Starting phenix.real_space_refine on Sun Aug 24 14:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgi_43201/08_2025/8vgi_43201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgi_43201/08_2025/8vgi_43201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgi_43201/08_2025/8vgi_43201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgi_43201/08_2025/8vgi_43201.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgi_43201/08_2025/8vgi_43201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgi_43201/08_2025/8vgi_43201.cif" } resolution = 2.7 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= -0.009 sd= 0.308 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 100 5.16 5 C 12960 2.51 5 N 3488 2.21 5 O 3934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20482 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "B" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "C" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "D" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1919 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 220} Chain: "E" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "F" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "G" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "H" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "I" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "J" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "K" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1570 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 1 Chain: "L" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 4.36, per 1000 atoms: 0.21 Number of scatterers: 20482 At special positions: 0 Unit cell: (111, 97, 183, 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 100 16.00 O 3934 8.00 N 3488 7.00 C 12960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.04 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 220 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 58 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 58 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 220 " distance=2.04 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 58 " distance=2.04 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 182 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 220 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 171 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS F 151 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 80 " - pdb=" SG CYS G 171 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 80 " - pdb=" SG CYS I 171 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS J 151 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.06 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 200 " distance=2.04 Simple disulfide: pdb=" SG CYS K 11 " - pdb=" SG CYS K 151 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.06 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 933.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4904 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 52 sheets defined 9.0% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 60E through 62 No H-bonds generated for 'chain 'A' and resid 60E through 62' Processing helix chain 'A' and resid 164 through 173A removed outlier: 3.571A pdb=" N LEU A 173A" --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 60E through 62 No H-bonds generated for 'chain 'B' and resid 60E through 62' Processing helix chain 'B' and resid 164 through 173A removed outlier: 3.510A pdb=" N HIS B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 173A" --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'C' and resid 60E through 62 No H-bonds generated for 'chain 'C' and resid 60E through 62' Processing helix chain 'C' and resid 164 through 173A removed outlier: 3.554A pdb=" N LEU C 173A" --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 60E through 62 No H-bonds generated for 'chain 'D' and resid 60E through 62' Processing helix chain 'D' and resid 164 through 173A removed outlier: 3.537A pdb=" N LEU D 173A" --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 205 through 208 Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 189 through 193 Processing helix chain 'H' and resid 205 through 208 Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 189 through 193 Processing helix chain 'J' and resid 205 through 208 Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 160 through 162 No H-bonds generated for 'chain 'K' and resid 160 through 162' Processing helix chain 'K' and resid 189 through 193 Processing helix chain 'K' and resid 205 through 208 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 removed outlier: 4.230A pdb=" N CYS A 136 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL A 213 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N THR A 229 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.767A pdb=" N CYS A 42 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 35 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A 40 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 21 removed outlier: 4.234A pdb=" N CYS B 136 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B 139 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 199 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL B 213 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N THR B 229 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 182 " --> pdb=" O MET B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.798A pdb=" N CYS B 42 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 35 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS B 40 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 21 removed outlier: 4.219A pdb=" N CYS C 136 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 139 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 199 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL C 213 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N THR C 229 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS C 182 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.776A pdb=" N CYS C 42 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL C 35 " --> pdb=" O HIS C 40 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS C 40 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 20 through 21 removed outlier: 4.235A pdb=" N CYS D 136 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR D 139 " --> pdb=" O PRO D 198 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 199 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL D 213 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR D 229 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS D 182 " --> pdb=" O MET D 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.780A pdb=" N CYS D 42 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 35 " --> pdb=" O HIS D 40 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS D 40 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 14 removed outlier: 3.504A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 3.504A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.554A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.522A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.836A pdb=" N ALA F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.832A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY F 143 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 186 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU F 145 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER F 184 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS F 147 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 182 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY F 143 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY F 143 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 186 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU F 145 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER F 184 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS F 147 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU F 182 " --> pdb=" O LYS F 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 155 through 158 Processing sheet with id=AC2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'G' and resid 10 through 14 removed outlier: 3.506A pdb=" N LEU G 11 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 10 through 14 removed outlier: 3.506A pdb=" N LEU G 11 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 114 through 118 removed outlier: 3.550A pdb=" N VAL G 133 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 153 through 155 removed outlier: 4.526A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 205 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.835A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.834A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.849A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 14 removed outlier: 4.128A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 14 removed outlier: 4.128A pdb=" N ALA I 84 " --> pdb=" O VAL I 104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.552A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.529A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.842A pdb=" N ALA J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.810A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.869A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY J 143 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL J 186 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU J 145 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER J 184 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS J 147 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 182 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.869A pdb=" N GLY J 143 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY J 143 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL J 186 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU J 145 " --> pdb=" O SER J 184 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER J 184 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS J 147 