204 SER Chi-restraints excluded: chain k residue 195 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 74 optimal weight: 0.6980 chunk 273 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 203 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 221 ASN c 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.060745 restraints weight = 45053.360| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.06 r_work: 0.2607 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27400 Z= 0.156 Angle : 0.529 9.324 37254 Z= 0.269 Chirality : 0.038 0.146 4062 Planarity : 0.003 0.044 4728 Dihedral : 9.347 87.298 5407 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 2.00 % Allowed : 19.83 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 3342 helix: 2.15 (0.12), residues: 1632 sheet: 0.53 (0.19), residues: 678 loop : 0.27 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG i 162 TYR 0.011 0.001 TYR e 235 PHE 0.011 0.001 PHE c 99 TRP 0.007 0.001 TRP k 40 HIS 0.006 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (27378) covalent geometry : angle 0.52910 / 0.27 (37230) SS BOND : bond 0.00236 / 0.13 ( 12) SS BOND : angle 0.46336 / 0.27 ( 24) hydrogen bonds : bond 0.03988 / 2.73 ( 1644) hydrogen bonds : angle 4.53538 / 3.37 ( 4731) Misc. bond : bond 0.00083 / 0.05 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 603 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9187 (mtmt) cc_final: 0.8958 (pttm) REVERT: B 102 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.8944 (p) REVERT: G 84 ARG cc_start: 0.8797 (ttp-110) cc_final: 0.8542 (ttp-110) REVERT: J 164 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8642 (tt0) REVERT: Q 102 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8838 (p) REVERT: a 71 LYS cc_start: 0.9061 (tppt) cc_final: 0.8524 (tppt) REVERT: a 77 ASP cc_start: 0.8219 (t70) cc_final: 0.7837 (t70) REVERT: a 86 GLU cc_start: 0.8628 (tp30) cc_final: 0.8226 (tm-30) REVERT: a 88 ARG cc_start: 0.7868 (ptt-90) cc_final: 0.7351 (ptt-90) REVERT: a 155 LEU cc_start: 0.8153 (tp) cc_final: 0.7205 (tp) REVERT: a 205 ARG cc_start: 0.8812 (ptp90) cc_final: 0.8438 (ptt-90) REVERT: a 249 GLU cc_start: 0.8264 (pm20) cc_final: 0.7866 (pm20) REVERT: c 44 ARG cc_start: 0.8449 (mtp85) cc_final: 0.7876 (mtp85) REVERT: c 77 ASP cc_start: 0.8328 (t70) cc_final: 0.7741 (t70) REVERT: c 86 GLU cc_start: 0.8691 (tt0) cc_final: 0.8361 (tt0) REVERT: c 162 ARG cc_start: 0.8989 (mtp-110) cc_final: 0.8726 (ttm110) REVERT: c 205 ARG cc_start: 0.8787 (ptp90) cc_final: 0.8355 (ptt-90) REVERT: c 223 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7223 (mm-30) REVERT: e 44 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7907 (mmm160) REVERT: e 77 ASP cc_start: 0.8228 (t70) cc_final: 0.7677 (t70) REVERT: e 86 GLU cc_start: 0.8678 (tt0) cc_final: 0.8401 (tt0) REVERT: e 88 ARG cc_start: 0.8607 (mtm110) cc_final: 0.7846 (ptt-90) REVERT: e 147 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8464 (mm110) REVERT: e 162 ARG cc_start: 0.8977 (mtp-110) cc_final: 0.8754 (ttm110) REVERT: g 15 LEU cc_start: 0.9043 (mp) cc_final: 0.8817 (tt) REVERT: g 50 GLU cc_start: 0.8866 (tt0) cc_final: 0.8655 (tt0) REVERT: g 67 LYS cc_start: 0.9366 (mtpp) cc_final: 0.9031 (mtpm) REVERT: g 71 LYS cc_start: 0.8504 (tppt) cc_final: 0.8076 (tppt) REVERT: g 77 ASP cc_start: 0.8186 (t70) cc_final: 0.7810 (t70) REVERT: g 94 ASP cc_start: 0.9123 (m-30) cc_final: 0.8913 (m-30) REVERT: g 205 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8058 (ttp-110) REVERT: g 237 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8778 (mtpm) REVERT: i 44 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7771 (mmm160) REVERT: i 71 LYS cc_start: 0.8790 (tppt) cc_final: 0.8517 (tppt) REVERT: i 77 ASP cc_start: 0.8265 (t70) cc_final: 0.7808 (t70) REVERT: i 88 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.8020 (mtm110) REVERT: i 205 ARG cc_start: 0.8903 (ptp90) cc_final: 0.8359 (ptp90) REVERT: i 221 ASN cc_start: 0.8618 (m-40) cc_final: 0.7418 (p0) REVERT: i 222 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7433 (tt) REVERT: i 223 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7200 (mm-30) REVERT: k 77 ASP cc_start: 0.8282 (t70) cc_final: 0.7856 (t70) REVERT: k 86 GLU cc_start: 0.8825 (tt0) cc_final: 0.8235 (tm-30) REVERT: k 88 ARG cc_start: 0.8512 (mtm110) cc_final: 0.7622 (mtm110) REVERT: k 202 VAL cc_start: 0.9172 (t) cc_final: 0.8868 (t) REVERT: k 203 PRO cc_start: 0.8802 (Cg_exo) cc_final: 0.8460 (Cg_endo) outliers start: 55 outliers final: 25 residues processed: 629 average time/residue: 0.7467 time to fit residues: 531.3922 Evaluate side-chains 586 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 556 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain J residue 134 MET Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 92 SER Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain g residue 205 ARG Chi-restraints excluded: chain i residue 108 ASN Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 108 ASN Chi-restraints excluded: chain k residue 161 ASP Chi-restraints excluded: chain k residue 195 THR Chi-restraints excluded: chain k residue 200 SER Chi-restraints excluded: chain k residue 214 ASP Chi-restraints excluded: chain k residue 216 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 273 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 chunk 194 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 321 optimal weight: 0.0570 chunk 30 optimal weight: 0.5980 chunk 156 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.062141 restraints weight = 45369.526| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.08 r_work: 0.2647 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27400 Z= 0.126 Angle : 0.511 10.243 37254 Z= 0.260 Chirality : 0.037 