Starting phenix.real_space_refine on Thu Jan 23 17:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgi_43201/01_2025/8vgi_43201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgi_43201/01_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_43201/01_2025/8vgi_43201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgi_43201/01_2025/8vgi_43201.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgi_43201/01_2025/8vgi_43201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgi_43201/01_2025/8vgi_43201.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 13.20, per 1000 atoms: 0.64 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: 5.04 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 3.97 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: 8.21 Time building geometry restraints manager: 5.83 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: 0.13 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: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 49.130 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.050 ------------------------------------------------------------------------------- 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 20992 Z= 0.753 Angle : 1.162 8.770 28644 Z= 0.641 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 : 4.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), 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 TRP 0.028 0.005 TRP A 38 HIS 0.023 0.005 HIS C 72 PHE 0.033 0.005 PHE I 118 TYR 0.030 0.005 TYR C 234 ARG 0.019 0.004 ARG K 97 *********************** 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 : 2.529 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: 0.8840 (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: 0.8840 (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: 0.8323 (pm20) REVERT: H 6 GLU cc_start: 0.7243 (mp0) cc_final: 0.6763 (mp0) REVERT: H 76 ASN cc_start: 0.8111 (t0) cc_final: 0.7553 (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: 0.8923 (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: 0.8920 (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: 1.2626 time to fit residues: 999.6727 Evaluate side-chains 465 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 453 time to evaluate : 2.374 ------------------------------------------------------------------------------- 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 222 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 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** F 203 ASN G 147 GLN G 158 ASN H 159 ASN H 203 ASN I 147 GLN I 158 ASN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 203 ASN ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 203 ASN L 158 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.060553 restraints weight = 41966.633| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.40 r_work: 0.2550 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20992 Z= 0.344 Angle : 0.841 9.762 28644 Z= 0.437 Chirality : 0.050 0.195 3220 Planarity : 0.006 0.068 3660 Dihedral : 8.233 118.593 2884 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.71 % Allowed : 15.58 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2636 helix: -1.27 (0.44), residues: 124 sheet: 0.22 (0.16), residues: 848 loop : -0.23 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 215 HIS 0.005 0.001 HIS G 189 PHE 0.023 0.003 PHE F 126 TYR 0.019 0.002 TYR L 29 ARG 0.010 0.001 ARG J 26 *********************** 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 586 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 524 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8993 (t0) cc_final: 0.8563 (t0) REVERT: A 149 GLU cc_start: 0.8658 (mp0) cc_final: 0.8300 (mp0) REVERT: A 150 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8855 (mmt-90) REVERT: A 164 GLU cc_start: 0.8212 (tp30) cc_final: 0.7872 (tm-30) REVERT: B 145 ASP cc_start: 0.9031 (t0) cc_final: 0.8545 (t0) REVERT: B 149 GLU cc_start: 0.8697 (mp0) cc_final: 0.8085 (mp0) REVERT: B 164 GLU cc_start: 0.8235 (tp30) cc_final: 0.7917 (tm-30) REVERT: C 145 ASP cc_start: 0.9038 (t0) cc_final: 0.8514 (t0) REVERT: C 149 GLU cc_start: 0.8675 (mp0) cc_final: 0.8013 (mp0) REVERT: C 164 GLU cc_start: 0.8258 (tp30) cc_final: 0.7959 (tm-30) REVERT: D 145 ASP cc_start: 0.9001 (t0) cc_final: 0.8410 (t0) REVERT: D 149 GLU cc_start: 0.8658 (mp0) cc_final: 0.7926 (mp0) REVERT: D 164 GLU cc_start: 0.8172 (tp30) cc_final: 0.7845 (tm-30) REVERT: E 30 ASN cc_start: 0.9207 (t0) cc_final: 0.8697 (t0) REVERT: E 50 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8745 (mp0) REVERT: E 142 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8058 (ttm-80) REVERT: E 145 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8208 (pptt) REVERT: E 186 TYR cc_start: 0.9217 (t80) cc_final: 0.8961 (t80) REVERT: E 192 TYR cc_start: 0.7498 (m-80) cc_final: 0.7257 (m-80) REVERT: E 210 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8124 (t0) REVERT: E 211 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7350 (ttm-80) REVERT: F 6 GLU cc_start: 0.7165 (mp0) cc_final: 0.6543 (mp0) REVERT: F 51 ILE cc_start: 0.9604 (tt) cc_final: 0.9390 (tp) REVERT: F 72 ASP cc_start: 0.8512 (t0) cc_final: 0.8100 (t0) REVERT: F 75 LYS cc_start: 0.9570 (mttt) cc_final: 0.9251 (mttt) REVERT: F 76 ASN cc_start: 0.8880 (t0) cc_final: 0.8154 (t0) REVERT: F 105 GLN cc_start: 0.7781 (pm20) cc_final: 0.7448 (pm20) REVERT: F 148 ASP cc_start: 0.8361 (p0) cc_final: 0.8106 (p0) REVERT: F 152 GLU cc_start: 0.8722 (pm20) cc_final: 0.8190 (pm20) REVERT: F 170 PHE cc_start: 0.8947 (m-80) cc_final: 0.8370 (m-80) REVERT: F 198 TYR cc_start: 0.6665 (m-80) cc_final: 0.6443 (m-80) REVERT: F 205 LYS cc_start: 0.9648 (tppt) cc_final: 0.9323 (mmmt) REVERT: G 30 ASN cc_start: 0.9225 (t0) cc_final: 0.8719 (t0) REVERT: G 50 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8730 (mp0) REVERT: G 145 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8219 (pptt) REVERT: G 186 TYR cc_start: 0.9223 (t80) cc_final: 0.8968 (t80) REVERT: G 192 TYR cc_start: 0.7496 (m-80) cc_final: 0.7247 (m-80) REVERT: G 210 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8123 (t0) REVERT: G 211 ARG cc_start: 0.7649 (ttp80) cc_final: 0.7438 (ttm-80) REVERT: H 6 GLU cc_start: 0.7176 (mp0) cc_final: 0.6507 (mp0) REVERT: H 51 ILE cc_start: 0.9624 (tt) cc_final: 0.9410 (tp) REVERT: H 72 ASP cc_start: 0.8503 (t0) cc_final: 0.8072 (t0) REVERT: H 75 LYS cc_start: 0.9568 (mttt) cc_final: 0.9244 (mttt) REVERT: H 76 ASN cc_start: 0.8872 (t0) cc_final: 0.8161 (t0) REVERT: H 105 GLN cc_start: 0.7859 (pm20) cc_final: 0.7417 (pm20) REVERT: H 148 ASP cc_start: 0.8355 (p0) cc_final: 0.8081 (p0) REVERT: H 152 GLU cc_start: 0.8718 (pm20) cc_final: 0.8189 (pm20) REVERT: H 170 PHE cc_start: 0.8974 (m-80) cc_final: 0.8327 (m-80) REVERT: H 198 TYR cc_start: 0.6663 (m-80) cc_final: 0.6437 (m-80) REVERT: H 205 LYS cc_start: 0.9648 (tppt) cc_final: 0.9323 (mmmt) REVERT: I 30 ASN cc_start: 0.9210 (t0) cc_final: 0.8712 (t0) REVERT: I 50 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8695 (mp0) REVERT: I 53 ILE cc_start: 0.8827 (mp) cc_final: 0.8574 (mp) REVERT: I 210 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8135 (t0) REVERT: J 6 GLU cc_start: 0.7072 (mp0) cc_final: 0.6552 (mp0) REVERT: J 51 ILE cc_start: 0.9611 (tt) cc_final: 0.9395 (tp) REVERT: J 72 ASP cc_start: 0.8520 (t0) cc_final: 0.7736 (t0) REVERT: J 75 LYS cc_start: 0.9555 (mttt) cc_final: 0.9334 (mttt) REVERT: J 76 ASN cc_start: 0.8915 (t0) cc_final: 0.8218 (t0) REVERT: J 105 GLN cc_start: 0.7816 (pm20) cc_final: 0.7408 (pm20) REVERT: J 148 ASP cc_start: 0.8342 (p0) cc_final: 0.8076 (p0) REVERT: J 152 GLU cc_start: 0.8800 (pm20) cc_final: 0.8344 (pm20) REVERT: J 170 PHE cc_start: 0.9140 (m-80) cc_final: 0.8592 (m-80) REVERT: J 203 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8060 (t0) REVERT: J 205 LYS cc_start: 0.9673 (tppt) cc_final: 0.9318 (mmmt) REVERT: J 210 LYS cc_start: 0.9027 (mptt) cc_final: 0.8600 (tptp) REVERT: K 6 GLU cc_start: 0.7072 (mp0) cc_final: 