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 182 " --> pdb=" O LYS J 147 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 155 through 158 Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.838A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.807A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.866A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY K 143 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL K 186 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU K 145 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER K 184 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS K 147 " --> pdb=" O LEU K 182 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU K 182 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.866A pdb=" N GLY K 143 " --> pdb=" O LEU K 128 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY K 143 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL K 186 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU K 145 " --> pdb=" O SER K 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER K 184 " --> pdb=" O LEU K 145 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS K 147 " --> pdb=" O LEU K 182 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU K 182 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 155 through 158 Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.129A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 14 removed outlier: 4.129A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.554A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.532A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6378 1.34 - 1.46: 5247 1.46 - 1.59: 9247 1.59 - 1.71: 0 1.71 - 1.84: 120 Bond restraints: 20992 Sorted by residual: bond pdb=" CB PRO C 152A" pdb=" CG PRO C 152A" ideal model delta sigma weight residual 1.492 1.384 0.108 5.00e-02 4.00e+02 4.65e+00 bond pdb=" CB PRO B 152A" pdb=" CG PRO B 152A" ideal model delta sigma weight residual 1.492 1.385 0.107 5.00e-02 4.00e+02 4.54e+00 bond pdb=" CB PRO A 152A" pdb=" CG PRO A 152A" ideal model delta sigma weight residual 1.492 1.387 0.105 5.00e-02 4.00e+02 4.42e+00 bond pdb=" CA GLN A 81 " pdb=" CB GLN A 81 " ideal model delta sigma weight residual 1.539 1.437 0.103 4.88e-02 4.20e+02 4.42e+00 bond pdb=" CB PRO D 152A" pdb=" CG PRO D 152A" ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.33e+00 ... (remaining 20987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 25426 1.75 - 3.51: 2709 3.51 - 5.26: 425 5.26 - 7.02: 64 7.02 - 8.77: 20 Bond angle restraints: 28644 Sorted by residual: angle pdb=" N PRO C 152A" pdb=" CA PRO C 152A" pdb=" C PRO C 152A" ideal model delta sigma weight residual 110.70 119.34 -8.64 1.22e+00 6.72e-01 5.01e+01 angle pdb=" N PRO B 152A" pdb=" CA PRO B 152A" pdb=" C PRO B 152A" ideal model delta sigma weight residual 110.70 119.07 -8.37 1.22e+00 6.72e-01 4.71e+01 angle pdb=" N PRO D 152A" pdb=" CA PRO D 152A" pdb=" C PRO D 152A" ideal model delta sigma weight residual 110.70 118.32 -7.62 1.22e+00 6.72e-01 3.90e+01 angle pdb=" N PRO A 152A" pdb=" CA PRO A 152A" pdb=" C PRO A 152A" ideal model delta sigma weight residual 110.70 118.23 -7.53 1.22e+00 6.72e-01 3.81e+01 angle pdb=" CA PRO B 152A" pdb=" C PRO B 152A" pdb=" N PRO B 152B" ideal model delta sigma weight residual 117.93 123.45 -5.52 1.20e+00 6.94e-01 2.11e+01 ... (remaining 28639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11615 18.00 - 36.00: 705 36.00 - 54.00: 131 54.00 - 71.99: 40 71.99 - 89.99: 29 Dihedral angle restraints: 12520 sinusoidal: 4856 harmonic: 7664 Sorted by residual: dihedral pdb=" CA SER B 25 " pdb=" C SER B 25 " pdb=" N LYS B 26 " pdb=" CA LYS B 26 " ideal model delta harmonic sigma weight residual -180.00 -149.65 -30.35 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA SER C 25 " pdb=" C SER C 25 " pdb=" N LYS C 26 " pdb=" CA LYS C 26 " ideal model delta harmonic sigma weight residual 180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA SER A 25 " pdb=" C SER A 25 " pdb=" N LYS A 26 " pdb=" CA LYS A 26 " ideal model delta harmonic sigma weight residual -180.00 -149.79 -30.21 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 12517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1887 0.057 - 0.115: 916 0.115 - 0.172: 364 0.172 - 0.229: 41 0.229 - 0.286: 12 Chirality restraints: 3220 Sorted by residual: chirality pdb=" CA PRO C 152A" pdb=" N PRO C 152A" pdb=" C PRO C 152A" pdb=" CB PRO C 152A" both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB VAL A 121 " pdb=" CA VAL A 121 " pdb=" CG1 VAL A 121 " pdb=" CG2 VAL A 121 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL C 121 " pdb=" CA VAL C 121 " pdb=" CG1 VAL C 121 " pdb=" CG2 VAL C 121 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 3217 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 24 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ARG C 24 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG C 24 " 0.019 2.00e-02 2.50e+03 pdb=" N SER C 25 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 24 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ARG D 24 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG D 24 " 0.019 2.00e-02 2.50e+03 pdb=" N SER D 25 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 24 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C ARG B 24 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG B 24 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 25 " -0.017 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 201 2.60 - 3.18: 17790 3.18 - 3.75: 30420 3.75 - 4.33: 44853 4.33 - 4.90: 73539 Nonbonded interactions: 166803 Sorted by model distance: nonbonded pdb=" OH TYR A 95 " pdb=" OE2 GLU D 217 " model vdw 2.029 3.040 nonbonded pdb=" OH TYR B 95 " pdb=" OE2 GLU C 217 " model vdw 2.036 3.040 nonbonded pdb=" OE2 GLU A 217 " pdb=" OH TYR D 95 " model vdw 2.038 3.040 nonbonded pdb=" OE2 GLU B 217 " pdb=" OH TYR C 95 " model vdw 2.055 3.040 nonbonded pdb=" O MET B 163 " pdb=" O HOH B 301 " model vdw 2.124 3.040 ... (remaining 166798 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 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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: 4.990 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: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.940 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.011 0.108 21032 Z= 0.479 Angle : 1.167 8.770 28724 Z= 0.643 Chirality : 0.074 0.286 3220 Planarity : 0.010 0.072 3660 Dihedral : 13.302 89.992 7496 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.53 % Favored : 93.21 % Rotamer: Outliers : 0.70 % Allowed : 2.14 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.16), residues: 2636 helix: -2.14 (0.43), residues: 92 sheet: 0.07 (0.17), residues: 860 loop : -0.75 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.004 ARG K 97 TYR 0.030 0.005 TYR C 234 PHE 0.033 0.005 PHE I 118 TRP 0.028 0.005 TRP A 38 HIS 0.023 0.005 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.01141 (20992) covalent geometry : angle 1.16179 (28644) SS BOND : bond 0.01102 ( 40) SS BOND : angle 2.31785 ( 80) hydrogen bonds : bond 0.24367 ( 707) hydrogen bonds : angle 9.68060 ( 1935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 684 time to evaluate : 0.565 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 220 CYS cc_start: 0.6907 (m) cc_final: 0.6341 (m) REVERT: E 123 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8853 (mm-30) REVERT: E 148 TRP cc_start: 0.8541 (m100) cc_final: 0.8278 (m100) REVERT: F 3 GLN cc_start: 0.8568 (pm20) cc_final: 0.8332 (pm20) REVERT: F 6 GLU cc_start: 0.7273 (mp0) cc_final: 0.6883 (mp0) REVERT: F 76 ASN cc_start: 0.8114 (t0) cc_final: 0.7561 (t0) REVERT: F 170 PHE cc_start: 0.9088 (m-80) cc_final: 0.8517 (m-80) REVERT: F 180 TYR cc_start: 0.8843 (m-80) cc_final: 0.8616 (m-80) REVERT: G 123 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8853 (mm-30) REVERT: G 140 TYR cc_start: 0.8429 (t80) cc_final: 0.8201 (t80) REVERT: G 148 TRP cc_start: 0.8541 (m100) cc_final: 0.8270 (m100) REVERT: H 3 GLN cc_start: 0.8566 (pm20) cc_final: 0.8322 (pm20) REVERT: H 6 GLU cc_start: 0.7243 (mp0) cc_final: 0.6764 (mp0) REVERT: H 76 ASN cc_start: 0.8111 (t0) cc_final: 0.7552 (t0) REVERT: H 170 PHE cc_start: 0.9092 (m-80) cc_final: 0.8630 (m-80) REVERT: H 180 TYR cc_start: 0.8852 (m-80) cc_final: 0.8620 (m-80) REVERT: I 123 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8941 (mm-30) REVERT: I 148 TRP cc_start: 0.8545 (m100) cc_final: 0.8258 (m100) REVERT: J 6 GLU cc_start: 0.7236 (mp0) cc_final: 0.6816 (mp0) REVERT: J 76 ASN cc_start: 0.8203 (t0) cc_final: 0.7605 (t0) REVERT: J 170 PHE cc_start: 0.9119 (m-80) cc_final: 0.8763 (m-80) REVERT: J 180 TYR cc_start: 0.8819 (m-80) cc_final: 0.8146 (m-80) REVERT: K 6 GLU cc_start: 0.7215 (mp0) cc_final: 0.6798 (mp0) REVERT: K 76 ASN cc_start: 0.8173 (t0) cc_final: 0.7580 (t0) REVERT: K 170 PHE cc_start: 0.9118 (m-80) cc_final: 0.8502 (m-80) REVERT: K 180 TYR cc_start: 0.8813 (m-80) cc_final: 0.8149 (m-80) REVERT: L 123 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8934 (mm-30) REVERT: L 148 TRP cc_start: 0.8519 (m100) cc_final: 0.8243 (m100) outliers start: 16 outliers final: 8 residues processed: 696 average time/residue: 0.5849 time to fit residues: 461.3686 Evaluate side-chains 464 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 452 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 123 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 165 ASN B 165 ASN B 192 GLN C 146 ASN C 165 ASN D 20 GLN D 165 ASN D 192 GLN E 147 GLN E 158 ASN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 158 ASN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN I 158 ASN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.060944 restraints weight = 42257.544| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.43 r_work: 0.2554 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21032 Z= 0.210 Angle : 0.849 9.878 28724 Z= 0.439 Chirality : 0.050 0.202 3220 Planarity : 0.006 0.069 3660 Dihedral : 8.214 118.224 2884 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.49 % Allowed : 15.88 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.16), residues: 