0.185 4062 Planarity : 0.003 0.042 4728 Dihedral : 9.150 89.994 5407 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 2.58 % Allowed : 20.04 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.14), residues: 3342 helix: 2.26 (0.12), residues: 1632 sheet: 0.71 (0.19), residues: 678 loop : 0.28 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG i 162 TYR 0.012 0.001 TYR F 127 PHE 0.011 0.001 PHE c 99 TRP 0.006 0.001 TRP c 240 HIS 0.006 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (27378) covalent geometry : angle 0.51064 / 0.26 (37230) SS BOND : bond 0.00231 / 0.15 ( 12) SS BOND : angle 0.42835 / 0.25 ( 24) hydrogen bonds : bond 0.03695 / 2.53 ( 1644) hydrogen bonds : angle 4.38079 / 3.25 ( 4731) Misc. bond : bond 0.00064 / 0.04 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 592 time to evaluate : 0.954 Fit side-chains REVERT: B 15 LYS cc_start: 0.9175 (mtmt) cc_final: 0.8944 (pttm) REVERT: B 25 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8267 (tp-100) REVERT: B 102 SER cc_start: 0.9268 (OUTLIER) cc_final: 0.8883 (p) REVERT: B 115 GLU cc_start: 0.8936 (mp0) cc_final: 0.8402 (tt0) REVERT: C 37 ARG cc_start: 0.8470 (ptt90) cc_final: 0.8268 (ptt90) REVERT: F 90 MET cc_start: 0.9610 (OUTLIER) cc_final: 0.9361 (mmm) REVERT: G 84 ARG cc_start: 0.8773 (ttp-110) cc_final: 0.8525 (ttp-110) REVERT: J 149 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.6660 (ttt-90) REVERT: J 164 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8639 (tt0) REVERT: L 37 ARG cc_start: 0.8457 (ptt90) cc_final: 0.8244 (ptt90) REVERT: Q 25 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8287 (tp-100) REVERT: Q 102 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.8801 (p) REVERT: Q 115 GLU cc_start: 0.8936 (mp0) cc_final: 0.8349 (tt0) REVERT: a 71 LYS cc_start: 0.9017 (tppt) cc_final: 0.8512 (tppt) REVERT: a 77 ASP cc_start: 0.8228 (t70) cc_final: 0.7839 (t70) REVERT: a 86 GLU cc_start: 0.8567 (tp30) cc_final: 0.8163 (tm-30) REVERT: a 88 ARG cc_start: 0.7879 (ptt-90) cc_final: 0.7443 (ptt-90) REVERT: a 155 LEU cc_start: 0.8052 (tp) cc_final: 0.7134 (tp) REVERT: a 249 GLU cc_start: 0.8244 (pm20) cc_final: 0.7884 (pm20) REVERT: c 44 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7766 (mmm160) REVERT: c 77 ASP cc_start: 0.8317 (t70) cc_final: 0.7706 (t70) REVERT: c 86 GLU cc_start: 0.8576 (tt0) cc_final: 0.8356 (tt0) REVERT: c 88 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7105 (ptt-90) REVERT: c 162 ARG cc_start: 0.8993 (mtp-110) cc_final: 0.8754 (ttm110) REVERT: c 205 ARG cc_start: 0.8742 (ptp90) cc_final: 0.8328 (ptt-90) REVERT: c 223 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7333 (mm-30) REVERT: e 44 ARG cc_start: 0.8238 (mtp180) cc_final: 0.7885 (mmm160) REVERT: e 77 ASP cc_start: 0.8198 (t70) cc_final: 0.7655 (t70) REVERT: e 86 GLU cc_start: 0.8651 (tt0) cc_final: 0.8361 (tt0) REVERT: e 88 ARG cc_start: 0.8626 (mtm110) cc_final: 0.8241 (mtm110) REVERT: e 205 ARG cc_start: 0.8744 (ptt-90) cc_final: 0.8191 (ptt-90) REVERT: g 15 LEU cc_start: 0.9048 (mp) cc_final: 0.8814 (tt) REVERT: g 17 ARG cc_start: 0.6961 (mmt180) cc_final: 0.6237 (mmp-170) REVERT: g 50 GLU cc_start: 0.8853 (tt0) cc_final: 0.8563 (tt0) REVERT: g 67 LYS cc_start: 0.9339 (mtpp) cc_final: 0.8928 (mtpm) REVERT: g 69 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8638 (mtpp) REVERT: g 71 LYS cc_start: 0.8500 (tppt) cc_final: 0.8085 (tppt) REVERT: g 77 ASP cc_start: 0.8159 (t70) cc_final: 0.7765 (t70) REVERT: g 223 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7420 (mm-30) REVERT: g 237 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8718 (mtpm) REVERT: i 71 LYS cc_start: 0.8794 (tppt) cc_final: 0.8483 (tppt) REVERT: i 77 ASP cc_start: 0.8224 (t70) cc_final: 0.7733 (t70) REVERT: i 88 ARG cc_start: 0.8440 (mtp-110) cc_final: 0.8108 (mtm110) REVERT: i 155 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8397 (pp) REVERT: i 205 ARG cc_start: 0.8901 (ptp90) cc_final: 0.8356 (ptt-90) REVERT: i 221 ASN cc_start: 0.8593 (m-40) cc_final: 0.7461 (p0) REVERT: i 222 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7332 (tt) REVERT: i 223 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7203 (mm-30) REVERT: k 14 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7542 (mt-10) REVERT: k 77 ASP cc_start: 0.8265 (t70) cc_final: 0.7811 (t70) REVERT: k 88 ARG cc_start: 0.8496 (mtm110) cc_final: 0.7996 (mtm110) REVERT: k 205 ARG cc_start: 0.8703 (ptp90) cc_final: 0.8274 (ptt-90) outliers start: 71 outliers final: 20 residues processed: 638 average time/residue: 0.7617 time to fit residues: 550.8092 Evaluate side-chains 578 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 551 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain i residue 155 LEU Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 154 SER Chi-restraints excluded: chain k residue 195 THR Chi-restraints excluded: chain k residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 123 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 150 GLN k 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.060492 restraints weight = 45190.909| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.07 r_work: 0.2614 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27400 Z= 0.160 Angle : 0.526 10.198 37254 Z= 0.267 Chirality : 0.038 0.148 4062 Planarity : 0.003 0.042 4728 Dihedral : 8.927 86.491 5407 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 2.29 % Allowed : 20.99 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.14), residues: 3342 helix: 2.22 (0.12), residues: 1632 sheet: 0.77 (0.20), residues: 678 loop : 0.28 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG i 162 TYR 0.012 0.001 TYR F 127 PHE 0.012 0.001 PHE c 99 TRP 0.008 0.001 TRP c 240 HIS 0.006 