0.6554 (mp0) REVERT: K 51 ILE cc_start: 0.9621 (tt) cc_final: 0.9408 (tp) REVERT: K 72 ASP cc_start: 0.8500 (t0) cc_final: 0.7690 (t0) REVERT: K 75 LYS cc_start: 0.9554 (mttt) cc_final: 0.9330 (mttt) REVERT: K 76 ASN cc_start: 0.8905 (t0) cc_final: 0.8210 (t0) REVERT: K 105 GLN cc_start: 0.7795 (pm20) cc_final: 0.7389 (pm20) REVERT: K 148 ASP cc_start: 0.8335 (p0) cc_final: 0.7837 (p0) REVERT: K 152 GLU cc_start: 0.8788 (pm20) cc_final: 0.8337 (pm20) REVERT: K 170 PHE cc_start: 0.8978 (m-80) cc_final: 0.8497 (m-80) REVERT: K 203 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8056 (t0) REVERT: K 205 LYS cc_start: 0.9673 (tppt) cc_final: 0.9316 (mmmt) REVERT: K 210 LYS cc_start: 0.9036 (mptt) cc_final: 0.8599 (tptp) REVERT: L 30 ASN cc_start: 0.9212 (t0) cc_final: 0.8709 (t0) REVERT: L 50 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8711 (mp0) REVERT: L 53 ILE cc_start: 0.8820 (mp) cc_final: 0.8567 (mp) REVERT: L 210 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8144 (t0) outliers start: 62 outliers final: 27 residues processed: 546 average time/residue: 1.2515 time to fit residues: 785.4932 Evaluate side-chains 447 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 411 time to evaluate : 2.583 ------------------------------------------------------------------------------- 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 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 122 ASP 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 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 203 ASN Chi-restraints excluded: chain J residue 208 ASN Chi-restraints excluded: chain K residue 203 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 64 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 238 optimal weight: 30.0000 chunk 183 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** D 221AGLN 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 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 147 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.059824 restraints weight = 41566.070| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.43 r_work: 0.2537 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20992 Z= 0.337 Angle : 0.767 7.439 28644 Z= 0.396 Chirality : 0.048 0.155 3220 Planarity : 0.006 0.065 3660 Dihedral : 5.796 21.699 2860 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.18 % Allowed : 17.50 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2636 helix: -1.14 (0.44), residues: 148 sheet: 0.60 (0.17), residues: 800 loop : -0.09 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 215 HIS 0.003 0.001 HIS G 189 PHE 0.024 0.002 PHE L 139 TYR 0.022 0.002 TYR I 140 ARG 0.013 0.001 ARG L 142 *********************** 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 514 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 441 time to evaluate : 2.652 Fit side-chains REVERT: A 20 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: A 145 ASP cc_start: 0.8959 (t0) cc_final: 0.8343 (t0) REVERT: A 149 GLU cc_start: 0.8732 (mp0) cc_final: 0.8220 (mp0) REVERT: A 164 GLU cc_start: 0.8289 (tp30) cc_final: 0.7903 (tm-30) REVERT: B 145 ASP cc_start: 0.8980 (t0) cc_final: 0.8443 (t0) REVERT: B 149 GLU cc_start: 0.8846 (mp0) cc_final: 0.8312 (mp0) REVERT: B 164 GLU cc_start: 0.8276 (tp30) cc_final: 0.7919 (tm-30) REVERT: C 145 ASP cc_start: 0.8973 (t0) cc_final: 0.8306 (t0) REVERT: C 149 GLU cc_start: 0.8796 (mp0) cc_final: 0.8041 (mp0) REVERT: C 164 GLU cc_start: 0.8323 (tp30) cc_final: 0.7991 (tm-30) REVERT: D 20 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: D 145 ASP cc_start: 0.8931 (t0) cc_final: 0.8373 (t0) REVERT: D 149 GLU cc_start: 0.8812 (mp0) cc_final: 0.8231 (mp0) REVERT: D 164 GLU cc_start: 0.8260 (tp30) cc_final: 0.7926 (tm-30) REVERT: E 18 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8061 (mmt90) REVERT: E 30 ASN cc_start: 0.9195 (t0) cc_final: 0.8656 (t0) REVERT: E 50 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8802 (mp0) REVERT: E 117 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7092 (mp) REVERT: E 142 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: E 148 TRP cc_start: 0.8251 (m100) cc_final: 0.7168 (m100) REVERT: E 158 ASN cc_start: 0.9253 (m110) cc_final: 0.8785 (t0) REVERT: E 210 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8179 (t0) REVERT: F 3 GLN cc_start: 0.8883 (pm20) cc_final: 0.8555 (pm20) REVERT: F 6 GLU cc_start: 0.7138 (mp0) cc_final: 0.6376 (mp0) REVERT: F 51 ILE cc_start: 0.9642 (tt) cc_final: 0.9401 (tp) REVERT: F 72 ASP cc_start: 0.8799 (t0) cc_final: 0.8307 (t0) REVERT: F 76 ASN cc_start: 0.8954 (t0) cc_final: 0.8259 (t0) REVERT: F 105 GLN cc_start: 0.7885 (pm20) cc_final: 0.7293 (pm20) REVERT: F 152 GLU cc_start: 0.8839 (pm20) cc_final: 0.8481 (pm20) REVERT: F 170 PHE cc_start: 0.8839 (m-80) cc_final: 0.8169 (m-80) REVERT: G 18 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.8071 (mmt90) REVERT: G 30 ASN cc_start: 0.9197 (t0) cc_final: 0.8661 (t0) REVERT: G 50 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8777 (mp0) REVERT: G 117 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7105 (mp) REVERT: G 148 TRP cc_start: 0.8209 (m100) cc_final: 0.7171 (m100) REVERT: G 158 ASN cc_start: 0.9256 (m110) cc_final: 0.8788 (t0) REVERT: G 210 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8182 (t0) REVERT: H 3 GLN cc_start: 0.8880 (pm20) cc_final: 0.8551 (pm20) REVERT: H 6 GLU cc_start: 0.7242 (mp0) cc_final: 0.6379 (mp0) REVERT: H 51 ILE cc_start: 0.9657 (tt) cc_final: 0.9410 (tp) REVERT: H 72 ASP cc_start: 0.8831 (t0) cc_final: 0.8346 (t0) REVERT: H 76 ASN cc_start: 0.8945 (t0) cc_final: 0.8261 (t0) REVERT: H 105 GLN cc_start: 0.7792 (pm20) cc_final: 0.7286 (pm20) REVERT: H 148 ASP cc_start: 0.8384 (p0) cc_final: 0.8183 (p0) REVERT: H 152 GLU cc_start: 0.8824 (pm20) cc_final: 0.8338 (pm20) REVERT: H 170 PHE cc_start: 0.9015 (m-80) cc_final: 0.8407 (m-80) REVERT: H 180 TYR cc_start: 0.9206 (m-80) cc_final: 0.8953 (m-10) REVERT: I 18 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7081 (mmt90) REVERT: I 30 ASN cc_start: 0.9213 (t0) cc_final: 0.8721 (t0) REVERT: I 50 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8727 (mp0) REVERT: I 53 ILE cc_start: 0.8884 (mp) cc_final: 0.8572 (mp) REVERT: I 117 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7306 (mp) REVERT: I 142 ARG cc_start: 0.9047 (ttm-80) cc_final: 0.8628 (ttm-80) REVERT: I 148 TRP cc_start: 0.8197 (m100) cc_final: 0.7100 (m100) REVERT: I 158 ASN cc_start: 0.9256 (m110) cc_final: 0.8781 (t0) REVERT: I 210 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8243 (t0) REVERT: J 6 GLU cc_start: 0.6956 (mp0) cc_final: 0.6420 (mp0) REVERT: J 51 ILE cc_start: 0.9635 (tt) cc_final: 0.9394 (tp) REVERT: J 72 ASP cc_start: 0.8637 (t0) cc_final: 0.8072 (t0) REVERT: J 76 ASN cc_start: 0.8986 (t0) cc_final: 0.8274 (t0) REVERT: J 105 GLN cc_start: 0.7873 (pm20) cc_final: 0.7228 (pm20) REVERT: J 152 GLU cc_start: 0.8945 (pm20) cc_final: 0.8615 (pm20) REVERT: J 159 ASN cc_start: 0.8952 (m110) cc_final: 0.8720 (m110) REVERT: J 170 PHE cc_start: 0.9157 (m-80) cc_final: 0.8591 (m-80) REVERT: K 6 GLU cc_start: 0.7023 (mp0) cc_final: 0.6433 (mp0) REVERT: K 51 ILE cc_start: 0.9649 (tt) cc_final: 0.9405 (tp) REVERT: K 72 ASP cc_start: 0.8633 (t0) cc_final: 0.8071 (t0) REVERT: K 76 ASN cc_start: 0.8978 (t0) cc_final: 0.8266 (t0) REVERT: K 105 GLN cc_start: 0.7872 (pm20) cc_final: 0.7262 (pm20) REVERT: K 152 GLU cc_start: 0.8926 (pm20) cc_final: 0.8456 (pm20) REVERT: K 159 ASN cc_start: 0.8946 (m110) cc_final: 0.8713 (m110) REVERT: K 170 PHE cc_start: 0.9158 (m-80) cc_final: 0.8630 (m-80) REVERT: K 180 TYR cc_start: 0.9276 (m-80) cc_final: 0.8930 (m-10) REVERT: L 18 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7093 (mmt90) REVERT: L 30 ASN cc_start: 0.9204 (t0) cc_final: 0.8707 (t0) REVERT: L 50 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8730 (mp0) REVERT: L 53 ILE cc_start: 0.8896 (mp) cc_final: 0.8586 (mp) REVERT: L 117 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7316 (mp) REVERT: L 142 ARG cc_start: 0.8901 (ttm-80) cc_final: 0.8439 (tpp80) REVERT: L 148 TRP cc_start: 0.8187 (m100) cc_final: 0.7086 (m100) REVERT: L 158 ASN cc_start: 0.9258 (m110) cc_final: 0.8782 (t0) REVERT: L 210 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8241 (t0) outliers start: 73 outliers final: 24 residues processed: 467 average time/residue: 1.0958 time to fit residues: 593.1212 Evaluate side-chains 433 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 399 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A 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 117 ILE 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 G residue 23 CYS Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 117 ILE 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 I residue 23 CYS Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 117 ILE 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 144 CYS 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 109 THR Chi-restraints excluded: chain L residue 117 ILE 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 221 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 245 optimal weight: 0.0170 chunk 161 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 83 optimal weight: 0.3980 chunk 169 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN B 221AGLN ** 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 K 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.101475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.062111 restraints weight = 41887.603| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.46 r_work: 0.2588 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 0.040 20992 Z= 0.187 Angle : 0.716 8.148 28644 Z= 0.364 Chirality : 0.047 0.170 3220 Planarity : 0.006 0.064 3660 Dihedral : 5.405 20.292 2860 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 18.72 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2636 helix: -0.25 (0.50), residues: 124 sheet: 0.73 (0.16), residues: 816 loop : -0.18 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 215 HIS 0.003 0.001 HIS B 57 PHE 0.024 0.002 PHE I 139 TYR 0.024 0.002 TYR I 140 ARG 0.006 0.001 ARG I 211 *********************** 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 553 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 496 time to evaluate : 2.486 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: 0.8800 (t0) cc_final: 0.8246 (t0) REVERT: A 149 GLU cc_start: 0.8885 (mp0) cc_final: 0.8360 (mp0) REVERT: A 164 GLU cc_start: 0.8269 (tp30) cc_final: 0.7884 (tm-30) REVERT: A 204 ASN cc_start: 0.9484 (OUTLIER) cc_final: 0.9199 (t160) REVERT: B 109 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8568 (mm-30) REVERT: B 128 GLU cc_start: 0.9436 (tp30) cc_final: 0.9103 (tp30) REVERT: B 145 ASP cc_start: 0.8784 (t0) cc_final: 0.8358 (t0) REVERT: B 149 GLU cc_start: 0.8933 (mp0) cc_final: 0.8668 (mm-30) REVERT: B 164 GLU cc_start: 0.8263 (tp30) cc_final: 0.7869 (tm-30) REVERT: B 204 ASN cc_start: 0.9488 (OUTLIER) cc_final: 0.9208 (t160) REVERT: C 145 ASP cc_start: 0.8790 (t0) cc_final: 0.8370 (t0) REVERT: C 149 GLU cc_start: 0.8898 (mp0) cc_final: 0.8599 (mm-30) REVERT: C 164 GLU cc_start: 0.8309 (tp30) cc_final: 0.7949 (tm-30) REVERT: C 204 ASN cc_start: 0.9481 (OUTLIER) cc_final: 0.9186 (t160) REVERT: D 20 GLN cc_start: 0.8723 (pm20) cc_final: 0.8509 (pm20) REVERT: D 145 ASP cc_start: 0.8727 (t0) cc_final: 0.8105 (t0) REVERT: D 149 GLU cc_start: 0.8893 (mp0) cc_final: 0.8248 (mp0) REVERT: D 164 GLU cc_start: 0.8191 (tp30) cc_final: 0.7877 (tp30) REVERT: D 204 ASN cc_start: 0.9495 (OUTLIER) cc_final: 0.9211 (t160) REVERT: E 18 ARG cc_start: 0.8456 (mmm-85) cc_final: 0.8184 (mmt90) REVERT: E 30 ASN cc_start: 0.9180 (t0) cc_final: 0.8734 (t0) REVERT: E 50 GLU cc_start: 0.9260 (mt-10) cc_final: 0.9030 (mp0) REVERT: E 142 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.8194 (ttm-80) REVERT: E 148 TRP cc_start: 0.8184 (m100) cc_final: 0.7189 (m100) REVERT: E 158 ASN cc_start: 0.9237 (m110) cc_final: 0.8609 (t0) REVERT: E 161 GLU cc_start: 0.8794 (mp0) cc_final: 0.8555 (mp0) REVERT: E 210 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8236 (t0) REVERT: F 3 GLN cc_start: 0.8908 (pm20) cc_final: 0.8679 (pm20) REVERT: F 6 GLU cc_start: 0.7131 (mp0) cc_final: 0.6287 (mp0) REVERT: F 51 ILE cc_start: 0.9646 (tt) cc_final: 0.9404 (tp) REVERT: F 72 ASP cc_start: 0.8847 (t0) cc_final: 0.8410 (t0) REVERT: F 76 ASN cc_start: 0.8881 (t0) cc_final: 0.8295 (t0) REVERT: F 105 GLN cc_start: 0.7872 (pm20) cc_final: 0.7266 (pm20) REVERT: F 152 GLU cc_start: 0.8808 (pm20) cc_final: 0.8570 (pm20) REVERT: F 170 PHE cc_start: 0.8861 (m-80) cc_final: 0.8225 (m-80) REVERT: G 18 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8178 (mmt90) REVERT: G 30 ASN cc_start: 0.9174 (t0) cc_final: 0.8730 (t0) REVERT: G 50 GLU cc_start: 0.9237 (mt-10) cc_final: 0.9006 (mp0) REVERT: G 108 ARG cc_start: 0.6545 (ttp-110) cc_final: 0.6095 (tmm-80) REVERT: G 142 ARG cc_start: 0.9068 (ttm-80) cc_final: 0.8355 (ttm-80) REVERT: G 148 TRP cc_start: 0.8145 (m100) cc_final: 0.7196 (m100) REVERT: G 158 ASN cc_start: 0.9243 (m110) cc_final: 0.8618 (t0) REVERT: G 161 GLU cc_start: 0.8824 (mp0) cc_final: 0.8605 (mp0) REVERT: G 210 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8247 (t0) REVERT: H 3 GLN cc_start: 0.8909 (pm20) cc_final: 0.8462 (pm20) REVERT: H 6 GLU cc_start: 0.7236 (mp0) cc_final: 0.6216 (mp0) REVERT: H 51 ILE cc_start: 0.9656 (tt) cc_final: 0.9411 (tp) REVERT: H 72 ASP cc_start: 0.8844 (t0) cc_final: 0.8397 (t0) REVERT: H 76 ASN cc_start: 0.8875 (t0) cc_final: 0.8294 (t0) REVERT: H 105 GLN cc_start: 0.7785 (pm20) cc_final: 0.7240 (pm20) REVERT: H 148 ASP cc_start: 0.8281 (p0) cc_final: 0.8063 (p0) REVERT: H 152 GLU cc_start: 0.8759 (pm20) cc_final: 0.8332 (pm20) REVERT: H 170 PHE cc_start: 0.9028 (m-80) cc_final: 0.8321 (m-80) REVERT: I 18 ARG cc_start: 0.8008 (ttm110) cc_final: 0.6985 (mmt90) REVERT: I 30 ASN cc_start: 0.9192 (t0) cc_final: 0.8757 (t0) REVERT: I 33 LEU cc_start: 0.9539 (tt) cc_final: 0.9311 (tm) REVERT: I 50 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9013 (mp0) REVERT: I 142 ARG cc_start: 0.8960 (ttm-80) cc_final: 0.8264 (tpp80) REVERT: I 148 TRP cc_start: 0.8167 (m100) cc_final: 0.7218 (m100) REVERT: I 158 ASN cc_start: 0.9232 (m110) cc_final: 0.8629 (t0) REVERT: I 161 GLU cc_start: 0.8805 (mp0) cc_final: 0.8562 (mp0) REVERT: I 210 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8391 (t0) REVERT: J 6 GLU cc_start: 0.6923 (mp0) cc_final: 0.6302 (mp0) REVERT: J 51 ILE cc_start: 0.9638 (tt) cc_final: 0.9418 (tp) REVERT: J 72 ASP cc_start: 0.8667 (t0) cc_final: 0.8062 (t0) REVERT: J 76 ASN cc_start: 0.8927 (t0) cc_final: 0.8331 (t0) REVERT: J 105 GLN cc_start: 0.7925 (pm20) cc_final: 0.7346 (pm20) REVERT: J 152 GLU cc_start: 0.8855 (pm20) cc_final: 0.8591 (pm20) REVERT: J 170 PHE cc_start: 0.9146 (m-80) cc_final: 0.8616 (m-80) REVERT: J 175 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8525 (mm-40) REVERT: J 201 ASN cc_start: 0.8813 (t0) cc_final: 0.8019 (m110) REVERT: K 6 GLU cc_start: 0.6998 (mp0) cc_final: 0.6356 (mp0) REVERT: K 51 ILE cc_start: 0.9655 (tt) cc_final: 0.9438 (tp) REVERT: K 72 ASP cc_start: 0.8668 (t0) cc_final: 0.8056 (t0) REVERT: K 76 ASN cc_start: 0.8926 (t0) cc_final: 0.8332 (t0) REVERT: K 105 GLN cc_start: 0.7916 (pm20) cc_final: 0.7329 (pm20) REVERT: K 152 GLU cc_start: 0.8835 (pm20) cc_final: 0.8369 (pm20) REVERT: K 170 PHE cc_start: 0.9174 (m-80) cc_final: 0.8618 (m-80) REVERT: K 201 ASN cc_start: 0.8845 (t0) cc_final: 0.8044 (m110) REVERT: L 18 ARG cc_start: 0.8006 (ttm110) cc_final: 0.6979 (mmt90) REVERT: L 30 ASN cc_start: 0.9187 (t0) cc_final: 0.8745 (t0) REVERT: L 50 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9007 (mp0) REVERT: L 148 TRP cc_start: 0.8167 (m100) cc_final: 0.7139 (m100) REVERT: L 158 ASN cc_start: 0.9232 (m110) cc_final: 0.8632 (t0) REVERT: L 161 GLU cc_start: 0.8806 (mp0) cc_final: 0.8577 (mp0) REVERT: L 210 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8399 (t0) outliers start: 57 outliers final: 27 residues processed: 522 average time/residue: 1.0643 time to fit residues: 646.0851 Evaluate side-chains 481 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 446 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 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 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 I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS 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 232 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 259 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 chunk 193 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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** ** 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 = 0.3551 r_free = 0.3551 target = 0.101805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062471 restraints weight = 41820.040| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.46 r_work: 0.2600 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20992 Z= 0.183 Angle : 0.684 8.558 28644 Z= 0.348 Chirality : 0.046 0.162 3220 Planarity : 0.005 0.064 3660 Dihedral : 5.094 19.150 2860 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.01 % Allowed : 20.38 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2636 helix: -0.14 (0.50), residues: 124 sheet: 0.87 (0.16), residues: 828 loop : -0.17 (0.16), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 137 HIS 0.005 0.001 HIS B 166 PHE 0.022 0.002 PHE E 139 TYR 0.025 0.002 TYR L 140 ARG 0.009 0.001 ARG E 211 *********************** 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 557 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 488 time to evaluate : 2.296 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: A 149 GLU cc_start: 0.8950 (mp0) cc_final: 0.8673 (mp0) REVERT: A 164 GLU cc_start: 0.8291 (tp30) cc_final: 0.7909 (tm-30) REVERT: A 189 ASP cc_start: 0.8989 (t0) cc_final: 0.8697 (t0) REVERT: A 204 ASN cc_start: 0.9492 (OUTLIER) cc_final: 0.9182 (t160) REVERT: B 109 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8583 (mm-30) REVERT: B 145 ASP cc_start: 0.8725 (t0) cc_final: 0.8307 (t0) REVERT: B 149 GLU cc_start: 0.8947 (mp0) cc_final: 0.8665 (mm-30) REVERT: B 164 GLU cc_start: 0.8240 (tp30) cc_final: 0.7874 (tm-30) REVERT: B 204 ASN cc_start: 0.9482 (OUTLIER) cc_final: 0.9181 (t160) REVERT: C 128 GLU cc_start: 0.9415 (tp30) cc_final: 0.9006 (tp30) REVERT: C 145 ASP cc_start: 0.8734 (t0) cc_final: 0.8313 (t0) REVERT: C 149 GLU cc_start: 0.8947 (mp0) cc_final: 0.8633 (mm-30) REVERT: C 164 GLU cc_start: 0.8275 (tp30) cc_final: 0.7846 (tm-30) REVERT: C 204 ASN cc_start: 0.9493 (OUTLIER) cc_final: 0.9175 (t160) REVERT: D 70 GLU cc_start: 0.8657 (pt0) cc_final: 0.8405 (pp20) REVERT: D 145 ASP cc_start: 0.8687 (t0) cc_final: 0.8223 (t0) REVERT: D 149 GLU cc_start: 0.8933 (mp0) cc_final: 0.8531 (mm-30) REVERT: D 164 GLU cc_start: 0.8233 (tp30) cc_final: 0.7902 (tm-30) REVERT: D 204 ASN cc_start: 0.9498 (OUTLIER) cc_final: 0.9192 (t160) REVERT: D 228 TYR cc_start: 0.9580 (m-80) cc_final: 0.9378 (m-80) REVERT: E 18 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8148 (mmt90) REVERT: E 30 ASN cc_start: 0.9172 (t0) cc_final: 0.8777 (t0) REVERT: E 50 GLU cc_start: 0.9250 (mt-10) cc_final: 0.9035 (mp0) REVERT: E 108 ARG cc_start: 0.6663 (ttp-110) cc_final: 0.6039 (ttp-110) REVERT: E 109 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7482 (t) REVERT: E 140 TYR cc_start: 0.8450 (t80) cc_final: 0.7745 (t80) REVERT: E 148 TRP cc_start: 0.8131 (m100) cc_final: 0.7113 (m100) REVERT: E 158 ASN cc_start: 0.9240 (m110) cc_final: 0.8618 (t0) REVERT: E 211 ARG cc_start: 0.7767 (ttp-170) cc_final: 0.7098 (ptm160) REVERT: F 3 GLN cc_start: 0.8926 (pm20) cc_final: 0.8381 (pm20) REVERT: F 6 GLU cc_start: 0.7132 (mp0) cc_final: 0.6214 (mp0) REVERT: F 51 ILE cc_start: 0.9663 (tt) cc_final: 0.9439 (tp) REVERT: F 72 ASP cc_start: 0.8854 (t0) cc_final: 0.8426 (t0) REVERT: F 76 ASN cc_start: 0.8865 (t0) cc_final: 0.8330 (t0) REVERT: F 105 GLN cc_start: 0.7837 (pm20) cc_final: 0.7215 (pm20) REVERT: F 170 PHE cc_start: 0.8846 (m-80) cc_final: 0.8250 (m-80) REVERT: G 18 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8118 (mmt90) REVERT: G 30 ASN cc_start: 0.9167 (t0) cc_final: 0.8777 (t0) REVERT: G 50 GLU cc_start: 0.9248 (mt-10) cc_final: 0.9032 (mp0) REVERT: G 125 LEU cc_start: 0.9524 (pp) cc_final: 0.9261 (mm) REVERT: G 142 ARG cc_start: 0.9008 (ttm-80) cc_final: 0.8652 (tpp80) REVERT: G 148 TRP cc_start: 0.8096 (m100) cc_final: 0.7118 (m100) REVERT: G 158 ASN cc_start: 0.9252 (m110) cc_final: 0.8643 (t0) REVERT: G 211 ARG cc_start: 0.7795 (ttp-170) cc_final: 0.7167 (ptm160) REVERT: H 3 GLN cc_start: 0.8926 (pm20) cc_final: 0.8387 (pm20) REVERT: H 35 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9263 (t) REVERT: H 51 ILE cc_start: 0.9667 (tt) cc_final: 0.9442 (tp) REVERT: H 72 ASP cc_start: 0.8890 (t0) cc_final: 0.8453 (t0) REVERT: H 76 ASN cc_start: 0.8876 (t0) cc_final: 0.8335 (t0) REVERT: H 152 GLU cc_start: 0.8904 (pm20) cc_final: 0.8593 (pm20) REVERT: H 170 PHE cc_start: 0.9036 (m-80) cc_final: 0.8341 (m-80) REVERT: I 30 ASN cc_start: 0.9181 (t0) cc_final: 0.8801 (t0) REVERT: I 50 GLU cc_start: 0.9260 (mt-10) cc_final: 0.9009 (mp0) REVERT: I 125 LEU cc_start: 0.9525 (pp) cc_final: 0.9258 (mm) REVERT: I 148 TRP cc_start: 0.8104 (m100) cc_final: 0.7163 (m100) REVERT: I 158 ASN cc_start: 0.9229 (m110) cc_final: 0.8541 (t0) REVERT: I 210 ASN cc_start: 0.8660 (p0) cc_final: 0.8458 (t0) REVERT: J 6 GLU cc_start: 0.6916 (mp0) cc_final: 0.6265 (mp0) REVERT: J 27 PHE cc_start: 0.8374 (m-80) cc_final: 0.6597 (m-80) REVERT: J 51 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9426 (tp) REVERT: J 72 ASP cc_start: 0.8682 (t0) cc_final: 0.8117 (t0) REVERT: J 76 ASN cc_start: 0.8904 (t0) cc_final: 0.8399 (t0) REVERT: J 105 GLN cc_start: 0.7874 (pm20) cc_final: 0.7262 (pm20) REVERT: J 170 PHE cc_start: 0.9119 (m-80) cc_final: 0.8603 (m-80) REVERT: J 201 ASN cc_start: 0.9017 (t0) cc_final: 0.8261 (m110) REVERT: K 27 PHE cc_start: 0.8384 (m-80) cc_final: 0.6620 (m-80) REVERT: K 51 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9439 (tp) REVERT: K 72 ASP cc_start: 0.8682 (t0) cc_final: 0.8122 (t0) REVERT: K 76 ASN cc_start: 0.8897 (t0) cc_final: 0.8393 (t0) REVERT: K 152 GLU cc_start: 0.8934 (pm20) cc_final: 0.8575 (pm20) REVERT: K 170 PHE cc_start: 0.9154 (m-80) cc_final: 0.8595 (m-80) REVERT: K 175 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8643 (mm-40) REVERT: K 201 ASN cc_start: 0.9022 (t0) cc_final: 0.8259 (m110) REVERT: L 18 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7208 (mmt90) REVERT: L 30 ASN cc_start: 0.9178 (t0) cc_final: 0.8790 (t0) REVERT: L 50 GLU cc_start: 0.9259 (mt-10) cc_final: 0.9010 (mp0) REVERT: L 125 LEU cc_start: 0.9526 (pp) cc_final: 0.9262 (mm) REVERT: L 148 TRP cc_start: 0.8132 (m100) cc_final: 0.7123 (m100) REVERT: L 158 ASN cc_start: 0.9241 (m110) cc_final: 0.8567 (t0) outliers start: 69 outliers final: 25 residues processed: 522 average time/residue: 1.0820 time to fit residues: 654.4918 Evaluate side-chains 485 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 452 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 190 SER 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 75 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain F residue 110 THR 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 H residue 35 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 75 ILE 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 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 L residue 23 CYS Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.099009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.059622 restraints weight = 42062.116| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 3.39 r_work: 0.2537 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20992 Z= 0.371 Angle : 0.732 8.546 28644 Z= 0.380 Chirality : 0.048 0.281 