2636 helix: -1.27 (0.44), residues: 124 sheet: 0.27 (0.16), residues: 848 loop : -0.23 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.016 0.002 TYR L 29 PHE 0.023 0.003 PHE H 126 TRP 0.015 0.002 TRP A 215 HIS 0.005 0.001 HIS G 189 Details of bonding type rmsd covalent geometry : bond 0.00478 (20992) covalent geometry : angle 0.84595 (28644) SS BOND : bond 0.00480 ( 40) SS BOND : angle 1.63563 ( 80) hydrogen bonds : bond 0.04269 ( 707) hydrogen bonds : angle 6.85691 ( 1935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 526 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8962 (t0) cc_final: 0.8456 (t0) REVERT: A 149 GLU cc_start: 0.8620 (mp0) cc_final: 0.8162 (mp0) REVERT: A 150 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8846 (mmt-90) REVERT: A 164 GLU cc_start: 0.8201 (tp30) cc_final: 0.7872 (tm-30) REVERT: B 145 ASP cc_start: 0.9025 (t0) cc_final: 0.8538 (t0) REVERT: B 149 GLU cc_start: 0.8679 (mp0) cc_final: 0.8067 (mp0) REVERT: B 164 GLU cc_start: 0.8238 (tp30) cc_final: 0.7943 (tm-30) REVERT: C 145 ASP cc_start: 0.9044 (t0) cc_final: 0.8487 (t0) REVERT: C 149 GLU cc_start: 0.8645 (mp0) cc_final: 0.7914 (mp0) REVERT: C 164 GLU cc_start: 0.8245 (tp30) cc_final: 0.7958 (tm-30) REVERT: C 171 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8913 (mttt) REVERT: D 75 TYR cc_start: 0.8933 (t80) cc_final: 0.8720 (t80) REVERT: D 145 ASP cc_start: 0.8977 (t0) cc_final: 0.8379 (t0) REVERT: D 149 GLU cc_start: 0.8653 (mp0) cc_final: 0.7788 (mp0) REVERT: D 164 GLU cc_start: 0.8136 (tp30) cc_final: 0.7838 (tm-30) REVERT: E 30 ASN cc_start: 0.9196 (t0) cc_final: 0.8678 (t0) REVERT: E 50 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8742 (mp0) REVERT: E 145 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8169 (pptt) REVERT: E 210 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8148 (t0) REVERT: F 6 GLU cc_start: 0.7157 (mp0) cc_final: 0.6608 (mp0) REVERT: F 51 ILE cc_start: 0.9609 (tt) cc_final: 0.9386 (tp) REVERT: F 72 ASP cc_start: 0.8485 (t0) cc_final: 0.8017 (t0) REVERT: F 75 LYS cc_start: 0.9567 (mttt) cc_final: 0.9221 (mttt) REVERT: F 76 ASN cc_start: 0.8855 (t0) cc_final: 0.8124 (t0) REVERT: F 105 GLN cc_start: 0.7761 (pm20) cc_final: 0.7442 (pm20) REVERT: F 144 CYS cc_start: 0.8122 (t) cc_final: 0.7865 (t) REVERT: F 148 ASP cc_start: 0.8340 (p0) cc_final: 0.7823 (p0) REVERT: F 152 GLU cc_start: 0.8719 (pm20) cc_final: 0.8186 (pm20) REVERT: F 170 PHE cc_start: 0.8943 (m-80) cc_final: 0.8333 (m-80) REVERT: G 30 ASN cc_start: 0.9207 (t0) cc_final: 0.8690 (t0) REVERT: G 50 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8722 (mp0) REVERT: G 145 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8195 (pptt) REVERT: G 210 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8151 (t0) REVERT: H 6 GLU cc_start: 0.7133 (mp0) cc_final: 0.6434 (mp0) REVERT: H 51 ILE cc_start: 0.9619 (tt) cc_final: 0.9399 (tp) REVERT: H 72 ASP cc_start: 0.8477 (t0) cc_final: 0.8016 (t0) REVERT: H 75 LYS cc_start: 0.9566 (mttt) cc_final: 0.9224 (mttt) REVERT: H 76 ASN cc_start: 0.8852 (t0) cc_final: 0.8125 (t0) REVERT: H 105 GLN cc_start: 0.7812 (pm20) cc_final: 0.7363 (pm20) REVERT: H 144 CYS cc_start: 0.8104 (t) cc_final: 0.7863 (t) REVERT: H 148 ASP cc_start: 0.8350 (p0) cc_final: 0.7837 (p0) REVERT: H 152 GLU cc_start: 0.8710 (pm20) cc_final: 0.8183 (pm20) REVERT: H 170 PHE cc_start: 0.8973 (m-80) cc_final: 0.8329 (m-80) REVERT: I 18 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7955 (mmm-85) REVERT: I 30 ASN cc_start: 0.9198 (t0) cc_final: 0.8680 (t0) REVERT: I 50 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8680 (mp0) REVERT: I 53 ILE cc_start: 0.8827 (mp) cc_final: 0.8559 (mp) REVERT: I 210 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8168 (t0) REVERT: J 6 GLU cc_start: 0.7042 (mp0) cc_final: 0.6511 (mp0) REVERT: J 51 ILE cc_start: 0.9605 (tt) cc_final: 0.9387 (tp) REVERT: J 72 ASP cc_start: 0.8518 (t0) cc_final: 0.7681 (t0) REVERT: J 75 LYS cc_start: 0.9549 (mttt) cc_final: 0.9324 (mttt) REVERT: J 76 ASN cc_start: 0.8889 (t0) cc_final: 0.8180 (t0) REVERT: J 105 GLN cc_start: 0.7794 (pm20) cc_final: 0.7402 (pm20) REVERT: J 148 ASP cc_start: 0.8347 (p0) cc_final: 0.7237 (p0) REVERT: J 152 GLU cc_start: 0.8788 (pm20) cc_final: 0.8310 (pm20) REVERT: J 159 ASN cc_start: 0.8870 (m110) cc_final: 0.8426 (m110) REVERT: J 170 PHE cc_start: 0.9129 (m-80) cc_final: 0.8580 (m-80) REVERT: J 200 CYS cc_start: 0.8245 (t) cc_final: 0.7991 (t) REVERT: K 6 GLU cc_start: 0.7050 (mp0) cc_final: 0.6522 (mp0) REVERT: K 51 ILE cc_start: 0.9615 (tt) cc_final: 0.9397 (tp) REVERT: K 72 ASP cc_start: 0.8510 (t0) cc_final: 0.7693 (t0) REVERT: K 75 LYS cc_start: 0.9550 (mttt) cc_final: 0.9330 (mttt) REVERT: K 76 ASN cc_start: 0.8882 (t0) cc_final: 0.8179 (t0) REVERT: K 105 GLN cc_start: 0.7764 (pm20) cc_final: 0.7376 (pm20) REVERT: K 148 ASP cc_start: 0.8351 (p0) cc_final: 0.7874 (p0) REVERT: K 152 GLU cc_start: 0.8774 (pm20) cc_final: 0.8274 (pm20) REVERT: K 159 ASN cc_start: 0.8880 (m110) cc_final: 0.8487 (m110) REVERT: K 170 PHE cc_start: 0.8965 (m-80) cc_final: 0.8466 (m-80) REVERT: K 200 CYS cc_start: 0.8224 (t) cc_final: 0.7962 (t) REVERT: L 18 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7953 (mmm-85) REVERT: L 30 ASN cc_start: 0.9200 (t0) cc_final: 0.8677 (t0) REVERT: L 50 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8708 (mp0) REVERT: L 53 ILE cc_start: 0.8823 (mp) cc_final: 0.8556 (mp) REVERT: L 210 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8171 (t0) outliers start: 57 outliers final: 27 residues processed: 546 average time/residue: 0.5790 time to fit residues: 360.4406 Evaluate side-chains 440 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 405 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 151 CYS Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 122 ASP Chi-restraints excluded: chain G residue 145 LYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 151 CYS Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 206 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN B 20 GLN B 36 HIS C 20 GLN C 192 GLN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN ** J 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 147 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.059260 restraints weight = 42054.644| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.44 r_work: 0.2523 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21032 Z= 0.258 Angle : 0.789 7.694 28724 Z= 0.407 Chirality : 0.049 0.152 3220 Planarity : 0.006 0.068 3660 Dihedral : 5.855 21.980 2860 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.88 % Allowed : 18.02 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2636 helix: -1.20 (0.43), residues: 148 sheet: 0.48 (0.16), residues: 832 loop : -0.08 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 142 TYR 0.021 0.002 TYR L 140 PHE 0.025 0.002 PHE I 139 TRP 0.011 0.002 TRP A 215 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00603 (20992) covalent geometry : angle 0.78500 (28644) SS BOND : bond 0.00592 ( 40) SS BOND : angle 1.69990 ( 80) hydrogen bonds : bond 0.04054 ( 707) hydrogen bonds : angle 6.44210 ( 1935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 430 time to evaluate : 0.905 Fit side-chains REVERT: A 20 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: A 128 GLU cc_start: 0.9411 (tp30) cc_final: 0.9071 (tp30) REVERT: A 145 ASP cc_start: 0.9004 (t0) cc_final: 0.8390 (t0) REVERT: A 149 GLU cc_start: 0.8739 (mp0) cc_final: 0.8214 (mp0) REVERT: A 164 GLU cc_start: 0.8342 (tp30) cc_final: 0.8003 (tm-30) REVERT: B 20 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8528 (pm20) REVERT: B 109 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8530 (mm-30) REVERT: B 128 GLU cc_start: 0.9419 (tp30) cc_final: 0.9074 (tp30) REVERT: B 145 ASP cc_start: 0.8988 (t0) cc_final: 0.8251 (t0) REVERT: B 149 GLU cc_start: 0.8804 (mp0) cc_final: 0.7983 (mp0) REVERT: B 164 GLU cc_start: 0.8301 (tp30) cc_final: 0.7928 (tm-30) REVERT: C 145 ASP cc_start: 0.9012 (t0) cc_final: 0.8294 (t0) REVERT: C 149 GLU cc_start: 0.8777 (mp0) cc_final: 0.7958 (mp0) REVERT: C 164 GLU cc_start: 0.8340 (tp30) cc_final: 0.7999 (tm-30) REVERT: C 171 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8955 (mttt) REVERT: D 20 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: D 128 GLU cc_start: 0.9406 (tp30) cc_final: 0.9067 (tp30) REVERT: D 145 ASP cc_start: 0.8934 (t0) cc_final: 0.8160 (t0) REVERT: D 149 GLU cc_start: 0.8787 (mp0) cc_final: 0.7950 (mp0) REVERT: D 164 GLU cc_start: 0.8246 (tp30) cc_final: 0.7917 (tm-30) REVERT: E 18 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8136 (mmt90) REVERT: E 30 ASN cc_start: 0.9208 (t0) cc_final: 0.8716 (t0) REVERT: E 50 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8805 (mp0) REVERT: E 158 ASN cc_start: 0.9261 (m110) cc_final: 0.8791 (t0) REVERT: E 210 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8269 (t0) REVERT: F 3 GLN cc_start: 0.8885 (pm20) cc_final: 0.8634 (pm20) REVERT: F 6 GLU cc_start: 0.7136 (mp0) cc_final: 0.6391 (mp0) REVERT: F 51 ILE cc_start: 0.9650 (tt) cc_final: 0.9397 (tp) REVERT: F 72 ASP cc_start: 0.8765 (t0) cc_final: 0.8314 (t0) REVERT: F 76 ASN cc_start: 0.8963 (t0) cc_final: 0.8261 (t0) REVERT: F 79 SER cc_start: 0.9344 (m) cc_final: 0.9120 (p) REVERT: F 105 GLN cc_start: 0.7860 (pm20) cc_final: 0.7270 (pm20) REVERT: F 152 GLU cc_start: 0.8834 (pm20) cc_final: 0.8431 (pm20) REVERT: F 170 PHE cc_start: 0.8843 (m-80) cc_final: 0.8264 (m-80) REVERT: G 18 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8137 (mmt90) REVERT: G 30 ASN cc_start: 0.9209 (t0) cc_final: 0.8715 (t0) REVERT: G 50 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8780 (mp0) REVERT: G 158 ASN cc_start: 0.9257 (m110) cc_final: 0.8783 (t0) REVERT: G 210 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8288 (t0) REVERT: H 3 GLN cc_start: 0.8915 (pm20) cc_final: 0.8561 (pm20) REVERT: H 6 GLU cc_start: 0.7220 (mp0) cc_final: 0.6417 (mp0) REVERT: H 51 ILE cc_start: 0.9660 (tt) cc_final: 0.9406 (tp) REVERT: H 72 ASP cc_start: 0.8763 (t0) cc_final: 0.8316 (t0) REVERT: H 76 ASN cc_start: 0.8958 (t0) cc_final: 0.8252 (t0) REVERT: H 105 GLN cc_start: 0.7800 (pm20) cc_final: 0.7267 (pm20) REVERT: H 152 GLU cc_start: 0.8836 (pm20) cc_final: 0.8437 (pm20) REVERT: H 170 PHE cc_start: 0.9023 (m-80) cc_final: 0.8415 (m-80) REVERT: I 30 ASN cc_start: 0.9223 (t0) cc_final: 0.8723 (t0) REVERT: I 50 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8743 (mp0) REVERT: I 53 ILE cc_start: 0.8899 (mp) cc_final: 0.8583 (mp) REVERT: I 142 ARG cc_start: 0.9039 (ttm-80) cc_final: 0.8681 (ttm-80) REVERT: I 158 ASN cc_start: 0.9254 (m110) cc_final: 0.8782 (t0) REVERT: I 210 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8297 (t0) REVERT: J 6 GLU cc_start: 0.6985 (mp0) cc_final: 0.6445 (mp0) REVERT: J 51 ILE cc_start: 0.9647 (tt) cc_final: 0.9397 (tp) REVERT: J 72 ASP cc_start: 0.8632 (t0) cc_final: 0.7941 (t0) REVERT: J 76 ASN cc_start: 0.8997 (t0) cc_final: 0.8267 (t0) REVERT: J 105 GLN cc_start: 0.7874 (pm20) cc_final: 0.7237 (pm20) REVERT: J 148 ASP cc_start: 0.8201 (p0) cc_final: 0.7996 (p0) REVERT: J 152 GLU cc_start: 0.8969 (pm20) cc_final: 0.8609 (pm20) REVERT: J 170 PHE cc_start: 0.9155 (m-80) cc_final: 0.8592 (m-80) REVERT: J 180 TYR cc_start: 0.9280 (m-80) cc_final: 0.9052 (m-10) REVERT: J 201 ASN cc_start: 0.8828 (t0) cc_final: 0.8081 (m110) REVERT: K 6 GLU cc_start: 0.7010 (mp0) cc_final: 0.6431 (mp0) REVERT: K 51 ILE cc_start: 0.9660 (tt) cc_final: 0.9411 (tp) REVERT: K 72 ASP cc_start: 0.8615 (t0) cc_final: 0.7915 (t0) REVERT: K 76 ASN cc_start: 0.8990 (t0) cc_final: 0.8264 (t0) REVERT: K 105 GLN cc_start: 0.7867 (pm20) cc_final: 0.7270 (pm20) REVERT: K 152 GLU cc_start: 0.8959 (pm20) cc_final: 0.8588 (pm20) REVERT: K 170 PHE cc_start: 0.9157 (m-80) cc_final: 0.8624 (m-80) REVERT: K 180 TYR cc_start: 0.9278 (m-80) cc_final: 0.9057 (m-10) REVERT: K 201 ASN cc_start: 0.8830 (t0) cc_final: 0.8082 (m110) REVERT: L 30 ASN cc_start: 0.9217 (t0) cc_final: 0.8724 (t0) REVERT: L 50 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8753 (mp0) REVERT: L 53 ILE cc_start: 0.8911 (mp) cc_final: 0.8588 (mp) REVERT: L 142 ARG cc_start: 0.8899 (ttm-80) cc_final: 0.8468 (tpp80) REVERT: L 158 ASN cc_start: 0.9258 (m110) cc_final: 0.8781 (t0) REVERT: L 210 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8293 (t0) outliers start: 66 outliers final: 27 residues processed: 457 average time/residue: 0.5327 time to fit residues: 280.5880 Evaluate side-chains 430 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 395 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 208 ASN Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 261 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 136 optimal weight: 20.0000 chunk 246 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 20 GLN B 221AGLN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221AGLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.061562 restraints weight = 41800.507| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.46 r_work: 0.2573 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21032 Z= 0.135 Angle : 0.718 7.907 28724 Z= 0.367 Chirality : 0.047 0.164 3220 Planarity : 0.006 0.064 3660 Dihedral : 5.467 20.433 2860 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.71 % Allowed : 19.15 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2636 helix: -0.26 (0.49), residues: 124 sheet: 0.72 (0.16), residues: 816 loop : -0.19 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 142 TYR 0.024 0.002 TYR G 140 PHE 0.024 0.002 PHE I 139 TRP 0.010 0.001 TRP A 215 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00310 (20992) covalent geometry : angle 0.71547 (28644) SS BOND : bond 0.00710 ( 40) SS BOND : angle 1.25268 ( 80) hydrogen bonds : bond 0.03438 ( 707) hydrogen bonds : angle 5.99250 ( 1935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 477 time to evaluate : 0.724 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8842 (t0) cc_final: 0.8375 (t0) REVERT: A 149 GLU cc_start: 0.8917 (mp0) cc_final: 0.8533 (mp0) REVERT: A 164 GLU cc_start: 0.8274 (tp30) cc_final: 0.7857 (tm-30) REVERT: A 204 ASN cc_start: 0.9489 (OUTLIER) cc_final: 0.9206 (t160) REVERT: B 109 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8595 (mm-30) REVERT: B 128 GLU cc_start: 0.9414 (tp30) cc_final: 0.9022 (tp30) REVERT: B 145 ASP cc_start: 0.8816 (t0) cc_final: 0.8247 (t0) REVERT: B 149 GLU cc_start: 0.8926 (mp0) cc_final: 0.8337 (mp0) REVERT: B 164 GLU cc_start: 0.8283 (tp30) cc_final: 0.7850 (tm-30) REVERT: B 204 ASN cc_start: 0.9490 (OUTLIER) cc_final: 0.9210 (t160) REVERT: C 145 ASP cc_start: 0.8806 (t0) cc_final: 0.8272 (t0) REVERT: C 149 GLU cc_start: 0.8889 (mp0) cc_final: 0.8325 (mp0) REVERT: C 164 GLU cc_start: 0.8317 (tp30) cc_final: 0.7947 (tm-30) REVERT: C 171 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8863 (mttt) REVERT: C 204 ASN cc_start: 0.9488 (OUTLIER) cc_final: 0.9199 (t160) REVERT: D 20 GLN cc_start: 0.8745 (pm20) cc_final: 0.8525 (pm20) REVERT: D 145 ASP cc_start: 0.8761 (t0) cc_final: 0.8206 (t0) REVERT: D 149 GLU cc_start: 0.8876 (mp0) cc_final: 0.8290 (mp0) REVERT: D 164 GLU cc_start: 0.8223 (tp30) cc_final: 0.7816 (tm-30) REVERT: D 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9207 (t160) REVERT: E 18 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.8166 (mmt90) REVERT: E 30 ASN cc_start: 0.9142 (t0) cc_final: 0.8670 (t0) REVERT: E 50 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9033 (mp0) REVERT: E 142 ARG cc_start: 0.8969 (ttm-80) cc_final: 0.8516 (ttm-80) REVERT: E 158 ASN cc_start: 0.9252 (m110) cc_final: 0.8675 (t0) REVERT: E 210 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8396 (t0) REVERT: E 211 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.6960 (ptm160) REVERT: F 3 GLN cc_start: 0.8913 (pm20) cc_final: 0.8668 (pm20) REVERT: F 6 GLU cc_start: 0.7161 (mp0) cc_final: 0.6372 (mp0) REVERT: F 51 ILE cc_start: 0.9656 (tt) cc_final: 0.9408 (tp) REVERT: F 72 ASP cc_start: 0.8821 (t0) cc_final: 0.8391 (t0) REVERT: F 76 ASN cc_start: 0.8906 (t0) cc_final: 0.8282 (t0) REVERT: F 79 SER cc_start: 0.9349 (m) cc_final: 0.9071 (p) REVERT: F 105 GLN cc_start: 0.7881 (pm20) cc_final: 0.7274 (pm20) REVERT: F 152 GLU cc_start: 0.8823 (pm20) cc_final: 0.8552 (pm20) REVERT: F 170 PHE cc_start: 0.8817 (m-80) cc_final: 0.8195 (m-80) REVERT: G 18 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.8128 (mmt90) REVERT: G 30 ASN cc_start: 0.9141 (t0) cc_final: 0.8669 (t0) REVERT: G 50 GLU cc_start: 0.9244 (mt-10) cc_final: 0.9011 (mp0) REVERT: G 142 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8429 (tpp80) REVERT: G 158 ASN cc_start: 0.9253 (m110) cc_final: 0.8684 (t0) REVERT: G 210 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8348 (t0) REVERT: H 3 GLN cc_start: 0.8941 (pm20) cc_final: 0.8715 (pm20) REVERT: H 6 GLU cc_start: 0.7212 (mp0) cc_final: 0.6220 (mp0) REVERT: H 51 ILE cc_start: 0.9664 (tt) cc_final: 0.9417 (tp) REVERT: H 72 ASP cc_start: 0.8823 (t0) cc_final: 0.8374 (t0) REVERT: H 76 ASN cc_start: 0.8903 (t0) cc_final: 0.8283 (t0) REVERT: H 105 GLN cc_start: 0.7740 (pm20) cc_final: 0.7184 (pm20) REVERT: H 152 GLU cc_start: 0.8828 (pm20) cc_final: 0.8560 (pm20) REVERT: H 170 PHE cc_start: 0.8995 (m-80) cc_final: 0.8291 (m-80) REVERT: I 30 ASN cc_start: 0.9199 (t0) cc_final: 0.8746 (t0) REVERT: I 33 LEU cc_start: 0.9538 (tt) cc_final: 0.9296 (tm) REVERT: I 50 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8735 (mp0) REVERT: I 53 ILE cc_start: 0.8914 (mp) cc_final: 0.8649 (mp) REVERT: I 158 ASN cc_start: 0.9216 (m110) cc_final: 0.8595 (t0) REVERT: I 161 GLU cc_start: 0.8831 (mp0) cc_final: 0.8528 (mp0) REVERT: I 210 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8401 (t0) REVERT: J 6 GLU cc_start: 0.6920 (mp0) cc_final: 0.6290 (mp0) REVERT: J 11 CYS cc_start: 0.6555 (t) cc_final: 0.6350 (t) REVERT: J 51 ILE cc_start: 0.9651 (tt) cc_final: 0.9401 (tp) REVERT: J 72 ASP cc_start: 0.8719 (t0) cc_final: 0.8074 (t0) REVERT: J 76 ASN cc_start: 0.8957 (t0) cc_final: 0.8362 (t0) REVERT: J 105 GLN cc_start: 0.7904 (pm20) cc_final: 0.7302 (pm20) REVERT: J 148 ASP cc_start: 0.7992 (p0) cc_final: 0.7768 (p0) REVERT: J 152 GLU cc_start: 0.8854 (pm20) cc_final: 0.8398 (pm20) REVERT: J 170 PHE cc_start: 0.9165 (m-80) cc_final: 0.8590 (m-80) REVERT: J 180 TYR cc_start: 0.9238 (m-80) cc_final: 0.9034 (m-80) REVERT: J 201 ASN cc_start: 0.8916 (t0) cc_final: 0.8129 (m110) REVERT: K 6 GLU cc_start: 0.6991 (mp0) cc_final: 0.6309 (mp0) REVERT: K 51 ILE cc_start: 0.9661 (tt) cc_final: 0.9415 (tp) REVERT: K 72 ASP cc_start: 0.8732 (t0) cc_final: 0.8089 (t0) REVERT: K 76 ASN cc_start: 0.8952 (t0) cc_final: 0.8357 (t0) REVERT: K 105 GLN cc_start: 0.7899 (pm20) cc_final: 0.7282 (pm20) REVERT: K 152 GLU cc_start: 0.8873 (pm20) cc_final: 0.8395 (pm20) REVERT: K 170 PHE cc_start: 0.9163 (m-80) cc_final: 0.8619 (m-80) REVERT: K 180 TYR cc_start: 0.9242 (m-80) cc_final: 0.9034 (m-80) REVERT: K 201 ASN cc_start: 0.8933 (t0) cc_final: 0.8136 (m110) REVERT: L 30 ASN cc_start: 0.9165 (t0) cc_final: 0.8694 (t0) REVERT: L 50 GLU cc_start: 0.9264 (mt-10) cc_final: 0.9014 (mp0) REVERT: L 158 ASN cc_start: 0.9224 (m110) cc_final: 0.8601 (t0) REVERT: L 161 GLU cc_start: 0.8810 (mp0) cc_final: 0.8553 (mp0) REVERT: L 210 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8383 (t0) outliers start: 62 outliers final: 28 residues processed: 505 average time/residue: 0.4856 time to fit residues: 284.9758 Evaluate side-chains 472 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 435 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 176 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.058092 restraints weight = 42179.688| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 3.36 r_work: 0.2489 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 21032 Z= 0.308 Angle : 0.754 7.960 28724 Z= 0.394 Chirality : 0.049 0.182 3220 Planarity : 0.006 0.064 3660 Dihedral : 5.525 20.976 2860 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.10 % Allowed : 20.81 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2636 helix: -0.15 (0.50), residues: 124 sheet: 0.43 (0.16), residues: 876 loop : -0.18 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 142 TYR 0.029 0.003 TYR D 75 PHE 0.017 0.002 PHE