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (27378) covalent geometry : angle 0.52564 / 0.27 (37230) SS BOND : bond 0.00214 / 0.13 ( 12) SS BOND : angle 0.47854 / 0.27 ( 24) hydrogen bonds : bond 0.03857 / 2.64 ( 1644) hydrogen bonds : angle 4.40735 / 3.28 ( 4731) Misc. bond : bond 0.00085 / 0.05 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 571 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8919 (pttm) REVERT: B 25 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8285 (tp-100) REVERT: B 102 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8938 (p) REVERT: B 115 GLU cc_start: 0.8931 (mp0) cc_final: 0.8415 (tt0) REVERT: C 78 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8817 (mtmt) REVERT: F 90 MET cc_start: 0.9619 (OUTLIER) cc_final: 0.9371 (mmm) REVERT: G 84 ARG cc_start: 0.8777 (ttp-110) cc_final: 0.8538 (ttp-110) REVERT: G 164 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8737 (tt0) REVERT: J 164 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8611 (tt0) REVERT: L 78 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8906 (mttt) REVERT: Q 25 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8305 (tp-100) REVERT: Q 102 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8877 (p) REVERT: Q 115 GLU cc_start: 0.8925 (mp0) cc_final: 0.8368 (tt0) REVERT: a 71 LYS cc_start: 0.9015 (tppt) cc_final: 0.8380 (tppt) REVERT: a 77 ASP cc_start: 0.8236 (t70) cc_final: 0.7856 (t70) REVERT: a 85 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8735 (ttp) REVERT: a 86 GLU cc_start: 0.8594 (tp30) cc_final: 0.8113 (tm-30) REVERT: a 88 ARG cc_start: 0.7804 (ptt-90) cc_final: 0.7289 (ptt-90) REVERT: a 155 LEU cc_start: 0.7918 (tp) cc_final: 0.6996 (tp) REVERT: a 205 ARG cc_start: 0.8821 (ptp90) cc_final: 0.8502 (ptt-90) REVERT: a 249 GLU cc_start: 0.8304 (pm20) cc_final: 0.7890 (pm20) REVERT: c 44 ARG cc_start: 0.8508 (mtp85) cc_final: 0.7856 (mmm160) REVERT: c 77 ASP cc_start: 0.8281 (t70) cc_final: 0.7698 (t70) REVERT: c 86 GLU cc_start: 0.8558 (tt0) cc_final: 0.8028 (tm-30) REVERT: c 88 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7204 (ptt-90) REVERT: c 223 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7370 (mm-30) REVERT: e 14 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8309 (mt-10) REVERT: e 44 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7887 (mmm160) REVERT: e 77 ASP cc_start: 0.8203 (t70) cc_final: 0.7700 (t70) REVERT: e 86 GLU cc_start: 0.8644 (tt0) cc_final: 0.8348 (tt0) REVERT: e 88 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8243 (mtm110) REVERT: e 205 ARG cc_start: 0.8798 (ptt-90) cc_final: 0.8204 (ptt-90) REVERT: e 223 GLU cc_start: 0.7510 (mp0) cc_final: 0.7250 (mp0) REVERT: g 15 LEU cc_start: 0.9057 (mp) cc_final: 0.8822 (tt) REVERT: g 50 GLU cc_start: 0.8871 (tt0) cc_final: 0.8591 (tt0) REVERT: g 67 LYS cc_start: 0.9333 (mtpp) cc_final: 0.8933 (mtpm) REVERT: g 69 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8595 (mtpp) REVERT: g 71 LYS cc_start: 0.8575 (tppt) cc_final: 0.8272 (tppt) REVERT: g 77 ASP cc_start: 0.8173 (t70) cc_final: 0.7790 (t70) REVERT: g 88 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8337 (mtm110) REVERT: g 155 LEU cc_start: 0.8408 (mt) cc_final: 0.8199 (mm) REVERT: g 221 ASN cc_start: 0.8177 (p0) cc_final: 0.7689 (p0) REVERT: g 223 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7211 (mm-30) REVERT: g 237 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8787 (mtpm) REVERT: i 71 LYS cc_start: 0.8810 (tppt) cc_final: 0.8481 (tppt) REVERT: i 77 ASP cc_start: 0.8234 (t70) cc_final: 0.7776 (t70) REVERT: i 88 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8164 (mtm110) REVERT: i 205 ARG cc_start: 0.8910 (ptp90) cc_final: 0.8313 (ptt-90) REVERT: i 221 ASN cc_start: 0.8644 (m-40) cc_final: 0.7399 (p0) REVERT: i 222 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7344 (tt) REVERT: i 223 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7305 (mm-30) REVERT: k 14 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7604 (mt-10) REVERT: k 77 ASP cc_start: 0.8274 (t70) cc_final: 0.7805 (t70) REVERT: k 86 GLU cc_start: 0.8777 (tt0) cc_final: 0.8149 (tm-30) REVERT: k 88 ARG cc_start: 0.8512 (mtm110) cc_final: 0.7796 (mtm110) REVERT: k 205 ARG cc_start: 0.8645 (ptp90) cc_final: 0.8383 (ptp90) outliers start: 63 outliers final: 28 residues processed: 607 average time/residue: 0.8220 time to fit residues: 564.3559 Evaluate side-chains 580 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 544 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain L residue 78 LYS Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 85 MET Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain a residue 216 SER Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain g residue 167 CYS Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 154 SER Chi-restraints excluded: chain k residue 159 LEU Chi-restraints excluded: chain k residue 195 THR Chi-restraints excluded: chain k residue 214 ASP Chi-restraints excluded: chain k residue 216 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 170 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 320 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 323 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 181 GLN k 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.056364 restraints weight = 45707.966| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.05 r_work: 0.2517 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 27400 Z= 0.323 Angle : 0.623 9.378 37254 Z= 0.315 Chirality : 0.042 0.179 4062 Planarity : 0.004 0.041 4728 Dihedral : 8.715 65.516 5407 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.40 % Allowed : 20.84 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.14), residues: 3342 helix: 