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.207 18.171 2860 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.49 % Allowed : 21.55 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2636 helix: -0.19 (0.49), residues: 128 sheet: 0.64 (0.16), residues: 872 loop : -0.10 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 141 HIS 0.004 0.001 HIS B 72 PHE 0.022 0.002 PHE I 139 TYR 0.026 0.002 TYR A 75 ARG 0.015 0.001 ARG E 142 *********************** 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 534 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 454 time to evaluate : 2.480 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: 0.8804 (t0) cc_final: 0.8329 (t0) REVERT: A 149 GLU cc_start: 0.8955 (mp0) cc_final: 0.8550 (mp0) REVERT: A 164 GLU cc_start: 0.8448 (tp30) cc_final: 0.8012 (tm-30) REVERT: B 145 ASP cc_start: 0.8792 (t0) cc_final: 0.8264 (t0) REVERT: B 149 GLU cc_start: 0.8953 (mp0) cc_final: 0.8377 (mp0) REVERT: B 164 GLU cc_start: 0.8411 (tp30) cc_final: 0.7991 (tm-30) REVERT: B 204 ASN cc_start: 0.9497 (OUTLIER) cc_final: 0.9205 (t160) REVERT: C 128 GLU cc_start: 0.9408 (tp30) cc_final: 0.9026 (tp30) REVERT: C 145 ASP cc_start: 0.8781 (t0) cc_final: 0.8264 (t0) REVERT: C 149 GLU cc_start: 0.8930 (mp0) cc_final: 0.8363 (mp0) REVERT: C 164 GLU cc_start: 0.8484 (tp30) cc_final: 0.8004 (tm-30) REVERT: C 171 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8971 (mttt) REVERT: D 145 ASP cc_start: 0.8769 (t0) cc_final: 0.8230 (t0) REVERT: D 149 GLU cc_start: 0.8946 (mp0) cc_final: 0.8390 (mp0) REVERT: D 164 GLU cc_start: 0.8363 (tp30) cc_final: 0.7910 (tm-30) REVERT: D 189 ASP cc_start: 0.8909 (t0) cc_final: 0.8686 (t0) REVERT: D 204 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.9210 (t160) REVERT: E 18 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8185 (mmt90) REVERT: E 30 ASN cc_start: 0.9208 (t0) cc_final: 0.8760 (t0) REVERT: E 50 GLU cc_start: 0.9273 (mt-10) cc_final: 0.9028 (mp0) REVERT: E 108 ARG cc_start: 0.6684 (ttp-110) cc_final: 0.6414 (tmm-80) REVERT: E 148 TRP cc_start: 0.8172 (m100) cc_final: 0.7213 (m100) REVERT: E 158 ASN cc_start: 0.9222 (m110) cc_final: 0.8598 (t0) REVERT: E 161 GLU cc_start: 0.8690 (mp0) cc_final: 0.8405 (mp0) REVERT: F 3 GLN cc_start: 0.8994 (pm20) cc_final: 0.8456 (pm20) REVERT: F 6 GLU cc_start: 0.7127 (mp0) cc_final: 0.6178 (mp0) REVERT: F 51 ILE cc_start: 0.9700 (OUTLIER) cc_final: 0.9433 (tp) REVERT: F 72 ASP cc_start: 0.8910 (t0) cc_final: 0.8487 (t0) REVERT: F 76 ASN cc_start: 0.8990 (t0) cc_final: 0.8483 (t0) REVERT: F 105 GLN cc_start: 0.7845 (pm20) cc_final: 0.7175 (pm20) REVERT: F 170 PHE cc_start: 0.8877 (m-80) cc_final: 0.8398 (m-80) REVERT: G 18 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8187 (mmt90) REVERT: G 30 ASN cc_start: 0.9213 (t0) cc_final: 0.8770 (t0) REVERT: G 50 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9029 (mp0) REVERT: G 142 ARG cc_start: 0.8947 (ttm-80) cc_final: 0.8152 (ttm-80) REVERT: G 148 TRP cc_start: 0.8092 (m100) cc_final: 0.7179 (m100) REVERT: G 158 ASN cc_start: 0.9230 (m110) cc_final: 0.8602 (t0) REVERT: G 161 GLU cc_start: 0.8812 (mp0) cc_final: 0.8582 (mp0) REVERT: H 3 GLN cc_start: 0.8984 (pm20) cc_final: 0.8446 (pm20) REVERT: H 6 GLU cc_start: 0.7529 (mp0) cc_final: 0.6518 (pm20) REVERT: H 51 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9445 (tp) REVERT: H 72 ASP cc_start: 0.8894 (t0) cc_final: 0.8465 (t0) REVERT: H 76 ASN cc_start: 0.8984 (t0) cc_final: 0.8473 (t0) REVERT: H 105 GLN cc_start: 0.8359 (pm20) cc_final: 0.8024 (pm20) REVERT: H 152 GLU cc_start: 0.8967 (pm20) cc_final: 0.8624 (pm20) REVERT: H 170 PHE cc_start: 0.9014 (m-80) cc_final: 0.8440 (m-80) REVERT: I 18 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7377 (mmt90) REVERT: I 30 ASN cc_start: 0.9192 (t0) cc_final: 0.8765 (t0) REVERT: I 50 GLU cc_start: 0.9250 (mt-10) cc_final: 0.9032 (mp0) REVERT: I 142 ARG cc_start: 0.9011 (ttm110) cc_final: 0.8551 (ttm-80) REVERT: I 148 TRP cc_start: 0.8086 (m100) cc_final: 0.7155 (m100) REVERT: I 158 ASN cc_start: 0.9224 (m110) cc_final: 0.8664 (t0) REVERT: I 210 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8503 (t0) REVERT: J 6 GLU cc_start: 0.7067 (mp0) cc_final: 0.6356 (mp0) REVERT: J 51 ILE cc_start: 0.9693 (tt) cc_final: 0.9433 (tp) REVERT: J 76 ASN cc_start: 0.8936 (t0) cc_final: 0.8441 (t0) REVERT: J 105 GLN cc_start: 0.7925 (pm20) cc_final: 0.7267 (pm20) REVERT: J 170 PHE cc_start: 0.9119 (m-80) cc_final: 0.8619 (m-80) REVERT: J 201 ASN cc_start: 0.9154 (t0) cc_final: 0.8441 (m110) REVERT: K 6 GLU cc_start: 0.7608 (mp0) cc_final: 0.7051 (pm20) REVERT: K 51 ILE cc_start: 0.9700 (OUTLIER) cc_final: 0.9443 (tp) REVERT: K 76 ASN cc_start: 0.8937 (t0) cc_final: 0.8438 (t0) REVERT: K 105 GLN cc_start: 0.8360 (pm20) cc_final: 0.8051 (pm20) REVERT: K 152 GLU cc_start: 0.9002 (pm20) cc_final: 0.8571 (pm20) REVERT: K 170 PHE cc_start: 0.9168 (m-80) cc_final: 0.8642 (m-80) REVERT: K 201 ASN cc_start: 0.9086 (t0) cc_final: 0.8361 (m110) REVERT: L 30 ASN cc_start: 0.9208 (t0) cc_final: 0.8768 (t0) REVERT: L 50 GLU cc_start: 0.9261 (mt-10) cc_final: 0.9045 (mp0) REVERT: L 142 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8015 (ttm110) REVERT: L 148 TRP cc_start: 0.8147 (m100) cc_final: 0.7202 (m100) REVERT: L 158 ASN cc_start: 0.9225 (m110) cc_final: 0.8663 (t0) outliers start: 80 outliers final: 53 residues processed: 494 average time/residue: 1.0928 time to fit residues: 625.1667 Evaluate side-chains 490 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 430 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 190 SER 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 B residue 204 ASN 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 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 11 CYS Chi-restraints excluded: chain F residue 12 VAL 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 148 ASP Chi-restraints excluded: chain F residue 156 VAL 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 11 CYS Chi-restraints excluded: chain H residue 12 VAL 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 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 CYS 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 156 VAL 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 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 75 ILE Chi-restraints excluded: chain L residue 117 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 2 optimal weight: 0.9980 chunk 255 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 226 optimal weight: 0.9990 chunk 259 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN D 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.060837 restraints weight = 41754.499| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.38 r_work: 0.2562 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20992 Z= 0.252 Angle : 0.720 8.685 28644 Z= 0.370 Chirality : 0.047 0.175 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.086 19.094 2860 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.32 % Allowed : 22.82 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2636 helix: -0.08 (0.49), residues: 128 sheet: 0.87 (0.16), residues: 832 loop : -0.18 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 137 HIS 0.005 0.001 HIS A 166 PHE 0.023 0.002 PHE E 139 TYR 0.027 0.002 TYR J 180 ARG 0.011 0.001 ARG E 61 *********************** 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 532 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 456 time to evaluate : 2.433 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: 0.8750 (t0) cc_final: 0.8189 (t0) REVERT: A 149 GLU cc_start: 0.8978 (mp0) cc_final: 0.8422 (mp0) REVERT: A 164 GLU cc_start: 0.8423 (tp30) cc_final: 0.7946 (tm-30) REVERT: A 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9172 (t160) REVERT: B 128 GLU cc_start: 0.9443 (tp30) cc_final: 0.9039 (tp30) REVERT: B 145 ASP cc_start: 0.8744 (t0) cc_final: 0.8188 (t0) REVERT: B 149 GLU cc_start: 0.8968 (mp0) cc_final: 0.8359 (mp0) REVERT: B 164 GLU cc_start: 0.8366 (tp30) cc_final: 