E 83 TRP 0.012 0.002 TRP A 141 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00712 (20992) covalent geometry : angle 0.75171 (28644) SS BOND : bond 0.00673 ( 40) SS BOND : angle 1.32550 ( 80) hydrogen bonds : bond 0.03854 ( 707) hydrogen bonds : angle 6.08965 ( 1935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 425 time to evaluate : 0.778 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8873 (t0) cc_final: 0.8381 (t0) REVERT: A 149 GLU cc_start: 0.8881 (mp0) cc_final: 0.8409 (mp0) REVERT: A 164 GLU cc_start: 0.8449 (tp30) cc_final: 0.8005 (tm-30) REVERT: B 109 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8500 (mm-30) REVERT: B 145 ASP cc_start: 0.8849 (t0) cc_final: 0.8161 (t0) REVERT: B 149 GLU cc_start: 0.8878 (mp0) cc_final: 0.8056 (mp0) REVERT: B 164 GLU cc_start: 0.8419 (tp30) cc_final: 0.7966 (tm-30) REVERT: C 145 ASP cc_start: 0.8927 (t0) cc_final: 0.8306 (t0) REVERT: C 149 GLU cc_start: 0.8858 (mp0) cc_final: 0.8159 (mp0) REVERT: C 164 GLU cc_start: 0.8457 (tp30) cc_final: 0.8007 (tm-30) REVERT: C 171 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8973 (mttt) REVERT: D 145 ASP cc_start: 0.8806 (t0) cc_final: 0.8074 (t0) REVERT: D 149 GLU cc_start: 0.8856 (mp0) cc_final: 0.8036 (mp0) REVERT: D 164 GLU cc_start: 0.8414 (tp30) cc_final: 0.7944 (tm-30) REVERT: E 18 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8186 (mmt90) REVERT: E 30 ASN cc_start: 0.9205 (t0) cc_final: 0.8693 (t0) REVERT: E 50 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8971 (mp0) REVERT: E 142 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8480 (ttm110) REVERT: E 158 ASN cc_start: 0.9226 (m110) cc_final: 0.8657 (t0) REVERT: E 210 ASN cc_start: 0.8633 (p0) cc_final: 0.8366 (t0) REVERT: F 3 GLN cc_start: 0.8995 (pm20) cc_final: 0.8477 (pm20) REVERT: F 6 GLU cc_start: 0.7211 (mp0) cc_final: 0.6452 (mp0) REVERT: F 51 ILE cc_start: 0.9697 (tt) cc_final: 0.9408 (tp) REVERT: F 72 ASP cc_start: 0.8890 (t0) cc_final: 0.8448 (t0) REVERT: F 76 ASN cc_start: 0.9033 (t0) cc_final: 0.8503 (t0) REVERT: F 79 SER cc_start: 0.9365 (m) cc_final: 0.8967 (p) REVERT: F 105 GLN cc_start: 0.7883 (pm20) cc_final: 0.7266 (pm20) REVERT: F 152 GLU cc_start: 0.9015 (pm20) cc_final: 0.8629 (pm20) REVERT: F 170 PHE cc_start: 0.8814 (m-80) cc_final: 0.8555 (m-80) REVERT: G 18 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8180 (mmt90) REVERT: G 30 ASN cc_start: 0.9210 (t0) cc_final: 0.8698 (t0) REVERT: G 50 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8954 (mp0) REVERT: G 108 ARG cc_start: 0.6561 (ttp-110) cc_final: 0.6142 (tmm-80) REVERT: G 158 ASN cc_start: 0.9230 (m110) cc_final: 0.8666 (t0) REVERT: G 210 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8468 (t0) REVERT: H 3 GLN cc_start: 0.9030 (pm20) cc_final: 0.8526 (pm20) REVERT: H 6 GLU cc_start: 0.7281 (mp0) cc_final: 0.6295 (mp0) REVERT: H 51 ILE cc_start: 0.9698 (tt) cc_final: 0.9414 (tp) REVERT: H 72 ASP cc_start: 0.8889 (t0) cc_final: 0.8469 (t0) REVERT: H 76 ASN cc_start: 0.9023 (t0) cc_final: 0.8497 (t0) REVERT: H 105 GLN cc_start: 0.7846 (pm20) cc_final: 0.7290 (pm20) REVERT: H 152 GLU cc_start: 0.9020 (pm20) cc_final: 0.8629 (pm20) REVERT: H 170 PHE cc_start: 0.8928 (m-80) cc_final: 0.8355 (m-80) REVERT: I 18 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7291 (mmt90) REVERT: I 30 ASN cc_start: 0.9213 (t0) cc_final: 0.8730 (t0) REVERT: I 50 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8695 (mp0) REVERT: I 53 ILE cc_start: 0.8940 (mp) cc_final: 0.8686 (mp) REVERT: I 142 ARG cc_start: 0.9088 (tpp80) cc_final: 0.8540 (ttm110) REVERT: I 158 ASN cc_start: 0.9217 (m110) cc_final: 0.8656 (t0) REVERT: I 210 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8466 (t0) REVERT: J 6 GLU cc_start: 0.7025 (mp0) cc_final: 0.6360 (mp0) REVERT: J 11 CYS cc_start: 0.6879 (t) cc_final: 0.6322 (t) REVERT: J 51 ILE cc_start: 0.9683 (tt) cc_final: 0.9400 (tp) REVERT: J 76 ASN cc_start: 0.9064 (t0) cc_final: 0.8457 (t0) REVERT: J 105 GLN cc_start: 0.7935 (pm20) cc_final: 0.7270 (pm20) REVERT: J 152 GLU cc_start: 0.8971 (pm20) cc_final: 0.8231 (pm20) REVERT: J 170 PHE cc_start: 0.9035 (m-80) cc_final: 0.8582 (m-80) REVERT: J 201 ASN cc_start: 0.9098 (t0) cc_final: 0.8328 (m110) REVERT: K 6 GLU cc_start: 0.7056 (mp0) cc_final: 0.6418 (mp0) REVERT: K 51 ILE cc_start: 0.9693 (tt) cc_final: 0.9411 (tp) REVERT: K 76 ASN cc_start: 0.9061 (t0) cc_final: 0.8456 (t0) REVERT: K 105 GLN cc_start: 0.7918 (pm20) cc_final: 0.7311 (pm20) REVERT: K 152 GLU cc_start: 0.8991 (pm20) cc_final: 0.8347 (pm20) REVERT: K 170 PHE cc_start: 0.9062 (m-80) cc_final: 0.8581 (m-80) REVERT: K 201 ASN cc_start: 0.9090 (t0) cc_final: 0.8334 (m110) REVERT: L 18 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7285 (mmt90) REVERT: L 30 ASN cc_start: 0.9220 (t0) cc_final: 0.8712 (t0) REVERT: L 50 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8702 (mp0) REVERT: L 53 ILE cc_start: 0.9034 (mp) cc_final: 0.8751 (mp) REVERT: L 117 ILE cc_start: 0.8833 (pp) cc_final: 0.8175 (mp) REVERT: L 142 ARG cc_start: 0.9114 (tpp80) cc_final: 0.8754 (ttm110) REVERT: L 158 ASN cc_start: 0.9222 (m110) cc_final: 0.8666 (t0) REVERT: L 210 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8446 (t0) outliers start: 71 outliers final: 45 residues processed: 463 average time/residue: 0.5698 time to fit residues: 303.2568 Evaluate side-chains 466 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 417 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 210 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 165 optimal weight: 0.7980 chunk 69 optimal weight: 0.0010 chunk 253 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 221AGLN B 50 GLN C 50 GLN C 221AGLN D 50 GLN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.100452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.061081 restraints weight = 41609.847| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.44 r_work: 0.2565 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21032 Z= 0.133 Angle : 0.691 8.863 28724 Z= 0.355 Chirality : 0.046 0.163 3220 Planarity : 0.006 0.062 3660 Dihedral : 5.175 18.954 2860 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.36 % Allowed : 21.77 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.16), residues: 2636 helix: -0.16 (0.49), residues: 128 sheet: 0.71 (0.17), residues: 796 loop : -0.15 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 61 TYR 0.026 0.002 TYR E 140 PHE 0.018 0.002 PHE I 83 TRP 0.010 0.001 TRP A 137 HIS 0.006 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00307 (20992) covalent geometry : angle 0.68877 (28644) SS BOND : bond 0.00510 ( 40) SS BOND : angle 1.17627 ( 80) hydrogen bonds : bond 0.03281 ( 707) hydrogen bonds : angle 5.71758 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 467 time to evaluate : 1.028 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: A 145 ASP cc_start: 0.8769 (t0) cc_final: 0.8138 (t0) REVERT: A 149 GLU cc_start: 0.8956 (mp0) cc_final: 0.8299 (mp0) REVERT: A 164 GLU cc_start: 0.8409 (tp30) cc_final: 0.7974 (tm-30) REVERT: A 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9173 (t160) REVERT: B 109 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8562 (mm-30) REVERT: B 145 ASP cc_start: 0.8787 (t0) cc_final: 0.8268 (t0) REVERT: B 149 GLU cc_start: 0.8958 (mp0) cc_final: 0.8383 (mp0) REVERT: B 164 GLU cc_start: 0.8372 (tp30) cc_final: 0.7977 (tm-30) REVERT: B 204 ASN cc_start: 0.9507 (OUTLIER) cc_final: 0.9191 (t160) REVERT: C 128 GLU cc_start: 0.9410 (tp30) cc_final: 0.9043 (tp30) REVERT: C 145 ASP cc_start: 0.8760 (t0) cc_final: 0.8236 (t0) REVERT: C 149 GLU cc_start: 0.8934 (mp0) cc_final: 0.8349 (mp0) REVERT: C 164 GLU cc_start: 0.8429 (tp30) cc_final: 0.7947 (tm-30) REVERT: C 171 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8930 (mttt) REVERT: C 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9173 (t160) REVERT: D 145 ASP cc_start: 0.8761 (t0) cc_final: 0.8222 (t0) REVERT: D 149 GLU cc_start: 0.8945 (mp0) cc_final: 0.8350 (mp0) REVERT: D 164 GLU cc_start: 0.8351 (tp30) cc_final: 0.7904 (tm-30) REVERT: D 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9174 (t160) REVERT: E 18 ARG cc_start: 0.8581 (mmm-85) cc_final: 0.8209 (mmt90) REVERT: E 30 ASN cc_start: 0.9168 (t0) cc_final: 0.8753 (t0) REVERT: E 50 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9028 (mp0) REVERT: E 125 LEU cc_start: 0.9525 (pp) cc_final: 0.9220 (mm) REVERT: E 142 ARG cc_start: 0.8974 (ttm-80) cc_final: 0.8413 (ttm-80) REVERT: E 158 ASN cc_start: 0.9220 (m110) cc_final: 0.8622 (t0) REVERT: E 211 ARG cc_start: 0.7550 (ttp-170) cc_final: 0.7002 (ptm160) REVERT: F 3 GLN cc_start: 0.8999 (pm20) cc_final: 0.8471 (pm20) REVERT: F 6 GLU cc_start: 0.7187 (mp0) cc_final: 0.6264 (mp0) REVERT: F 51 ILE cc_start: 0.9696 (tt) cc_final: 0.9461 (tp) REVERT: F 72 ASP cc_start: 0.8912 (t0) cc_final: 0.8478 (t0) REVERT: F 76 ASN cc_start: 0.8987 (t0) cc_final: 0.8480 (t0) REVERT: F 79 SER cc_start: 0.9326 (m) cc_final: 0.8878 (p) REVERT: F 105 GLN cc_start: 0.7978 (pm20) cc_final: 0.7352 (pm20) REVERT: F 152 GLU cc_start: 0.8978 (pm20) cc_final: 0.8600 (pm20) REVERT: F 170 PHE cc_start: 0.8768 (m-80) cc_final: 0.8497 (m-80) REVERT: G 18 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8206 (mmt90) REVERT: G 30 ASN cc_start: 0.9176 (t0) cc_final: 0.8757 (t0) REVERT: G 50 GLU cc_start: 0.9269 (mt-10) cc_final: 0.9014 (mp0) REVERT: G 125 LEU cc_start: 0.9544 (pp) cc_final: 0.9224 (mm) REVERT: G 142 ARG cc_start: 0.8970 (ttm110) cc_final: 0.8306 (ttm-80) REVERT: G 158 ASN cc_start: 0.9223 (m110) cc_final: 0.8638 (t0) REVERT: G 210 ASN cc_start: 0.8641 (p0) cc_final: 0.8429 (t0) REVERT: G 211 ARG cc_start: 0.6989 (ttp-170) cc_final: 0.6629 (ptm160) REVERT: H 3 GLN cc_start: 0.9014 (pm20) cc_final: 0.8520 (pm20) REVERT: H 6 GLU cc_start: 0.7265 (mp0) cc_final: 0.6179 (mp0) REVERT: H 51 ILE cc_start: 0.9698 (tt) cc_final: 0.9464 (tp) REVERT: H 72 ASP cc_start: 0.8905 (t0) cc_final: 0.8469 (t0) REVERT: H 76 ASN cc_start: 0.8977 (t0) cc_final: 0.8392 (t0) REVERT: H 105 GLN cc_start: 0.7867 (pm20) cc_final: 0.7252 (pm20) REVERT: H 152 GLU cc_start: 0.8989 (pm20) cc_final: 0.8603 (pm20) REVERT: H 170 