1.90 (0.12), residues: 1632 sheet: 0.53 (0.20), residues: 618 loop : 0.36 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG i 162 TYR 0.015 0.002 TYR g 235 PHE 0.013 0.002 PHE c 99 TRP 0.011 0.001 TRP c 240 HIS 0.006 0.002 HIS I 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00717 / 0.32 (27378) covalent geometry : angle 0.62275 / 0.31 (37230) SS BOND : bond 0.00379 / 0.23 ( 12) SS BOND : angle 0.85078 / 0.50 ( 24) hydrogen bonds : bond 0.04634 / 3.17 ( 1644) hydrogen bonds : angle 4.72915 / 3.52 ( 4731) Misc. bond : bond 0.00166 / 0.09 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 545 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8919 (pttm) REVERT: B 102 SER cc_start: 0.9398 (OUTLIER) cc_final: 0.9091 (p) REVERT: D 23 ASP cc_start: 0.8877 (m-30) cc_final: 0.8580 (m-30) REVERT: F 90 MET cc_start: 0.9655 (OUTLIER) cc_final: 0.9410 (mmm) REVERT: G 84 ARG cc_start: 0.8777 (ttp-110) cc_final: 0.8570 (ttp-110) REVERT: Q 102 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9068 (p) REVERT: a 71 LYS cc_start: 0.8942 (tppt) cc_final: 0.8610 (tppt) REVERT: a 77 ASP cc_start: 0.8285 (t70) cc_final: 0.7941 (t70) REVERT: a 86 GLU cc_start: 0.8648 (tp30) cc_final: 0.8270 (tm-30) REVERT: a 88 ARG cc_start: 0.7828 (ptt-90) cc_final: 0.7526 (ptt-90) REVERT: a 155 LEU cc_start: 0.8220 (tp) cc_final: 0.7281 (tp) REVERT: a 249 GLU cc_start: 0.8385 (pm20) cc_final: 0.7968 (pm20) REVERT: c 14 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8318 (mt-10) REVERT: c 44 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8194 (mtp-110) REVERT: c 77 ASP cc_start: 0.8359 (t70) cc_final: 0.7796 (t0) REVERT: c 86 GLU cc_start: 0.8632 (tt0) cc_final: 0.8272 (tt0) REVERT: c 162 ARG cc_start: 0.9090 (mtp-110) cc_final: 0.8748 (ttm110) REVERT: c 223 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7357 (mm-30) REVERT: e 44 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7360 (mtp180) REVERT: e 77 ASP cc_start: 0.8224 (t70) cc_final: 0.7719 (t0) REVERT: e 86 GLU cc_start: 0.8729 (tt0) cc_final: 0.8374 (tt0) REVERT: e 88 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8163 (mtm110) REVERT: g 15 LEU cc_start: 0.9126 (mp) cc_final: 0.8892 (tt) REVERT: g 67 LYS cc_start: 0.9357 (mtpp) cc_final: 0.9129 (mtpm) REVERT: g 69 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8802 (mtpp) REVERT: g 71 LYS cc_start: 0.8605 (tppt) cc_final: 0.8278 (tppt) REVERT: g 77 ASP cc_start: 0.8253 (t70) cc_final: 0.7888 (t70) REVERT: g 88 ARG cc_start: 0.8470 (mtm110) cc_final: 0.8211 (mtm110) REVERT: g 145 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: g 155 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8153 (tp) REVERT: g 205 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8539 (ttp80) REVERT: g 221 ASN cc_start: 0.8256 (p0) cc_final: 0.8040 (p0) REVERT: i 71 LYS cc_start: 0.8848 (tppt) cc_final: 0.8575 (tppt) REVERT: i 77 ASP cc_start: 0.8238 (t70) cc_final: 0.7842 (t70) REVERT: i 88 ARG cc_start: 0.8413 (mtp-110) cc_final: 0.8115 (mtm110) REVERT: i 205 ARG cc_start: 0.8898 (ptp90) cc_final: 0.8297 (ptt-90) REVERT: i 222 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8051 (tt) REVERT: k 17 ARG cc_start: 0.6782 (mmp-170) cc_final: 0.6360 (mmp-170) REVERT: k 77 ASP cc_start: 0.8232 (t70) cc_final: 0.7817 (t70) REVERT: k 88 ARG cc_start: 0.8550 (mtm110) cc_final: 0.8091 (mtm110) outliers start: 66 outliers final: 33 residues processed: 589 average time/residue: 0.8378 time to fit residues: 558.1918 Evaluate side-chains 575 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 534 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 147 SER Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 161 ASP Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 92 SER Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain c residue 216 SER Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 71 LYS Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 167 CYS Chi-restraints excluded: chain g residue 205 ARG Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 154 SER Chi-restraints excluded: chain k residue 195 THR Chi-restraints excluded: chain k residue 216 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 83 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 268 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 256 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 150 GLN k 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.060702 restraints weight = 45392.975| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.05 r_work: 0.2614 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27400 Z= 0.140 Angle : 0.528 9.814 37254 Z= 0.269 Chirality : 0.037 0.154 4062 Planarity : 0.003 0.042 4728 Dihedral : 8.662 70.836 5407 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.82 % Allowed : 21.50 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.14), residues: 3342 helix: 2.17 (0.12), residues: 1632 sheet: 0.81 (0.20), residues: 678 loop : 0.28 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG i 162 TYR 0.012 0.001 TYR I 127 PHE 0.011 0.001 PHE e 99 TRP 0.009 0.001 TRP i 40 HIS 0.007 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (27378) covalent geometry : angle 0.52789 / 0.27 (37230) SS BOND : bond 0.00448 / 0.33 ( 12) SS BOND : angle 0.45019 / 0.27 ( 24) hydrogen bonds : bond 0.03771 / 2.59 ( 1644) hydrogen bonds : angle 4.42527 / 3.29 ( 4731) Misc. bond : bond 0.00070 / 0.04 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 564 time to evaluate : 1.035 Fit side-chains REVERT: B 15 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8926 (pttm) REVERT: B 25 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8294 (tp-100) REVERT: B 102 SER cc_start: 0.9303 (OUTLIER) cc_final: 0.8966 (p) REVERT: C 78 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8883 (mtmt) REVERT: G 84 ARG cc_start: 0.8803 (ttp-110) cc_final: 0.8560 (ttp-110) REVERT: J 149 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.6641 (ttt-90) REVERT: J 164 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8752 (tt0) REVERT: Q 25 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8331 (tp-100) REVERT: Q 102 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.8933 (p) REVERT: a 14 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8311 (mt-10) REVERT: a 71 LYS cc_start: 0.8996 (tppt) cc_final: 0.8538 (tppt) REVERT: a 77 ASP cc_start: 0.8300 (t70) cc_final: 0.7903 (t70) REVERT: a 86 GLU cc_start: 0.8589 (tp30) cc_final: 0.8209 (tm-30) REVERT: a 88 ARG cc_start: 0.7826 (ptt-90) cc_final: 0.7540 (ptt-90) REVERT: a 155 LEU cc_start: 0.7895 (tp) cc_final: 0.6951 (tp) REVERT: a 249 GLU cc_start: 0.8270 (pm20) cc_final: 0.7875 (pm20) REVERT: c 14 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8269 (mt-10) REVERT: c 44 ARG cc_start: 0.8450 (mtp85) cc_final: 0.7818 (mmm160) REVERT: c 77 ASP cc_start: 0.8373 (t70) cc_final: 0.7718 (t70) REVERT: c 86 GLU cc_start: 0.8596 (tt0) cc_final: 0.8080 (tm-30) REVERT: c 88 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7126 (ptt-90) REVERT: c 145 ASP cc_start: 0.8677 (p0) cc_final: 0.7839 (p0) REVERT: c 223 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7385 (mm-30) REVERT: e 14 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8276 (mt-10) REVERT: e 44 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7864 (mmm160) REVERT: e 77 ASP cc_start: 0.8237 (t70) cc_final: 0.7696 (t70) REVERT: e 86 GLU cc_start: 0.8642 (tt0) cc_final: 0.8022 (tm-30) REVERT: e 88 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8011 (mtm110) REVERT: g 15 LEU cc_start: 0.9079 (mp) cc_final: 0.8853 (tt) REVERT: g 69 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8801 (mtpp) REVERT: g 71 LYS cc_start: 0.8590 (tppt) cc_final: 0.8277 (tppt) REVERT: g 77 ASP cc_start: 0.8271 (t70) cc_final: 0.7869 (t70) REVERT: g 88 ARG cc_start: 0.8562 (mtm110) cc_final: 0.8340 (mtm110) REVERT: g 145 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: g 221 ASN cc_start: 0.8222 (p0) cc_final: 0.8018 (p0) REVERT: i 71 LYS cc_start: 0.8861 (tppt) cc_final: 0.8580 (tppt) REVERT: i 77 ASP cc_start: 0.8278 (t70) cc_final: 0.7826 (t70) REVERT: i 86 GLU cc_start: 0.8822 (tt0) cc_final: 0.8173 (tm-30) REVERT: i 88 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8031 (mtm110) REVERT: i 205 ARG cc_start: 0.8878 (ptp90) cc_final: 0.8460 (ptt-90) REVERT: i 221 ASN cc_start: 0.8669 (m-40) cc_final: 0.7753 (p0) REVERT: i 222 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7870 (tt) REVERT: k 14 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7723 (mt-10) REVERT: k 77 ASP cc_start: 0.8273 (t70) cc_final: 0.7804 (t70) REVERT: k 86 GLU cc_start: 0.8787 (tt0) cc_final: 0.8150 (tm-30) REVERT: k 88 ARG cc_start: 0.8499 (mtm110) cc_final: 0.7878 (mtm110) outliers start: 50 outliers final: 27 residues processed: 594 average time/residue: 0.7682 time to fit residues: 515.7623 Evaluate side-chains 564 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 531 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 66 GLU Chi-restraints excluded: chain c residue 92 SER Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain c residue 216 SER Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain g residue 167 CYS Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 214 ASP Chi-restraints excluded: chain k residue 216 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 34 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 329 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 316 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 212 optimal weight: 0.2980 chunk 304 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 150 GLN k 221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.080039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.061527 restraints weight = 45725.223| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.06 r_work: 0.2637 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27400 Z= 0.131 Angle : 0.522 9.402 37254 Z= 0.267 Chirality : 0.037 0.162 4062 Planarity : 0.003 0.048 4728 Dihedral : 8.523 72.139 5407 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 1.63 % Allowed : 22.37 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.14), residues: 3342 helix: 2.25 (0.12), residues: 1638 sheet: 0.93 (0.20), residues: 678 loop : 0.28 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG i 162 TYR 0.011 0.001 TYR I 127 PHE 0.010 0.001 PHE e 99 TRP 0.009 0.001 TRP i 40 HIS 0.007 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (27378) covalent geometry : angle 0.52179 / 0.27 (37230) SS BOND : bond 0.00184 / 0.11 ( 12) SS BOND : angle 0.41146 / 0.24 ( 24) hydrogen bonds : bond 0.03641 / 2.50 ( 1644) hydrogen bonds : angle 4.31240 / 3.21 ( 4731) Misc. bond : bond 0.00065 / 0.04 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 559 time to evaluate : 1.008 Fit side-chains REVERT: B 15 LYS cc_start: 0.9223 (mtmt) cc_final: 0.8928 (pttm) REVERT: B 25 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8309 (tp-100) REVERT: B 102 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.9010 (p) REVERT: B 115 GLU cc_start: 0.8912 (mp0) cc_final: 0.8418 (tt0) REVERT: G 84 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8559 (ttp-110) REVERT: G 164 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8884 (tt0) REVERT: I 137 ARG cc_start: 0.9057 (ttt90) cc_final: 0.8837 (ttt90) REVERT: J 149 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.6620 (ttt-90) REVERT: J 164 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8759 (tt0) REVERT: Q 25 