PHE cc_start: 0.8957 (m-80) cc_final: 0.8351 (m-80) REVERT: I 30 ASN cc_start: 0.9190 (t0) cc_final: 0.8786 (t0) REVERT: I 33 LEU cc_start: 0.9562 (tt) cc_final: 0.9333 (tm) REVERT: I 50 GLU cc_start: 0.9223 (mt-10) cc_final: 0.9014 (mp0) REVERT: I 142 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8375 (ttm-80) REVERT: I 158 ASN cc_start: 0.9219 (m110) cc_final: 0.8578 (t0) REVERT: I 161 GLU cc_start: 0.8801 (mp0) cc_final: 0.8496 (mp0) REVERT: J 6 GLU cc_start: 0.7024 (mp0) cc_final: 0.6353 (mp0) REVERT: J 27 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: J 51 ILE cc_start: 0.9694 (OUTLIER) cc_final: 0.9456 (tp) REVERT: J 76 ASN cc_start: 0.9025 (t0) cc_final: 0.8545 (t0) REVERT: J 77 GLN cc_start: 0.9017 (pt0) cc_final: 0.8122 (pp30) REVERT: J 105 GLN cc_start: 0.7972 (pm20) cc_final: 0.7325 (pm20) REVERT: J 152 GLU cc_start: 0.8928 (pm20) cc_final: 0.8570 (pm20) REVERT: J 170 PHE cc_start: 0.9103 (m-80) cc_final: 0.8660 (m-80) REVERT: J 201 ASN cc_start: 0.9093 (t0) cc_final: 0.8317 (m110) REVERT: K 6 GLU cc_start: 0.7015 (mp0) cc_final: 0.6362 (mp0) REVERT: K 27 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: K 51 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9479 (tp) REVERT: K 76 ASN cc_start: 0.9018 (t0) cc_final: 0.8536 (t0) REVERT: K 77 GLN cc_start: 0.9012 (pt0) cc_final: 0.8119 (pp30) REVERT: K 105 GLN cc_start: 0.7956 (pm20) cc_final: 0.7318 (pm20) REVERT: K 152 GLU cc_start: 0.9041 (pm20) cc_final: 0.8619 (pm20) REVERT: K 170 PHE cc_start: 0.9104 (m-80) cc_final: 0.8612 (m-80) REVERT: K 201 ASN cc_start: 0.9175 (t0) cc_final: 0.8384 (m110) REVERT: L 18 ARG cc_start: 0.8280 (ttm110) cc_final: 0.8051 (ttm110) REVERT: L 30 ASN cc_start: 0.9174 (t0) cc_final: 0.8749 (t0) REVERT: L 50 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9020 (mp0) REVERT: L 117 ILE cc_start: 0.8835 (pp) cc_final: 0.8177 (mp) REVERT: L 125 LEU cc_start: 0.9546 (pp) cc_final: 0.9229 (mm) REVERT: L 158 ASN cc_start: 0.9229 (m110) cc_final: 0.8593 (t0) REVERT: L 161 GLU cc_start: 0.8813 (mp0) cc_final: 0.8513 (mp0) REVERT: L 210 ASN cc_start: 0.8694 (p0) cc_final: 0.8490 (t0) outliers start: 77 outliers final: 41 residues processed: 508 average time/residue: 0.5311 time to fit residues: 312.5605 Evaluate side-chains 485 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 435 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 27 PHE Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 27 PHE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 137 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 58 optimal weight: 0.0020 chunk 163 optimal weight: 0.9990 chunk 247 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.060809 restraints weight = 41774.010| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.39 r_work: 0.2563 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21032 Z= 0.156 Angle : 0.707 8.762 28724 Z= 0.361 Chirality : 0.047 0.173 3220 Planarity : 0.006 0.062 3660 Dihedral : 5.040 19.974 2860 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.27 % Allowed : 23.12 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2636 helix: -0.02 (0.49), residues: 128 sheet: 0.81 (0.17), residues: 788 loop : -0.18 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 142 TYR 0.025 0.002 TYR G 140 PHE 0.027 0.002 PHE L 139 TRP 0.009 0.001 TRP A 141 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00366 (20992) covalent geometry : angle 0.70529 (28644) SS BOND : bond 0.00585 ( 40) SS BOND : angle 1.10751 ( 80) hydrogen bonds : bond 0.03318 ( 707) hydrogen bonds : angle 5.65321 ( 1935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 451 time to evaluate : 0.776 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8764 (t0) cc_final: 0.8110 (t0) REVERT: A 149 GLU cc_start: 0.8977 (mp0) cc_final: 0.8312 (mp0) REVERT: A 164 GLU cc_start: 0.8429 (tp30) cc_final: 0.7995 (tm-30) REVERT: B 70 GLU cc_start: 0.8513 (pt0) cc_final: 0.8277 (pp20) REVERT: B 109 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 145 ASP cc_start: 0.8778 (t0) cc_final: 0.8258 (t0) REVERT: B 149 GLU cc_start: 0.8954 (mp0) cc_final: 0.8416 (mp0) REVERT: B 164 GLU cc_start: 0.8363 (tp30) cc_final: 0.7939 (tm-30) REVERT: C 145 ASP cc_start: 0.8740 (t0) cc_final: 0.8217 (t0) REVERT: C 149 GLU cc_start: 0.8952 (mp0) cc_final: 0.8392 (mp0) REVERT: C 164 GLU cc_start: 0.8508 (tp30) cc_final: 0.8034 (tm-30) REVERT: C 171 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8957 (mttt) REVERT: D 145 ASP cc_start: 0.8751 (t0) cc_final: 0.8200 (t0) REVERT: D 149 GLU cc_start: 0.8967 (mp0) cc_final: 0.8386 (mp0) REVERT: D 164 GLU cc_start: 0.8378 (tp30) cc_final: 0.7933 (tm-30) REVERT: E 18 ARG cc_start: 0.8625 (mmm-85) cc_final: 0.8196 (mmt90) REVERT: E 30 ASN cc_start: 0.9196 (t0) cc_final: 0.8790 (t0) REVERT: E 50 GLU cc_start: 0.9285 (mt-10) cc_final: 0.9052 (mp0) REVERT: E 142 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8314 (ttm-80) REVERT: E 158 ASN cc_start: 0.9227 (m110) cc_final: 0.8651 (t0) REVERT: E 211 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7007 (ptm160) REVERT: F 3 GLN cc_start: 0.9012 (pm20) cc_final: 0.8446 (pm20) REVERT: F 6 GLU cc_start: 0.7217 (mp0) cc_final: 0.6293 (mp0) REVERT: F 51 ILE cc_start: 0.9705 (OUTLIER) cc_final: 0.9472 (tp) REVERT: F 72 ASP cc_start: 0.8941 (t0) cc_final: 0.8503 (t0) REVERT: F 76 ASN cc_start: 0.8960 (t0) cc_final: 0.8541 (t0) REVERT: F 79 SER cc_start: 0.9313 (m) cc_final: 0.8833 (p) REVERT: F 105 GLN cc_start: 0.7945 (pm20) cc_final: 0.7343 (pm20) REVERT: F 152 GLU cc_start: 0.9035 (pm20) cc_final: 0.8703 (pm20) REVERT: F 170 PHE cc_start: 0.8760 (m-80) cc_final: 0.8469 (m-80) REVERT: F 195 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7760 (p) REVERT: G 11 LEU cc_start: 0.9277 (pp) cc_final: 0.8600 (pp) REVERT: G 18 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8229 (mmt90) REVERT: G 30 ASN cc_start: 0.9209 (t0) cc_final: 0.8802 (t0) REVERT: G 50 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9039 (mp0) REVERT: G 105 GLU cc_start: 0.8763 (tp30) cc_final: 0.8090 (mp0) REVERT: G 142 ARG cc_start: 0.8869 (ttm110) cc_final: 0.8311 (ttm-80) REVERT: G 158 ASN cc_start: 0.9230 (m110) cc_final: 0.8635 (t0) REVERT: H 3 GLN cc_start: 0.9026 (pm20) cc_final: 0.8502 (pm20) REVERT: H 51 ILE cc_start: 0.9706 (OUTLIER) cc_final: 0.9471 (tp) REVERT: H 72 ASP cc_start: 0.8911 (t0) cc_final: 0.8502 (t0) REVERT: H 76 ASN cc_start: 0.8972 (t0) cc_final: 0.8558 (t0) REVERT: H 152 GLU cc_start: 0.9014 (pm20) cc_final: 0.8677 (pm20) REVERT: H 170 PHE cc_start: 0.8951 (m-80) cc_final: 0.8479 (m-80) REVERT: H 195 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7738 (p) REVERT: I 18 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7245 (mmt90) REVERT: I 30 ASN cc_start: 0.9204 (t0) cc_final: 0.8822 (t0) REVERT: I 33 LEU cc_start: 0.9570 (tt) cc_final: 0.9296 (tm) REVERT: I 50 GLU cc_start: 0.9235 (mt-10) cc_final: 0.9007 (mp0) REVERT: I 158 ASN cc_start: 0.9216 (m110) cc_final: 0.8561 (t0) REVERT: I 161 GLU cc_start: 0.8761 (mp0) cc_final: 0.8506 (mp0) REVERT: I 211 ARG cc_start: 0.7395 (ttp-170) cc_final: 0.6767 (ptm160) REVERT: J 6 GLU cc_start: 0.7091 (mp0) cc_final: 0.6369 (mp0) REVERT: J 51 ILE cc_start: 0.9692 (OUTLIER) cc_final: 0.9456 (tp) REVERT: J 76 ASN cc_start: 0.8979 (t0) cc_final: 0.8612 (t0) REVERT: J 105 GLN cc_start: 0.7963 (pm20) cc_final: 0.7340 (pm20) REVERT: J 147 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8144 (tmtm) REVERT: J 152 GLU cc_start: 0.9032 (pm20) cc_final: 0.8662 (pm20) REVERT: J 170 PHE cc_start: 0.9073 (m-80) cc_final: 0.8623 (m-80) REVERT: J 195 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7724 (p) REVERT: J 201 ASN cc_start: 0.9130 (t0) cc_final: 0.8345 (m110) REVERT: K 6 GLU cc_start: 0.7123 (mp0) cc_final: 0.6433 (mp0) REVERT: K 51 ILE cc_start: 0.9704 (OUTLIER) cc_final: 0.9469 (tp) REVERT: K 76 ASN cc_start: 0.8978 (t0) cc_final: 0.8625 (t0) REVERT: K 77 GLN cc_start: 0.8999 (pt0) cc_final: 0.8139 (pp30) REVERT: K 105 GLN cc_start: 0.7945 (pm20) cc_final: 0.7331 (pm20) REVERT: K 152 GLU cc_start: 0.9043 (pm20) cc_final: 0.8653 (pm20) REVERT: K 170 PHE cc_start: 0.9102 (m-80) cc_final: 0.8583 (m-80) REVERT: K 195 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7723 (p) REVERT: K 201 ASN cc_start: 0.9169 (t0) cc_final: 0.8442 (m110) REVERT: L 30 ASN cc_start: 0.9216 (t0) cc_final: 0.8810 (t0) REVERT: L 50 GLU cc_start: 0.9248 (mt-10) cc_final: 0.9015 (mp0) REVERT: L 117 ILE cc_start: 0.8986 (pp) cc_final: 0.8366 (mp) REVERT: L 137 ASN cc_start: 0.7168 (m-40) cc_final: 0.6934 (m-40) REVERT: L 158 ASN cc_start: 0.9231 (m110) cc_final: 0.8649 (t0) REVERT: L 161 GLU cc_start: 0.8786 (mp0) cc_final: 0.8536 (mp0) REVERT: L 173 TYR cc_start: 0.7788 (m-10) cc_final: 0.7382 (m-10) outliers start: 75 outliers final: 46 residues processed: 489 average time/residue: 0.4936 time to fit residues: 280.2170 Evaluate side-chains 483 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 427 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 147 LYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 217 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 161 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.059494 restraints weight = 42096.496| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.37 r_work: 0.2533 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21032 Z= 0.230 Angle : 0.730 8.649 28724 Z= 0.377 Chirality : 0.048 0.181 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.085 20.995 2860 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.45 % Allowed : 23.12 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2636 helix: -0.02 (0.49), residues: 128 sheet: 0.61 (0.17), residues: 840 loop : -0.23 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 26 TYR 0.026 0.002 TYR I 140 PHE 0.014 0.002 PHE L 83 TRP 0.010 0.001 TRP C 141 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00542 (20992) covalent geometry : angle 0.72883 (28644) SS BOND : bond 0.00497 ( 40) SS BOND : angle 1.12852 ( 80) hydrogen bonds : bond 0.03502 ( 707) hydrogen bonds : angle 5.68783 ( 1935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 438 time to evaluate : 