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8350 (tp-100) REVERT: Q 102 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8913 (p) REVERT: Q 115 GLU cc_start: 0.8948 (mp0) cc_final: 0.8386 (tt0) REVERT: a 14 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8293 (mt-10) REVERT: a 71 LYS cc_start: 0.9041 (tppt) cc_final: 0.8568 (tppt) REVERT: a 77 ASP cc_start: 0.8327 (t70) cc_final: 0.7913 (t70) REVERT: a 86 GLU cc_start: 0.8480 (tp30) cc_final: 0.8147 (tm-30) REVERT: a 88 ARG cc_start: 0.7814 (ptt-90) cc_final: 0.7563 (ptt-90) REVERT: a 155 LEU cc_start: 0.7718 (tp) cc_final: 0.7024 (pt) REVERT: a 249 GLU cc_start: 0.8276 (pm20) cc_final: 0.7828 (pm20) REVERT: c 44 ARG cc_start: 0.8426 (mtp85) cc_final: 0.7946 (mmm160) REVERT: c 77 ASP cc_start: 0.8366 (t70) cc_final: 0.7725 (t0) REVERT: c 86 GLU cc_start: 0.8594 (tt0) cc_final: 0.8073 (tm-30) REVERT: c 88 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7256 (ptt-90) REVERT: c 145 ASP cc_start: 0.8615 (p0) cc_final: 0.7892 (p0) REVERT: c 223 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7425 (mm-30) REVERT: e 14 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8253 (mt-10) REVERT: e 44 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7858 (mmm160) REVERT: e 77 ASP cc_start: 0.8218 (t70) cc_final: 0.7701 (t70) REVERT: e 86 GLU cc_start: 0.8657 (tt0) cc_final: 0.7977 (tm-30) REVERT: e 88 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8088 (mtm110) REVERT: g 15 LEU cc_start: 0.9090 (mp) cc_final: 0.8856 (tt) REVERT: g 71 LYS cc_start: 0.8641 (tppt) cc_final: 0.8174 (tppt) REVERT: g 77 ASP cc_start: 0.8294 (t70) cc_final: 0.7876 (t70) REVERT: g 145 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: i 14 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8304 (mt-10) REVERT: i 71 LYS cc_start: 0.8876 (tppt) cc_final: 0.8611 (tppt) REVERT: i 77 ASP cc_start: 0.8258 (t70) cc_final: 0.7772 (t70) REVERT: i 86 GLU cc_start: 0.8753 (tt0) cc_final: 0.8128 (tm-30) REVERT: i 88 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.8261 (mtm110) REVERT: i 145 ASP cc_start: 0.8383 (p0) cc_final: 0.8070 (p0) REVERT: i 162 ARG cc_start: 0.9101 (mtp-110) cc_final: 0.8730 (ttm110) REVERT: i 205 ARG cc_start: 0.8894 (ptp90) cc_final: 0.8184 (ptt-90) REVERT: i 221 ASN cc_start: 0.8682 (m-40) cc_final: 0.7711 (p0) REVERT: i 222 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7832 (tt) REVERT: k 77 ASP cc_start: 0.8275 (t70) cc_final: 0.7810 (t70) REVERT: k 86 GLU cc_start: 0.8751 (tt0) cc_final: 0.8155 (tm-30) REVERT: k 88 ARG cc_start: 0.8486 (mtm110) cc_final: 0.8144 (mtm110) outliers start: 45 outliers final: 28 residues processed: 584 average time/residue: 0.7623 time to fit residues: 503.1644 Evaluate side-chains 561 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 527 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 154 SER Chi-restraints excluded: chain a residue 204 SER Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain g residue 167 CYS Chi-restraints excluded: chain g residue 214 ASP Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 154 SER Chi-restraints excluded: chain k residue 214 ASP Chi-restraints excluded: chain k residue 216 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 210 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 246 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 310 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 290 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN e 108 ASN k 150 GLN k 221 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.061665 restraints weight = 45713.060| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.05 r_work: 0.2639 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27400 Z= 0.136 Angle : 0.529 9.134 37254 Z= 0.270 Chirality : 0.037 0.171 4062 Planarity : 0.004 0.046 4728 Dihedral : 8.465 72.204 5407 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.60 % Allowed : 23.02 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.14), residues: 3342 helix: 2.22 (0.12), residues: 1638 sheet: 0.99 (0.20), residues: 678 loop : 0.26 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG i 162 TYR 0.011 0.001 TYR I 127 PHE 0.011 0.001 PHE g 99 TRP 0.007 0.001 TRP k 51 HIS 0.007 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (27378) covalent geometry : angle 0.52918 / 0.27 (37230) SS BOND : bond 0.00176 / 0.10 ( 12) SS BOND : angle 0.42998 / 0.25 ( 24) hydrogen bonds : bond 0.03653 / 2.50 ( 1644) hydrogen bonds : angle 4.29330 / 3.19 ( 4731) Misc. bond : bond 0.00067 / 0.04 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 541 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9230 (mtmt) cc_final: 0.8933 (pttm) REVERT: B 25 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8324 (tp-100) REVERT: B 102 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.9027 (p) REVERT: B 115 GLU cc_start: 0.8916 (mp0) cc_final: 0.8407 (tt0) REVERT: C 78 LYS cc_start: 0.9140 (mtmt) cc_final: 0.8900 (mtmt) REVERT: G 23 ASP cc_start: 0.8684 (m-30) cc_final: 0.8345 (m-30) REVERT: G 84 ARG cc_start: 0.8778 (ttp-110) cc_final: 0.8556 (ttp-110) REVERT: G 164 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8920 (tt0) REVERT: I 137 ARG cc_start: 0.9050 (ttt90) cc_final: 0.8831 (ttt90) REVERT: J 149 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.6587 (ttt-90) REVERT: J 164 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8777 (tt0) REVERT: Q 25 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8360 (tp-100) REVERT: Q 102 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8917 (p) REVERT: Q 115 GLU cc_start: 0.8946 (mp0) cc_final: 0.8383 (tt0) REVERT: a 14 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8309 (mt-10) REVERT: a 71 LYS cc_start: 0.9038 (tppt) cc_final: 0.8549 (tppt) REVERT: a 77 ASP cc_start: 0.8327 (t70) cc_final: 0.7951 (t70) REVERT: a 86 GLU cc_start: 0.8473 (tp30) cc_final: 0.8070 (tm-30) REVERT: a 155 LEU cc_start: 0.7681 (tp) cc_final: 0.7053 (pt) REVERT: a 247 ASN cc_start: 0.8442 (t0) cc_final: 0.8112 (t160) REVERT: a 249 GLU cc_start: 0.8256 (pm20) cc_final: 0.7788 (pm20) REVERT: c 44 ARG cc_start: 0.8425 (mtp85) cc_final: 0.7961 (mmm160) REVERT: c 77 ASP cc_start: 0.8374 (t70) cc_final: 0.7774 (t70) REVERT: c 86 GLU cc_start: 0.8580 (tt0) cc_final: 0.8113 (tm-30) REVERT: c 88 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7189 (ptt-90) REVERT: c 145 ASP cc_start: 0.8597 (p0) cc_final: 0.7911 (p0) REVERT: c 223 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7534 (mm-30) REVERT: e 14 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8252 (mt-10) REVERT: e 44 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7889 (mmm160) REVERT: e 77 ASP cc_start: 0.8206 (t70) cc_final: 0.7684 (t70) REVERT: e 86 GLU cc_start: 0.8636 (tt0) cc_final: 0.8001 (tm-30) REVERT: e 88 ARG cc_start: 0.8583 (mtm110) cc_final: 0.8118 (mtm110) REVERT: g 14 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8315 (mt-10) REVERT: g 15 LEU cc_start: 0.9100 (mp) cc_final: 0.8856 (tt) REVERT: g 71 LYS cc_start: 0.8676 (tppt) cc_final: 0.8374 (tppt) REVERT: g 77 ASP cc_start: 0.8279 (t70) cc_final: 0.7894 (t70) REVERT: g 85 MET cc_start: 0.9189 (ttm) cc_final: 0.8943 (ttm) REVERT: g 88 ARG cc_start: 0.8498 (mtm110) cc_final: 0.8279 (mtm110) REVERT: g 145 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: g 205 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8319 (ttp80) REVERT: i 14 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8321 (mt-10) REVERT: i 71 LYS cc_start: 0.8888 (tppt) cc_final: 0.8626 (tppt) REVERT: i 77 ASP cc_start: 0.8248 (t70) cc_final: 0.7781 (t70) REVERT: i 86 GLU cc_start: 0.8732 (tt0) cc_final: 0.8095 (tm-30) REVERT: i 88 ARG cc_start: 0.8473 (mtp-110) cc_final: 0.8256 (mtm110) REVERT: i 145 ASP cc_start: 0.8372 (p0) cc_final: 0.8053 (p0) REVERT: i 162 ARG cc_start: 0.9096 (mtp-110) cc_final: 0.8708 (ttm110) REVERT: i 205 ARG cc_start: 0.8910 (ptp90) cc_final: 0.8564 (ptt-90) REVERT: i 221 ASN cc_start: 0.8686 (m-40) cc_final: 0.7762 (p0) REVERT: i 222 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7789 (tt) REVERT: k 77 ASP cc_start: 0.8278 (t70) cc_final: 0.7787 (t0) REVERT: k 86 GLU cc_start: 0.8764 (tt0) cc_final: 0.8144 (tm-30) REVERT: k 88 ARG cc_start: 0.8483 (mtm110) cc_final: 0.8175 (mtm110) REVERT: k 200 SER cc_start: 0.9361 (t) cc_final: 0.9134 (p) REVERT: k 222 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7948 (tt) REVERT: k 237 LYS cc_start: 0.9025 (mmtt) cc_final: 0.8766 (mmmm) outliers start: 44 outliers final: 27 residues processed: 568 average time/residue: 0.7733 time to fit residues: 496.0634 Evaluate side-chains 559 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 525 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 145 ASP Chi-restraints excluded: chain g residue 167 CYS Chi-restraints excluded: chain g residue 214 ASP Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 154 SER Chi-restraints excluded: chain k residue 214 ASP Chi-restraints excluded: chain k residue 216 SER Chi-restraints excluded: chain k residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 241 optimal weight: 0.9980 chunk 164 optimal weight: 0.0010 chunk 273 optimal weight: 5.9990 chunk 329 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 210 optimal weight: 0.2980 chunk 206 optimal weight: 0.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 150 GLN k 150 GLN k 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.062682 restraints weight = 45492.915| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.06 r_work: 0.2662 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27400 Z= 0.123 Angle : 0.524 8.725 37254 Z= 0.268 Chirality : 0.037 0.174 4062 Planarity : 0.004 0.043 4728 Dihedral : 8.411 72.928 5406 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.42 % Allowed : 23.35 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.15), residues: 3342 helix: 2.28 (0.12), residues: 1638 sheet: 1.03 (0.20), residues: 678 loop : 0.24 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG i 162 TYR 0.011 0.001 TYR I 127 PHE 0.011 0.001 PHE e 99 TRP 0.008 0.001 TRP i 40 HIS 0.007 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (27378) covalent geometry : angle 0.52440 / 0.27 (37230) SS BOND : bond 0.00205 / 0.12 ( 12) SS BOND : angle 0.44791 / 0.26 ( 24) hydrogen bonds : bond 0.03552 / 2.44 ( 1644) hydrogen bonds : angle 4.23922 / 3.15 ( 4731) Misc. bond : bond 0.00059 / 0.03 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6684 Ramachandran restraints generated. 3342 Oldfield, 0 Emsley, 3342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 547 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.9221 (mtmt) cc_final: 0.8923 (pttm) REVERT: B 25 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8326 (tp-100) REVERT: B 102 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.9009 (p) REVERT: B 115 GLU cc_start: 0.8898 (mp0) cc_final: 0.8392 (tt0) REVERT: C 37 ARG cc_start: 0.8272 (ptt90) cc_final: 0.8038 (ptt90) REVERT: C 78 LYS cc_start: 0.9117 (mtmt) cc_final: 0.8874 (mtmt) REVERT: G 23 ASP cc_start: 0.8690 (m-30) cc_final: 0.8391 (m-30) REVERT: G 84 ARG cc_start: 0.8787 (ttp-110) cc_final: 0.8565 (ttp-110) REVERT: G 164 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8866 (tt0) REVERT: I 137 ARG cc_start: 0.9065 (ttt90) cc_final: 0.8850 (ttt90) REVERT: J 149 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.6568 (ttt-90) REVERT: J 164 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8791 (tt0) REVERT: M 115 GLU cc_start: 0.8968 (mp0) cc_final: 0.8760 (mp0) REVERT: Q 25 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8353 (tp-100) REVERT: Q 102 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8837 (p) REVERT: Q 115 GLU cc_start: 0.8936 (mp0) cc_final: 0.8377 (tt0) REVERT: a 14 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8275 (mt-10) REVERT: a 71 LYS cc_start: 0.9056 (tppt) cc_final: 0.8456 (tppt) REVERT: a 77 ASP cc_start: 0.8330 (t70) cc_final: 0.7936 (t70) REVERT: a 86 GLU cc_start: 0.8428 (tp30) cc_final: 0.7943 (tm-30) REVERT: a 88 ARG cc_start: 0.7854 (ptt-90) cc_final: 0.7311 (ptt-90) REVERT: a 97 VAL cc_start: 0.8867 (t) cc_final: 0.8589 (p) REVERT: a 155 LEU cc_start: 0.7624 (tp) cc_final: 0.7045 (pt) REVERT: a 249 GLU cc_start: 0.8265 (pm20) cc_final: 0.7782 (pm20) REVERT: c 44 ARG cc_start: 0.8355 (mtp85) cc_final: 0.7934 (mmm160) REVERT: c 77 ASP cc_start: 0.8391 (t70) cc_final: 0.7761 (t0) REVERT: c 86 GLU cc_start: 0.8548 (tt0) cc_final: 0.8058 (tm-30) REVERT: c 88 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7290 (ptt-90) REVERT: c 223 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7551 (mm-30) REVERT: e 44 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7841 (mmm160) REVERT: e 77 ASP cc_start: 0.8197 (t70) cc_final: 0.7674 (t70) REVERT: e 86 GLU cc_start: 0.8608 (tt0) cc_final: 0.7976 (tm-30) REVERT: e 88 ARG cc_start: 0.8575 (mtm110) cc_final: 0.8140 (mtm110) REVERT: e 120 VAL cc_start: 0.9483 (t) cc_final: 0.9221 (m) REVERT: e 148 MET cc_start: 0.8967 (mmm) cc_final: 0.8762 (mmm) REVERT: g 14 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8318 (mt-10) REVERT: g 15 LEU cc_start: 0.9096 (mp) cc_final: 0.8850 (tt) REVERT: g 71 LYS cc_start: 0.8708 (tppt) cc_final: 0.8425 (tppt) REVERT: g 77 ASP cc_start: 0.8320 (t70) cc_final: 0.7884 (t70) REVERT: g 88 ARG cc_start: 0.8465 (mtm110) cc_final: 0.8220 (mtm110) REVERT: g 97 VAL cc_start: 0.8842 (t) cc_final: 0.8600 (p) REVERT: g 120 VAL cc_start: 0.9483 (t) cc_final: 0.9175 (m) REVERT: g 145 ASP cc_start: 0.8124 (m-30) cc_final: 0.7652 (m-30) REVERT: g 205 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8382 (ttp80) REVERT: i 71 LYS cc_start: 0.8887 (tppt) cc_final: 0.8626 (tppt) REVERT: i 77 ASP cc_start: 0.8264 (t70) cc_final: 0.7777 (t0) REVERT: i 86 GLU cc_start: 0.8739 (tt0) cc_final: 0.8064 (tm-30) REVERT: i 88 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.8289 (mtm110) REVERT: i 145 ASP cc_start: 0.8337 (p0) cc_final: 0.8027 (p0) REVERT: i 162 ARG cc_start: 0.9095 (mtp-110) cc_final: 0.8809 (ttm110) REVERT: i 205 ARG cc_start: 0.8918 (ptp90) cc_final: 0.8578 (ptt-90) REVERT: i 221 ASN cc_start: 0.8688 (m-40) cc_final: 0.7757 (p0) REVERT: i 222 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7807 (tt) REVERT: k 77 ASP cc_start: 0.8280 (t70) cc_final: 0.7789 (t70) REVERT: k 86 GLU cc_start: 0.8753 (tt0) cc_final: 0.8123 (tm-30) REVERT: k 88 ARG cc_start: 0.8469 (mtm110) cc_final: 0.8198 (mtm110) REVERT: k 200 SER cc_start: 0.9314 (t) cc_final: 0.9104 (p) REVERT: k 222 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7899 (tt) REVERT: k 237 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8760 (mmmm) outliers start: 39 outliers final: 27 residues processed: 568 average time/residue: 0.8108 time to fit residues: 519.8971 Evaluate side-chains 559 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 526 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain J residue 149 ARG Chi-restraints excluded: chain J residue 162 SER Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain O residue 125 SER Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain c residue 45 THR Chi-restraints excluded: chain c residue 145 ASP Chi-restraints excluded: chain c residue 214 ASP Chi-restraints excluded: chain c residue 216 SER Chi-restraints excluded: chain e residue 44 ARG Chi-restraints excluded: chain e residue 45 THR Chi-restraints excluded: chain e residue 214 ASP Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 108 ASN Chi-restraints excluded: chain g residue 167 CYS Chi-restraints excluded: chain g residue 214 ASP Chi-restraints excluded: chain i residue 194 TYR Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain i residue 222 LEU Chi-restraints excluded: chain k residue 154 SER Chi-restraints excluded: chain k residue 214 ASP Chi-restraints excluded: chain k residue 216 SER Chi-restraints excluded: chain k residue 222 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 1 optimal weight: 0.0060 chunk 24 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN I 161 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN k 150 GLN k 221 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.062839 restraints weight = 45285.083| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.04 r_work: 0.2669 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27400 Z= 0.125 Angle : 0.528 9.844 37254 Z= 0.270 Chirality : 0.037 0.176 4062 Planarity : 0.004 0.042 4728 Dihedral : 8.364 73.224 5406 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 1.56 % Allowed : 23.57 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.15), residues: 3342 helix: 2.29 (0.12), residues: 1638 sheet: 1.02 (0.20), residues: 678 loop : 0.25 (0.21), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG i 162 TYR 0.011 0.001 TYR I 127 PHE 0.011 0.001 PHE e 99 TRP 0.007 0.001 TRP i 40 HIS 0.007 0.002 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (27378) covalent geometry : angle 0.52771 / 0.27 (37230) SS BOND : bond 0.00182 / 0.10 ( 12) SS BOND : angle 0.45210 / 0.26 ( 24) hydrogen bonds : bond 0.03548 / 2.43 ( 1644) hydrogen bonds : angle 4.22072 / 3.14 ( 4731) Misc. bond : bond 0.00060 / 0.03 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13906.67 seconds wall clock time: 236 minutes 43.37 seconds (14203.37 seconds total)