0.765 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: symmetry clash REVERT: A 145 ASP cc_start: 0.8845 (t0) cc_final: 0.8356 (t0) REVERT: A 149 GLU cc_start: 0.9007 (mp0) cc_final: 0.8541 (mp0) REVERT: A 164 GLU cc_start: 0.8501 (tp30) cc_final: 0.8064 (tm-30) REVERT: B 109 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8524 (mm-30) REVERT: B 145 ASP cc_start: 0.8860 (t0) cc_final: 0.8369 (t0) REVERT: B 149 GLU cc_start: 0.8985 (mp0) cc_final: 0.8499 (mp0) REVERT: B 164 GLU cc_start: 0.8416 (tp30) cc_final: 0.7970 (tm-30) REVERT: B 204 ASN cc_start: 0.9518 (OUTLIER) cc_final: 0.9207 (t160) REVERT: C 128 GLU cc_start: 0.9392 (tp30) cc_final: 0.9181 (tp30) REVERT: C 145 ASP cc_start: 0.8835 (t0) cc_final: 0.8200 (t0) REVERT: C 149 GLU cc_start: 0.8967 (mp0) cc_final: 0.8257 (mp0) REVERT: C 164 GLU cc_start: 0.8549 (tp30) cc_final: 0.8098 (tm-30) REVERT: C 171 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.9025 (mttt) REVERT: D 145 ASP cc_start: 0.8809 (t0) cc_final: 0.8272 (t0) REVERT: D 149 GLU cc_start: 0.8976 (mp0) cc_final: 0.8438 (mp0) REVERT: D 164 GLU cc_start: 0.8453 (tp30) cc_final: 0.8036 (tm-30) REVERT: D 204 ASN cc_start: 0.9506 (OUTLIER) cc_final: 0.9194 (t160) REVERT: E 18 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8249 (mmt90) REVERT: E 30 ASN cc_start: 0.9183 (t0) cc_final: 0.8763 (t0) REVERT: E 50 GLU cc_start: 0.9255 (mt-10) cc_final: 0.9035 (mt-10) REVERT: E 125 LEU cc_start: 0.9562 (pp) cc_final: 0.9209 (mm) REVERT: E 142 ARG cc_start: 0.8832 (ttm-80) cc_final: 0.8427 (ttm-80) REVERT: E 158 ASN cc_start: 0.9236 (m110) cc_final: 0.8652 (t0) REVERT: E 211 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.6857 (ptm160) REVERT: F 3 GLN cc_start: 0.9014 (pm20) cc_final: 0.8565 (pm20) REVERT: F 6 GLU cc_start: 0.7313 (mp0) cc_final: 0.6421 (mp0) REVERT: F 22 CYS cc_start: 0.8188 (t) cc_final: 0.7951 (t) REVERT: F 51 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9496 (tp) REVERT: F 72 ASP cc_start: 0.8962 (t0) cc_final: 0.8559 (t0) REVERT: F 76 ASN cc_start: 0.9021 (t0) cc_final: 0.8616 (t0) REVERT: F 79 SER cc_start: 0.9294 (m) cc_final: 0.8845 (p) REVERT: F 105 GLN cc_start: 0.7957 (pm20) cc_final: 0.7310 (pm20) REVERT: F 152 GLU cc_start: 0.9084 (pm20) cc_final: 0.8758 (pm20) REVERT: F 170 PHE cc_start: 0.8770 (m-80) cc_final: 0.8565 (m-80) REVERT: F 195 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7800 (p) REVERT: G 18 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8274 (mmt90) REVERT: G 30 ASN cc_start: 0.9192 (t0) cc_final: 0.8771 (t0) REVERT: G 50 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9032 (mt-10) REVERT: G 125 LEU cc_start: 0.9552 (pp) cc_final: 0.9206 (mm) REVERT: G 142 ARG cc_start: 0.8889 (ttm110) cc_final: 0.8504 (ttm-80) REVERT: G 158 ASN cc_start: 0.9238 (m110) cc_final: 0.8654 (t0) REVERT: H 3 GLN cc_start: 0.9017 (pm20) cc_final: 0.8744 (pm20) REVERT: H 6 GLU cc_start: 0.7738 (mp0) cc_final: 0.6691 (pm20) REVERT: H 51 ILE cc_start: 0.9728 (OUTLIER) cc_final: 0.9492 (tp) REVERT: H 72 ASP cc_start: 0.8938 (t0) cc_final: 0.8548 (t0) REVERT: H 76 ASN cc_start: 0.8996 (t0) cc_final: 0.8603 (t0) REVERT: H 105 GLN cc_start: 0.8454 (pm20) cc_final: 0.8215 (pm20) REVERT: H 152 GLU cc_start: 0.9090 (pm20) cc_final: 0.8756 (pm20) REVERT: H 170 PHE cc_start: 0.8893 (m-80) cc_final: 0.8529 (m-80) REVERT: H 195 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7796 (p) REVERT: I 18 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7268 (mmt90) REVERT: I 30 ASN cc_start: 0.9200 (t0) cc_final: 0.8800 (t0) REVERT: I 50 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8994 (mp0) REVERT: I 142 ARG cc_start: 0.8819 (ttm-80) cc_final: 0.8398 (tpp80) REVERT: I 158 ASN cc_start: 0.9230 (m110) cc_final: 0.8671 (t0) REVERT: I 211 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.6784 (ptm160) REVERT: J 6 GLU cc_start: 0.7229 (mp0) cc_final: 0.6515 (mp0) REVERT: J 51 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9469 (tp) REVERT: J 76 ASN cc_start: 0.9041 (t0) cc_final: 0.8672 (t0) REVERT: J 105 GLN cc_start: 0.7980 (pm20) cc_final: 0.7319 (pm20) REVERT: J 152 GLU cc_start: 0.9051 (pm20) cc_final: 0.8680 (pm20) REVERT: J 195 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7744 (p) REVERT: J 201 ASN cc_start: 0.9141 (t0) cc_final: 0.8881 (t0) REVERT: K 6 GLU cc_start: 0.7166 (mp0) cc_final: 0.6426 (mp0) REVERT: K 26 ARG cc_start: 0.8763 (mtp-110) cc_final: 0.8322 (ptm160) REVERT: K 51 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9491 (tp) REVERT: K 76 ASN cc_start: 0.9028 (t0) cc_final: 0.8672 (t0) REVERT: K 105 GLN cc_start: 0.7957 (pm20) cc_final: 0.7271 (pm20) REVERT: K 152 GLU cc_start: 0.9080 (pm20) cc_final: 0.8670 (pm20) REVERT: K 170 PHE cc_start: 0.9103 (m-80) cc_final: 0.8790 (m-80) REVERT: K 195 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7742 (p) REVERT: K 201 ASN cc_start: 0.9185 (t0) cc_final: 0.8929 (t0) REVERT: L 18 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7332 (mmt90) REVERT: L 30 ASN cc_start: 0.9204 (t0) cc_final: 0.8781 (t0) REVERT: L 50 GLU cc_start: 0.9221 (mt-10) cc_final: 0.9019 (mt-10) REVERT: L 117 ILE cc_start: 0.9038 (pp) cc_final: 0.8426 (mt) REVERT: L 125 LEU cc_start: 0.9560 (pp) cc_final: 0.9221 (mm) REVERT: L 137 ASN cc_start: 0.7367 (m-40) cc_final: 0.7127 (m-40) REVERT: L 158 ASN cc_start: 0.9243 (m110) cc_final: 0.8676 (t0) outliers start: 79 outliers final: 50 residues processed: 478 average time/residue: 0.4989 time to fit residues: 275.5286 Evaluate side-chains 490 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 146 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.099753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.060894 restraints weight = 41752.889| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.37 r_work: 0.2573 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21032 Z= 0.152 Angle : 0.755 10.000 28724 Z= 0.387 Chirality : 0.047 0.170 3220 Planarity : 0.006 0.077 3660 Dihedral : 5.075 28.426 2860 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.18 % Allowed : 23.91 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.16), residues: 2636 helix: 0.04 (0.49), residues: 128 sheet: 0.62 (0.16), residues: 900 loop : -0.10 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 26 TYR 0.031 0.002 TYR I 140 PHE 0.027 0.002 PHE L 139 TRP 0.012 0.001 TRP C 51 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00362 (20992) covalent geometry : angle 0.74633 (28644) SS BOND : bond 0.00522 ( 40) SS BOND : angle 2.31585 ( 80) hydrogen bonds : bond 0.03284 ( 707) hydrogen bonds : angle 5.55950 ( 1935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 445 time to evaluate : 0.675 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.9397 (tp30) cc_final: 0.9173 (tp30) REVERT: A 145 ASP cc_start: 0.8812 (t0) cc_final: 0.8161 (t0) REVERT: A 149 GLU cc_start: 0.8996 (mp0) cc_final: 0.8342 (mp0) REVERT: A 164 GLU cc_start: 0.8478 (tp30) cc_final: 0.8040 (tm-30) REVERT: A 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9135 (t160) REVERT: B 109 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8556 (mm-30) REVERT: B 145 ASP cc_start: 0.8828 (t0) cc_final: 0.8319 (t0) REVERT: B 149 GLU cc_start: 0.8963 (mp0) cc_final: 0.8452 (mp0) REVERT: B 164 GLU cc_start: 0.8377 (tp30) cc_final: 0.7942 (tm-30) REVERT: B 204 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.9188 (t160) REVERT: C 145 ASP cc_start: 0.8763 (t0) cc_final: 0.8267 (t0) REVERT: C 149 GLU cc_start: 0.8989 (mp0) cc_final: 0.8466 (mp0) REVERT: C 164 GLU cc_start: 0.8524 (tp30) cc_final: 0.8039 (tm-30) REVERT: C 204 ASN cc_start: 0.9505 (OUTLIER) cc_final: 0.9182 (t160) REVERT: D 128 GLU cc_start: 0.9406 (tp30) cc_final: 0.9183 (tp30) REVERT: D 145 ASP cc_start: 0.8794 (t0) cc_final: 0.8228 (t0) REVERT: D 149 GLU cc_start: 0.8972 (mp0) cc_final: 0.8416 (mp0) REVERT: D 164 GLU cc_start: 0.8416 (tp30) cc_final: 0.7932 (tm-30) REVERT: D 204 ASN cc_start: 0.9500 (OUTLIER) cc_final: 0.9171 (t160) REVERT: E 18 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8209 (mmt90) REVERT: E 30 ASN cc_start: 0.9159 (t0) cc_final: 0.8780 (t0) REVERT: E 50 GLU cc_start: 0.9230 (mt-10) cc_final: 0.9010 (mt-10) REVERT: E 105 GLU cc_start: 0.8600 (tp30) cc_final: 0.8205 (mp0) REVERT: E 125 LEU cc_start: 0.9559 (pp) cc_final: 0.9211 (mm) REVERT: E 142 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8485 (tpp80) REVERT: E 158 ASN cc_start: 0.9259 (m110) cc_final: 0.8688 (t0) REVERT: E 211 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.6780 (ptm160) REVERT: F 3 GLN cc_start: 0.8878 (pm20) cc_final: 0.8219 (pm20) REVERT: F 6 GLU cc_start: 0.7220 (mp0) cc_final: 0.6331 (mp0) REVERT: F 51 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9511 (tp) REVERT: F 72 ASP cc_start: 0.8978 (t0) cc_final: 0.8593 (t0) REVERT: F 76 ASN cc_start: 0.8957 (t0) cc_final: 0.8603 (t0) REVERT: F 77 GLN cc_start: 0.9021 (tt0) cc_final: 0.8637 (tp40) REVERT: F 79 SER cc_start: 0.9250 (m) cc_final: 0.8737 (p) REVERT: F 105 GLN cc_start: 0.8011 (pm20) cc_final: 0.7378 (pm20) REVERT: F 152 GLU cc_start: 0.9035 (pm20) cc_final: 0.8735 (pm20) REVERT: F 170 PHE cc_start: 0.8699 (m-80) cc_final: 0.8483 (m-80) REVERT: F 195 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7707 (p) REVERT: G 18 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8209 (mmt90) REVERT: G 30 ASN cc_start: 0.9177 (t0) cc_final: 0.8798 (t0) REVERT: G 50 GLU cc_start: 0.9238 (mt-10) cc_final: 0.9015 (mt-10) REVERT: G 125 LEU cc_start: 0.9561 (pp) cc_final: 0.9220 (mm) REVERT: G 142 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8529 (ttm-80) REVERT: G 158 ASN cc_start: 0.9253 (m110) cc_final: 0.8688 (t0) REVERT: H 3 GLN cc_start: 0.8997 (pm20) cc_final: 0.8234 (pm20) REVERT: H 6 GLU cc_start: 0.7663 (mp0) cc_final: 0.6482 (pm20) REVERT: H 27 PHE cc_start: 0.8159 (m-80) cc_final: 0.7217 (m-80) REVERT: H 51 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9507 (tp) REVERT: H 72 ASP cc_start: 0.8969 (t0) cc_final: 0.8593 (t0) REVERT: H 76 ASN cc_start: 0.8979 (t0) cc_final: 0.8674 (t0) REVERT: H 77 GLN cc_start: 0.8965 (tt0) cc_final: 0.8612 (tp40) REVERT: H 105 GLN cc_start: 0.8397 (pm20) cc_final: 0.8147 (pm20) REVERT: H 152 GLU cc_start: 0.9048 (pm20) cc_final: 0.8724 (pm20) REVERT: H 170 PHE cc_start: 0.8903 (m-80) cc_final: 0.8592 (m-80) REVERT: H 195 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7700 (p) REVERT: I 18 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7292 (mmt90) REVERT: I 30 ASN cc_start: 0.9173 (t0) cc_final: 0.8822 (t0) REVERT: I 50 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8985 (mp0) REVERT: I 142 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8472 (tpp80) REVERT: I 158 ASN cc_start: 0.9231 (m110) cc_final: 0.8659 (t0) REVERT: I 211 ARG cc_start: 0.7364 (ttp-170) cc_final: 0.6803 (ptm160) REVERT: J 51 ILE cc_start: 0.9706 (OUTLIER) cc_final: 0.9482 (tp) REVERT: J 76 ASN cc_start: 0.9012 (t0) cc_final: 0.8713 (t0) REVERT: J 152 GLU cc_start: 0.9058 (pm20) cc_final: 0.8765 (pm20) REVERT: J 195 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7687 (p) REVERT: J 201 ASN cc_start: 0.9186 (t0) cc_final: 0.8480 (m110) REVERT: K 26 ARG cc_start: 0.8842 (mtp-110) cc_final: 0.8504 (ptm160) REVERT: K 51 ILE cc_start: 0.9722 (OUTLIER) cc_final: 0.9498 (tp) REVERT: K 76 ASN cc_start: 0.9011 (t0) cc_final: 0.8717 (t0) REVERT: K 152 GLU cc_start: 0.9041 (pm20) cc_final: 0.8723 (pm20) REVERT: K 170 PHE cc_start: 0.9100 (m-80) cc_final: 0.8770 (m-80) REVERT: K 195 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7686 (p) REVERT: K 201 ASN cc_start: 0.9190 (t0) cc_final: 0.8493 (m110) REVERT: L 18 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7318 (mmt90) REVERT: L 30 ASN cc_start: 0.9180 (t0) cc_final: 0.8802 (t0) REVERT: L 50 GLU cc_start: 0.9208 (mt-10) cc_final: 0.9003 (mt-10) REVERT: L 117 ILE cc_start: 0.9041 (pp) cc_final: 0.8445 (mt) REVERT: L 125 LEU cc_start: 0.9557 (pp) cc_final: 0.9211 (mm) REVERT: L 137 ASN cc_start: 0.7206 (m-40) cc_final: 0.6982 (m-40) REVERT: L 158 ASN cc_start: 0.9250 (m110) cc_final: 0.8686 (t0) outliers start: 73 outliers final: 45 residues processed: 483 average time/residue: 0.5188 time to fit residues: 288.8377 Evaluate side-chains 485 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 428 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 10 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 227 optimal weight: 0.0970 chunk 170 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 164 optimal weight: 0.0980 chunk 115 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.061595 restraints weight = 41798.832| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.35 r_work: 0.2586 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21032 Z= 0.151 Angle : 0.750 10.986 28724 Z= 0.383 Chirality : 0.047 0.192 3220 Planarity : 0.006 0.106 3660 Dihedral : 5.043 24.391 2860 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.75 % Allowed : 24.87 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.16), residues: 2636 helix: 0.11 (0.50), residues: 128 sheet: 0.66 (0.16), residues: 892 loop : -0.14 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 26 TYR 0.031 0.002 TYR L 140 PHE 0.017 0.001 PHE F 27 TRP 0.013 0.001 TRP B 51 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00358 (20992) covalent geometry : angle 0.74618 (28644) SS BOND : bond 0.00439 ( 40) SS BOND : angle 1.65360 ( 80) hydrogen bonds : bond 0.03291 ( 707) hydrogen bonds : angle 5.49643 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 440 time to evaluate : 0.837 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8802 (t0) cc_final: 0.8160 (t0) REVERT: A 149 GLU cc_start: 0.8989 (mp0) cc_final: 0.8362 (mp0) REVERT: A 164 GLU cc_start: 0.8488 (tp30) cc_final: 0.8046 (tm-30) REVERT: A 204 ASN cc_start: 0.9495 (OUTLIER) cc_final: 0.9151 (t160) REVERT: B 109 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8694 (mm-30) REVERT: B 145 ASP cc_start: 0.8819 (t0) cc_final: 0.8265 (t0) REVERT: B 149 GLU cc_start: 0.8971 (mp0) cc_final: 0.8396 (mp0) REVERT: B 164 GLU cc_start: 0.8363 (tp30) cc_final: 0.7931 (tm-30) REVERT: B 204 ASN cc_start: 0.9499 (OUTLIER) cc_final: 0.9167 (t160) REVERT: C 128 GLU cc_start: 0.9398 (tp30) cc_final: 0.9187 (tp30) REVERT: C 145 ASP cc_start: 0.8785 (t0) cc_final: 0.8268 (t0) REVERT: C 149 GLU cc_start: 0.8982 (mp0) cc_final: 0.8464 (mp0) REVERT: C 164 GLU cc_start: 0.8506 (tp30) cc_final: 0.8065 (tm-30) REVERT: C 204 ASN cc_start: 0.9503 (OUTLIER) cc_final: 0.9163 (t160) REVERT: D 145 ASP cc_start: 0.8773 (t0) cc_final: 0.8198 (t0) REVERT: D 149 GLU cc_start: 0.8975 (mp0) cc_final: 0.8425 (mp0) REVERT: D 164 GLU cc_start: 0.8417 (tp30) cc_final: 0.7936 (tm-30) REVERT: D 204 ASN cc_start: 0.9499 (OUTLIER) cc_final: 0.9156 (t160) REVERT: E 18 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8263 (mmt90) REVERT: E 30 ASN cc_start: 0.9158 (t0) cc_final: 0.8794 (t0) REVERT: E 50 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8991 (mp0) REVERT: E 105 GLU cc_start: 0.8644 (tp30) cc_final: 0.8174 (mp0) REVERT: E 125 LEU cc_start: 0.9562 (pp) cc_final: 0.9209 (mm) REVERT: E 142 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8513 (tpp80) REVERT: E 158 ASN cc_start: 0.9267 (m110) cc_final: 0.8714 (t0) REVERT: E 211 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.6738 (ptm160) REVERT: F 3 GLN cc_start: 0.8911 (pm20) cc_final: 0.8592 (pm20) REVERT: F 6 GLU cc_start: 0.7195 (mp0) cc_final: 0.6248 (mp0) REVERT: F 51 ILE cc_start: 0.9716 (OUTLIER) cc_final: 0.9510 (tp) REVERT: F 72 ASP cc_start: 0.9024 (t0) cc_final: 0.8653 (OUTLIER) REVERT: F 76 ASN cc_start: 0.8916 (t0) cc_final: 0.8586 (t0) REVERT: F 77 GLN cc_start: 0.9003 (tt0) cc_final: 0.8654 (tp40) REVERT: F 79 SER cc_start: 0.9183 (m) cc_final: 0.8828 (t) REVERT: F 105 GLN cc_start: 0.7998 (pm20) cc_final: 0.7404 (pm20) REVERT: F 152 GLU cc_start: 0.9033 (pm20) cc_final: 0.8641 (pm20) REVERT: F 170 PHE cc_start: 0.8684 (m-80) cc_final: 0.8455 (m-80) REVERT: F 195 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7725 (p) REVERT: G 18 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8247 (mmt90) REVERT: G 30 ASN cc_start: 0.9179 (t0) cc_final: 0.8831 (t0) REVERT: G 50 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8974 (mp0) REVERT: G 125 LEU cc_start: 0.9560 (pp) cc_final: 0.9213 (mm) REVERT: G 142 ARG cc_start: 0.8904 (ttm110) cc_final: 0.8583 (ttm-80) REVERT: G 158 ASN cc_start: 0.9268 (m110) cc_final: 0.8721 (t0) REVERT: H 3 GLN cc_start: 0.8876 (pm20) cc_final: 0.7723 (pm20) REVERT: H 6 GLU cc_start: 0.7771 (mp0) cc_final: 0.6648 (mp0) REVERT: H 26 ARG cc_start: 0.8990 (ttm110) cc_final: 0.8523 (mtm-85) REVERT: H 51 ILE cc_start: 0.9724 (OUTLIER) cc_final: 0.9508 (tp) REVERT: H 72 ASP cc_start: 0.9011 (t0) cc_final: 0.8683 (t0) REVERT: H 76 ASN cc_start: 0.8933 (t0) cc_final: 0.8648 (t0) REVERT: H 77 GLN cc_start: 0.8929 (tt0) cc_final: 0.8437 (tp40) REVERT: H 152 GLU cc_start: 0.9038 (pm20) cc_final: 0.8664 (pm20) REVERT: H 195 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7732 (p) REVERT: I 18 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7333 (mmt90) REVERT: I 30 ASN cc_start: 0.9158 (t0) cc_final: 0.8814 (t0) REVERT: I 50 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8996 (mp0) REVERT: I 158 ASN cc_start: 0.9266 (m110) cc_final: 0.8711 (t0) REVERT: I 211 ARG cc_start: 0.7291 (ttp-170) cc_final: 0.6716 (ptm160) REVERT: J 3 GLN cc_start: 0.8530 (pm20) cc_final: 0.8266 (pm20) REVERT: J 6 GLU cc_start: 0.7497 (mp0) cc_final: 0.6960 (pm20) REVERT: J 51 ILE cc_start: 0.9705 (OUTLIER) cc_final: 0.9489 (tp) REVERT: J 76 ASN cc_start: 0.8988 (t0) cc_final: 0.8753 (t0) REVERT: J 105 GLN cc_start: 0.8332 (pm20) cc_final: 0.7824 (pm20) REVERT: J 152 GLU cc_start: 0.9047 (pm20) cc_final: 0.8744 (pm20) REVERT: J 195 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7680 (p) REVERT: J 201 ASN cc_start: 0.9178 (t0) cc_final: 0.8444 (m110) REVERT: K 6 GLU cc_start: 0.7523 (mp0) cc_final: 0.6947 (pm20) REVERT: K 26 ARG cc_start: 0.8855 (mtp-110) cc_final: 0.8353 (ptm160) REVERT: K 51 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9514 (tp) REVERT: K 76 ASN cc_start: 0.9000 (t0) cc_final: 0.8761 (t0) REVERT: K 105 GLN cc_start: 0.8313 (pm20) cc_final: 0.7798 (pm20) REVERT: K 152 GLU cc_start: 0.9020 (pm20) cc_final: 0.8735 (pm20) REVERT: K 195 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (p) REVERT: K 201 ASN cc_start: 0.9182 (t0) cc_final: 0.8460 (m110) REVERT: L 18 ARG cc_start: 0.8270 (ttm110) cc_final: 0.7337 (mmt90) REVERT: L 30 ASN cc_start: 0.9172 (t0) cc_final: 0.8801 (t0) REVERT: L 50 GLU cc_start: 0.9209 (mt-10) cc_final: 0.9005 (mp0) REVERT: L 117 ILE cc_start: 0.9057 (pp) cc_final: 0.8489 (mt) REVERT: L 125 LEU cc_start: 0.9560 (pp) cc_final: 0.9215 (mm) REVERT: L 137 ASN cc_start: 0.7199 (m-40) cc_final: 0.6968 (m-40) REVERT: L 158 ASN cc_start: 0.9275 (m110) cc_final: 0.8733 (t0) outliers start: 63 outliers final: 46 residues processed: 473 average time/residue: 0.4732 time to fit residues: 259.5955 Evaluate side-chains 483 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 426 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 55 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.100103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.061382 restraints weight = 42129.926| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.37 r_work: 0.2587 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21032 Z= 0.159 Angle : 0.750 10.984 28724 Z= 0.384 Chirality : 0.047 0.185 3220 Planarity : 0.006 0.088 3660 Dihedral : 4.995 28.416 2860 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.88 % Allowed : 24.87 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 2636 helix: 0.13 (0.50), residues: 128 sheet: 0.72 (0.16), residues: 928 loop : -0.22 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 26 TYR 0.030 0.002 TYR L 140 PHE 0.028 0.002 PHE L 139 TRP 0.019 0.001 TRP K 158 HIS 0.005 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00376 (20992) covalent geometry : angle 0.74424 (28644) SS BOND : bond 0.00458 ( 40) SS BOND : angle 1.90127 ( 80) hydrogen bonds : bond 0.03295 ( 707) hydrogen bonds : angle 5.51950 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8159.36 seconds wall clock time: 139 minutes 35.89 seconds (8375.89 seconds total)