0.7959 (tm-30) REVERT: B 204 ASN cc_start: 0.9498 (OUTLIER) cc_final: 0.9185 (t160) REVERT: C 128 GLU cc_start: 0.9428 (tp30) cc_final: 0.9033 (tp30) REVERT: C 145 ASP cc_start: 0.8739 (t0) cc_final: 0.8177 (t0) REVERT: C 149 GLU cc_start: 0.8966 (mp0) cc_final: 0.8332 (mp0) REVERT: C 164 GLU cc_start: 0.8491 (tp30) cc_final: 0.8006 (tm-30) REVERT: C 171 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8950 (mttt) REVERT: C 204 ASN cc_start: 0.9495 (OUTLIER) cc_final: 0.9170 (t160) REVERT: D 145 ASP cc_start: 0.8732 (t0) cc_final: 0.8148 (t0) REVERT: D 149 GLU cc_start: 0.8967 (mp0) cc_final: 0.8316 (mp0) REVERT: D 164 GLU cc_start: 0.8354 (tp30) cc_final: 0.7906 (tm-30) REVERT: D 189 ASP cc_start: 0.8865 (t0) cc_final: 0.8582 (t0) REVERT: D 204 ASN cc_start: 0.9493 (OUTLIER) cc_final: 0.9178 (t160) REVERT: E 18 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8213 (mmt90) REVERT: E 30 ASN cc_start: 0.9192 (t0) cc_final: 0.8776 (t0) REVERT: E 50 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9050 (mp0) REVERT: E 125 LEU cc_start: 0.9557 (pp) cc_final: 0.9227 (mm) REVERT: E 148 TRP cc_start: 0.8124 (m100) cc_final: 0.7220 (m100) REVERT: E 158 ASN cc_start: 0.9211 (m110) cc_final: 0.8542 (t0) REVERT: E 161 GLU cc_start: 0.8716 (mp0) cc_final: 0.8474 (mp0) REVERT: E 211 ARG cc_start: 0.7140 (ttp-170) cc_final: 0.6402 (ptm160) REVERT: F 3 GLN cc_start: 0.8992 (pm20) cc_final: 0.8199 (pm20) REVERT: F 6 GLU cc_start: 0.7077 (mp0) cc_final: 0.6141 (mp0) REVERT: F 27 PHE cc_start: 0.8258 (m-80) cc_final: 0.7476 (m-80) REVERT: F 51 ILE cc_start: 0.9694 (OUTLIER) cc_final: 0.9457 (tp) REVERT: F 72 ASP cc_start: 0.8910 (t0) cc_final: 0.8505 (t0) REVERT: F 76 ASN cc_start: 0.8984 (t0) cc_final: 0.8494 (t0) REVERT: F 105 GLN cc_start: 0.7892 (pm20) cc_final: 0.7258 (pm20) REVERT: F 170 PHE cc_start: 0.8777 (m-80) cc_final: 0.8431 (m-80) REVERT: G 11 LEU cc_start: 0.9307 (pp) cc_final: 0.8618 (pp) REVERT: G 18 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8223 (mmt90) REVERT: G 30 ASN cc_start: 0.9195 (t0) cc_final: 0.8781 (t0) REVERT: G 50 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9041 (mp0) REVERT: G 105 GLU cc_start: 0.8727 (tp30) cc_final: 0.8052 (mp0) REVERT: G 125 LEU cc_start: 0.9503 (pp) cc_final: 0.9234 (mm) REVERT: G 142 ARG cc_start: 0.8904 (ttm-80) cc_final: 0.8399 (ttm-80) REVERT: G 148 TRP cc_start: 0.8101 (m100) cc_final: 0.7135 (m100) REVERT: G 158 ASN cc_start: 0.9225 (m110) cc_final: 0.8635 (t0) REVERT: G 161 GLU cc_start: 0.8801 (mp0) cc_final: 0.8586 (mp0) REVERT: G 211 ARG cc_start: 0.7171 (ttp-170) cc_final: 0.6495 (ptm160) REVERT: H 3 GLN cc_start: 0.8983 (pm20) cc_final: 0.8509 (pm20) REVERT: H 6 GLU cc_start: 0.7519 (mp0) cc_final: 0.6498 (mp0) REVERT: H 27 PHE cc_start: 0.8257 (m-80) cc_final: 0.7480 (m-80) REVERT: H 51 ILE cc_start: 0.9703 (OUTLIER) cc_final: 0.9474 (tp) REVERT: H 72 ASP cc_start: 0.8905 (t0) cc_final: 0.8485 (t0) REVERT: H 76 ASN cc_start: 0.8996 (t0) cc_final: 0.8503 (t0) REVERT: H 152 GLU cc_start: 0.8996 (pm20) cc_final: 0.8649 (pm20) REVERT: H 170 PHE cc_start: 0.8946 (m-80) cc_final: 0.8340 (m-80) REVERT: I 30 ASN cc_start: 0.9193 (t0) cc_final: 0.8798 (t0) REVERT: I 50 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9057 (mt-10) REVERT: I 125 LEU cc_start: 0.9500 (pp) cc_final: 0.9220 (mm) REVERT: I 142 ARG cc_start: 0.8989 (ttm110) cc_final: 0.8533 (ttm-80) REVERT: I 148 TRP cc_start: 0.8017 (m100) cc_final: 0.7156 (m100) REVERT: I 158 ASN cc_start: 0.9222 (m110) cc_final: 0.8652 (t0) REVERT: I 211 ARG cc_start: 0.7385 (ttp-170) cc_final: 0.6908 (ptm160) REVERT: J 6 GLU cc_start: 0.7031 (mp0) cc_final: 0.6328 (mp0) REVERT: J 51 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9445 (tp) REVERT: J 76 ASN cc_start: 0.8950 (t0) cc_final: 0.8480 (t0) REVERT: J 77 GLN cc_start: 0.8988 (pt0) cc_final: 0.8149 (pp30) REVERT: J 105 GLN cc_start: 0.7910 (pm20) cc_final: 0.7275 (pm20) REVERT: J 170 PHE cc_start: 0.9064 (m-80) cc_final: 0.8533 (m-80) REVERT: J 201 ASN cc_start: 0.9130 (t0) cc_final: 0.8442 (m110) REVERT: K 6 GLU cc_start: 0.7583 (mp0) cc_final: 0.6849 (pm20) REVERT: K 51 ILE cc_start: 0.9692 (OUTLIER) cc_final: 0.9441 (tp) REVERT: K 76 ASN cc_start: 0.8947 (t0) cc_final: 0.8481 (t0) REVERT: K 77 GLN cc_start: 0.9013 (pt0) cc_final: 0.8122 (pp30) REVERT: K 105 GLN cc_start: 0.8364 (pm20) cc_final: 0.8146 (pm20) REVERT: K 152 GLU cc_start: 0.9001 (pm20) cc_final: 0.8632 (pm20) REVERT: K 170 PHE cc_start: 0.9095 (m-80) cc_final: 0.8529 (m-80) REVERT: K 201 ASN cc_start: 0.9099 (t0) cc_final: 0.8379 (m110) REVERT: L 30 ASN cc_start: 0.9204 (t0) cc_final: 0.8791 (t0) REVERT: L 50 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9072 (mt-10) REVERT: L 125 LEU cc_start: 0.9501 (pp) cc_final: 0.9231 (mm) REVERT: L 142 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8014 (ttm-80) REVERT: L 148 TRP cc_start: 0.8048 (m100) cc_final: 0.7143 (m100) REVERT: L 158 ASN cc_start: 0.9224 (m110) cc_final: 0.8649 (t0) outliers start: 76 outliers final: 46 residues processed: 495 average time/residue: 1.1073 time to fit residues: 635.7130 Evaluate side-chains 481 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 426 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 190 SER Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 171 LYS 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 D residue 217 GLU 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 51 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 148 ASP Chi-restraints excluded: chain F residue 156 VAL 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 51 ILE 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 75 ILE Chi-restraints excluded: chain J residue 2 VAL 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 2 VAL 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 199 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 45 LYS 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 138 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 46 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.058607 restraints weight = 42491.710| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.36 r_work: 0.2517 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 20992 Z= 0.475 Angle : 0.780 8.406 28644 Z= 0.406 Chirality : 0.049 0.193 3220 Planarity : 0.006 0.074 3660 Dihedral : 5.256 20.521 2860 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.27 % Allowed : 23.65 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2636 helix: -0.05 (0.49), residues: 128 sheet: 0.68 (0.17), residues: 832 loop : -0.20 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 141 HIS 0.005 0.001 HIS L 189 PHE 0.024 0.002 PHE L 139 TYR 0.042 0.003 TYR F 180 ARG 0.018 0.001 ARG H 26 *********************** 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 509 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 434 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8885 (t0) cc_final: 0.8207 (t0) REVERT: A 149 GLU cc_start: 0.9010 (mp0) cc_final: 0.8378 (mp0) REVERT: A 164 GLU cc_start: 0.8533 (tp30) cc_final: 0.8090 (tm-30) REVERT: B 145 ASP cc_start: 0.8862 (t0) cc_final: 0.8211 (t0) REVERT: B 149 GLU cc_start: 0.8970 (mp0) cc_final: 0.8256 (mp0) REVERT: B 164 GLU cc_start: 0.8462 (tp30) cc_final: 0.8021 (tm-30) REVERT: C 145 ASP cc_start: 0.8836 (t0) cc_final: 0.8187 (t0) REVERT: C 149 GLU cc_start: 0.8975 (mp0) cc_final: 0.8264 (mp0) REVERT: C 164 GLU cc_start: 0.8595 (tp30) cc_final: 0.8147 (tm-30) REVERT: C 171 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9042 (mttt) REVERT: D 145 ASP cc_start: 0.8854 (t0) cc_final: 0.8338 (t0) REVERT: D 149 GLU cc_start: 0.8982 (mp0) cc_final: 0.8479 (mp0) REVERT: D 164 GLU cc_start: 0.8504 (tp30) cc_final: 0.8083 (tm-30) REVERT: D 189 ASP cc_start: 0.8970 (t0) cc_final: 0.8697 (t0) REVERT: E 18 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8258 (mmt90) REVERT: E 30 ASN cc_start: 0.9217 (t0) cc_final: 0.8743 (t0) REVERT: E 50 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9044 (mt-10) REVERT: E 105 GLU cc_start: 0.8690 (tp30) cc_final: 0.8147 (mp0) REVERT: E 158 ASN cc_start: 0.9229 (m110) cc_final: 0.8675 (t0) REVERT: E 211 ARG cc_start: 0.7243 (ttp-170) cc_final: 0.6579 (ptm160) REVERT: F 3 GLN cc_start: 0.8904 (pm20) cc_final: 0.8332 (pm20) REVERT: F 6 GLU cc_start: 0.7287 (mp0) cc_final: 0.6479 (mp0) REVERT: F 26 ARG cc_start: 0.9002 (ttm110) cc_final: 0.8588 (mtp-110) REVERT: F 27 PHE cc_start: 0.7985 (m-80) cc_final: 0.7426 (m-80) REVERT: F 51 ILE cc_start: 0.9717 (OUTLIER) cc_final: 0.9457 (tp) REVERT: F 72 ASP cc_start: 0.8974 (t0) cc_final: 0.8588 (t0) REVERT: F 76 ASN cc_start: 0.9064 (t0) cc_final: 0.8607 (t0) REVERT: F 105 GLN cc_start: 0.7931 (pm20) cc_final: 0.7290 (pm20) REVERT: F 170 PHE cc_start: 0.8846 (m-80) cc_final: 0.8617 (m-80) REVERT: F 195 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7740 (p) REVERT: G 18 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8248 (mmt90) REVERT: G 30 ASN cc_start: 0.9218 (t0) cc_final: 0.8752 (t0) REVERT: G 50 GLU cc_start: 0.9261 (mt-10) cc_final: 0.9046 (mt-10) REVERT: G 142 ARG cc_start: 0.8878 (ttm-80) cc_final: 0.8390 (ttm-80) REVERT: G 158 ASN cc_start: 0.9243 (m110) cc_final: 0.8693 (t0) REVERT: G 211 ARG cc_start: 0.7244 (ttp-170) cc_final: 0.6576 (ptm160) REVERT: H 3 GLN cc_start: 0.8923 (pm20) cc_final: 0.8361 (pm20) REVERT: H 26 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8587 (mtp-110) REVERT: H 27 PHE cc_start: 0.8002 (m-80) cc_final: 0.7441 (m-80) REVERT: H 51 ILE cc_start: 0.9725 (OUTLIER) cc_final: 0.9471 (tp) REVERT: H 72 ASP cc_start: 0.8962 (t0) cc_final: 0.8559 (t0) REVERT: H 76 ASN cc_start: 0.9067 (t0) cc_final: 0.8612 (t0) REVERT: H 152 GLU cc_start: 0.9061 (pm20) cc_final: 0.8711 (pm20) REVERT: H 170 PHE cc_start: 0.8993 (m-80) cc_final: 0.8628 (m-80) REVERT: H 195 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7746 (p) REVERT: I 18 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7340 (mmt90) REVERT: I 30 ASN cc_start: 0.9222 (t0) cc_final: 0.8777 (t0) REVERT: I 125 LEU cc_start: 0.9533 (pp) cc_final: 0.9251 (mm) REVERT: I 142 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8345 (ttm-80) REVERT: I 148 TRP cc_start: 0.8084 (m100) cc_final: 0.7185 (m100) REVERT: I 158 ASN cc_start: 0.9236 (m110) cc_final: 0.8672 (t0) REVERT: I 211 ARG cc_start: 0.7724 (ttp-170) cc_final: 0.6930 (ptm160) REVERT: J 6 GLU cc_start: 0.7214 (mp0) cc_final: 0.6506 (mp0) REVERT: J 51 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9453 (tp) REVERT: J 76 ASN cc_start: 0.9030 (t0) cc_final: 0.8548 (t0) REVERT: J 77 GLN cc_start: 0.9042 (pt0) cc_final: 0.8191 (pp30) REVERT: J 105 GLN cc_start: 0.7953 (pm20) cc_final: 0.7298 (pm20) REVERT: J 170 PHE cc_start: 0.9073 (m-80) cc_final: 0.8814 (m-80) REVERT: J 195 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7718 (p) REVERT: J 201 ASN cc_start: 0.9190 (t0) cc_final: 0.8518 (m110) REVERT: K 6 GLU cc_start: 0.7593 (mp0) cc_final: 0.6809 (pm20) REVERT: K 51 ILE cc_start: 0.9727 (OUTLIER) cc_final: 0.9470 (tp) REVERT: K 76 ASN cc_start: 0.9031 (t0) cc_final: 0.8572 (t0) REVERT: K 77 GLN cc_start: 0.9055 (pt0) cc_final: 0.8155 (pp30) REVERT: K 105 GLN cc_start: 0.8302 (pm20) cc_final: 0.7804 (pm20) REVERT: K 152 GLU cc_start: 0.9086 (pm20) cc_final: 0.8697 (pm20) REVERT: K 170 PHE cc_start: 0.9077 (m-80) cc_final: 0.8779 (m-80) REVERT: K 195 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7736 (p) REVERT: K 201 ASN cc_start: 0.9140 (t0) cc_final: 0.8444 (m110) REVERT: L 18 ARG cc_start: 0.8188 (ttm110) cc_final: 0.7304 (mmt90) REVERT: L 30 ASN cc_start: 0.9226 (t0) cc_final: 0.8755 (t0) REVERT: L 50 GLU cc_start: 0.9237 (mt-10) cc_final: 0.9028 (mt-10) REVERT: L 125 LEU cc_start: 0.9533 (pp) cc_final: 0.9252 (mm) REVERT: L 148 TRP cc_start: 0.8100 (m100) cc_final: 0.6967 (m100) REVERT: L 158 ASN cc_start: 0.9248 (m110) cc_final: 0.8692 (t0) REVERT: L 211 ARG cc_start: 0.7190 (ttp-170) cc_final: 0.6383 (ptm160) outliers start: 75 outliers final: 54 residues processed: 474 average time/residue: 1.0859 time to fit residues: 598.3182 Evaluate side-chains 491 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 428 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 88 ILE 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 88 ILE 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 88 ILE 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 11 CYS 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 148 ASP 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 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 75 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 11 CYS 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 148 ASP 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 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 201 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 182 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221AGLN B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.100188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.061180 restraints weight = 42163.069| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.41 r_work: 0.2577 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20992 Z= 0.219 Angle : 0.764 9.303 28644 Z= 0.390 Chirality : 0.047 0.218 3220 Planarity : 0.006 0.072 3660 Dihedral : 5.112 27.648 2860 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.92 % Allowed : 24.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 2636 helix: 0.00 (0.49), residues: 128 sheet: 0.73 (0.16), residues: 884 loop : -0.06 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 148 HIS 0.006 0.001 HIS A 166 PHE 0.028 0.002 PHE E 139 TYR 0.034 0.002 TYR F 180 ARG 0.017 0.001 ARG F 26 *********************** 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 519 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 452 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8771 (t0) cc_final: 0.8282 (t0) REVERT: A 149 GLU cc_start: 0.9010 (mp0) cc_final: 0.8501 (mp0) REVERT: A 164 GLU cc_start: 0.8491 (tp30) cc_final: 0.8065 (tm-30) REVERT: A 204 ASN cc_start: 0.9505 (OUTLIER) cc_final: 0.9189 (t160) REVERT: B 128 GLU cc_start: 0.9407 (tp30) cc_final: 0.9078 (tp30) REVERT: B 145 ASP cc_start: 0.8777 (t0) cc_final: 0.8273 (t0) REVERT: B 149 GLU cc_start: 0.8969 (mp0) cc_final: 0.8446 (mp0) REVERT: B 164 GLU cc_start: 0.8402 (tp30) cc_final: 0.7968 (tm-30) REVERT: B 204 ASN cc_start: 0.9506 (OUTLIER) cc_final: 0.9175 (t160) REVERT: C 145 ASP cc_start: 0.8744 (t0) cc_final: 0.8232 (t0) REVERT: C 149 GLU cc_start: 0.8975 (mp0) cc_final: 0.8435 (mp0) REVERT: C 164 GLU cc_start: 0.8540 (tp30) cc_final: 0.8103 (tm-30) REVERT: C 171 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8988 (mttt) REVERT: C 204 ASN cc_start: 0.9510 (OUTLIER) cc_final: 0.9194 (t160) REVERT: D 145 ASP cc_start: 0.8774 (t0) cc_final: 0.8208 (t0) REVERT: D 149 GLU cc_start: 0.8985 (mp0) cc_final: 0.8384 (mp0) REVERT: D 164 GLU cc_start: 0.8435 (tp30) cc_final: 0.7971 (tm-30) REVERT: D 189 ASP cc_start: 0.8928 (t0) cc_final: 0.8685 (t0) REVERT: D 204 ASN cc_start: 0.9509 (OUTLIER) cc_final: 0.9177 (t160) REVERT: E 18 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8209 (mmt90) REVERT: E 30 ASN cc_start: 0.9133 (t0) cc_final: 0.8744 (t0) REVERT: E 50 GLU cc_start: 0.9254 (mt-10) cc_final: 0.9032 (mt-10) REVERT: E 125 LEU cc_start: 0.9555 (pp) cc_final: 0.9222 (mm) REVERT: E 148 TRP cc_start: 0.8182 (m100) cc_final: 0.7424 (m100) REVERT: E 158 ASN cc_start: 0.9225 (m110) cc_final: 0.8658 (t0) REVERT: E 211 ARG cc_start: 0.7287 (ttp-170) cc_final: 0.6606 (ptm160) REVERT: F 3 GLN cc_start: 0.8865 (pm20) cc_final: 0.8190 (pm20) REVERT: F 6 GLU cc_start: 0.7225 (mp0) cc_final: 0.6381 (mp0) REVERT: F 51 ILE cc_start: 0.9713 (tt) cc_final: 0.9493 (tp) REVERT: F 72 ASP cc_start: 0.8995 (t0) cc_final: 0.8616 (t0) REVERT: F 76 ASN cc_start: 0.9023 (t0) cc_final: 0.8579 (t0) REVERT: F 105 GLN cc_start: 0.7972 (pm20) cc_final: 0.7317 (pm20) REVERT: F 170 PHE cc_start: 0.8773 (m-80) cc_final: 0.8525 (m-80) REVERT: F 195 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7698 (p) REVERT: G 18 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8223 (mmt90) REVERT: G 30 ASN cc_start: 0.9156 (t0) cc_final: 0.8762 (t0) REVERT: G 50 GLU cc_start: 0.9249 (mt-10) cc_final: 0.9025 (mt-10) REVERT: G 105 GLU cc_start: 0.8692 (tp30) cc_final: 0.8138 (mp0) REVERT: G 125 LEU cc_start: 0.9509 (pp) cc_final: 0.9235 (mm) REVERT: G 142 ARG cc_start: 0.8836 (ttm-80) cc_final: 0.8312 (ttm-80) REVERT: G 148 TRP cc_start: 0.8154 (m100) cc_final: 0.7441 (m100) REVERT: G 158 ASN cc_start: 0.9228 (m110) cc_final: 0.8667 (t0) REVERT: G 211 ARG cc_start: 0.7286 (ttp-170) cc_final: 0.6579 (ptm160) REVERT: H 3 GLN cc_start: 0.8873 (pm20) cc_final: 0.8228 (pm20) REVERT: H 51 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9499 (tp) REVERT: H 72 ASP cc_start: 0.8951 (t0) cc_final: 0.8588 (OUTLIER) REVERT: H 76 ASN cc_start: 0.9000 (t0) cc_final: 0.8587 (t0) REVERT: H 152 GLU cc_start: 0.9034 (pm20) cc_final: 0.8654 (pm20) REVERT: H 170 PHE cc_start: 0.8913 (m-80) cc_final: 0.8506 (m-80) REVERT: H 195 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7699 (p) REVERT: I 18 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7249 (mmt90) REVERT: I 30 ASN cc_start: 0.9171 (t0) cc_final: 0.8798 (t0) REVERT: I 50 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8896 (mp0) REVERT: I 105 GLU cc_start: 0.8577 (tp30) cc_final: 0.8277 (mp0) REVERT: I 125 LEU cc_start: 0.9515 (pp) cc_final: 0.9244 (mm) REVERT: I 137 ASN cc_start: 0.7114 (m-40) cc_final: 0.6856 (m-40) REVERT: I 142 ARG cc_start: 0.8895 (ttm110) cc_final: 0.8461 (tpp80) REVERT: I 148 TRP cc_start: 0.8076 (m100) cc_final: 0.7142 (m100) REVERT: I 158 ASN cc_start: 0.9236 (m110) cc_final: 0.8675 (t0) REVERT: I 211 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.6873 (ptm160) REVERT: J 6 GLU cc_start: 0.7126 (mp0) cc_final: 0.6388 (mp0) REVERT: J 26 ARG cc_start: 0.8768 (mtm110) cc_final: 0.8502 (pmm-80) REVERT: J 51 ILE cc_start: 0.9700 (OUTLIER) cc_final: 0.9471 (tp) REVERT: J 76 ASN cc_start: 0.8992 (t0) cc_final: 0.8579 (t0) REVERT: J 77 GLN cc_start: 0.9042 (pt0) cc_final: 0.8227 (pp30) REVERT: J 105 GLN cc_start: 0.7973 (pm20) cc_final: 0.7325 (pm20) REVERT: J 170 PHE cc_start: 0.9065 (m-80) cc_final: 0.8740 (m-80) REVERT: J 195 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7691 (p) REVERT: J 201 ASN cc_start: 0.9142 (t0) cc_final: 0.8452 (m110) REVERT: K 3 GLN cc_start: 0.8528 (pm20) cc_final: 0.7988 (pm20) REVERT: K 6 GLU cc_start: 0.7593 (mp0) cc_final: 0.6930 (pm20) REVERT: K 51 ILE cc_start: 0.9717 (OUTLIER) cc_final: 0.9477 (tp) REVERT: K 76 ASN cc_start: 0.8989 (t0) cc_final: 0.8594 (t0) REVERT: K 152 GLU cc_start: 0.9044 (pm20) cc_final: 0.8673 (pm20) REVERT: K 170 PHE cc_start: 0.9068 (m-80) cc_final: 0.8707 (m-80) REVERT: K 195 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7661 (p) REVERT: K 201 ASN cc_start: 0.9146 (t0) cc_final: 0.8449 (m110) REVERT: L 18 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7237 (mmt90) REVERT: L 30 ASN cc_start: 0.9149 (t0) cc_final: 0.8759 (t0) REVERT: L 50 GLU cc_start: 0.9231 (mt-10) cc_final: 0.9026 (mt-10) REVERT: L 105 GLU cc_start: 0.8588 (tp30) cc_final: 0.8215 (mp0) REVERT: L 125 LEU cc_start: 0.9516 (pp) cc_final: 0.9250 (mm) REVERT: L 142 ARG cc_start: 0.8883 (tpp80) cc_final: 0.8639 (tpp80) REVERT: L 148 TRP cc_start: 0.8047 (m100) cc_final: 0.7049 (m100) REVERT: L 158 ASN cc_start: 0.9239 (m110) cc_final: 0.8682 (t0) REVERT: L 211 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.6684 (ptm160) outliers start: 67 outliers final: 44 residues processed: 488 average time/residue: 1.1211 time to fit residues: 634.6350 Evaluate side-chains 492 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 436 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 204 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 190 SER 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 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 11 CYS 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 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 29 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 148 ASP 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 50 GLU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 11 CYS 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 148 ASP 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 11 CYS 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 117 ILE 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 151 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 164 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 260 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.098439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.059775 restraints weight = 42138.151| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 3.36 r_work: 0.2544 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20992 Z= 0.396 Angle : 0.784 11.134 28644 Z= 0.405 Chirality : 0.048 0.184 3220 Planarity : 0.006 0.066 3660 Dihedral : 5.174 25.576 2860 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.66 % Allowed : 25.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2636 helix: 0.08 (0.49), residues: 128 sheet: 0.55 (0.16), residues: 924 loop : -0.09 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 51 HIS 0.004 0.001 HIS A 166 PHE 0.027 0.002 PHE L 139 TYR 0.028 0.002 TYR L 140 ARG 0.017 0.001 ARG E 142 ********************** 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 494 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 433 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8837 (t0) cc_final: 0.8207 (t0) REVERT: A 149 GLU cc_start: 0.9013 (mp0) cc_final: 0.8388 (mp0) REVERT: A 164 GLU cc_start: 0.8502 (tp30) cc_final: 0.8054 (tm-30) REVERT: A 204 ASN cc_start: 0.9513 (OUTLIER) cc_final: 0.9196 (t160) REVERT: B 128 GLU cc_start: 0.9404 (tp30) cc_final: 0.8987 (tp30) REVERT: B 145 ASP cc_start: 0.8831 (t0) cc_final: 0.8250 (t0) REVERT: B 149 GLU cc_start: 0.8965 (mp0) cc_final: 0.8357 (mp0) REVERT: B 164 GLU cc_start: 0.8431 (tp30) cc_final: 0.7974 (tm-30) REVERT: C 145 ASP cc_start: 0.8795 (t0) cc_final: 0.8296 (t0) REVERT: C 149 GLU cc_start: 0.8978 (mp0) cc_final: 0.8493 (mp0) REVERT: C 164 GLU cc_start: 0.8573 (tp30) cc_final: 0.8104 (tm-30) REVERT: C 171 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.9015 (mttt) REVERT: D 145 ASP cc_start: 0.8842 (t0) cc_final: 0.8242 (t0) REVERT: D 149 GLU cc_start: 0.8972 (mp0) cc_final: 0.8341 (mp0) REVERT: D 164 GLU cc_start: 0.8459 (tp30) cc_final: 0.7956 (tm-30) REVERT: D 189 ASP cc_start: 0.8964 (t0) cc_final: 0.8705 (t0) REVERT: D 204 ASN cc_start: 0.9520 (OUTLIER) cc_final: 0.9215 (t160) REVERT: E 18 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8289 (mmt90) REVERT: E 30 ASN cc_start: 0.9203 (t0) cc_final: 0.8775 (t0) REVERT: E 50 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9062 (mt-10) REVERT: E 105 GLU cc_start: 0.8581 (tp30) cc_final: 0.8298 (mp0) REVERT: E 125 LEU cc_start: 0.9558 (pp) cc_final: 0.9200 (mm) REVERT: E 148 TRP cc_start: 0.8166 (m100) cc_final: 0.7422 (m100) REVERT: E 158 ASN cc_start: 0.9214 (m110) cc_final: 0.8629 (t0) REVERT: E 211 ARG cc_start: 0.7256 (ttp-170) cc_final: 0.6575 (ptm160) REVERT: F 3 GLN cc_start: 0.8954 (pm20) cc_final: 0.8575 (pm20) REVERT: F 6 GLU cc_start: 0.7233 (mp0) cc_final: 0.6361 (mp0) REVERT: F 26 ARG cc_start: 0.8990 (ttm110) cc_final: 0.8693 (ptp-110) REVERT: F 51 ILE cc_start: 0.9716 (OUTLIER) cc_final: 0.9466 (tp) REVERT: F 72 ASP cc_start: 0.9000 (t0) cc_final: 0.8648 (t0) REVERT: F 76 ASN cc_start: 0.9003 (t0) cc_final: 0.8626 (t0) REVERT: F 77 GLN cc_start: 0.8994 (tt0) cc_final: 0.8446 (tp40) REVERT: F 105 GLN cc_start: 0.7989 (pm20) cc_final: 0.7345 (pm20) REVERT: F 170 PHE cc_start: 0.8756 (m-80) cc_final: 0.8499 (m-80) REVERT: F 195 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7700 (p) REVERT: G 18 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8300 (mmt90) REVERT: G 30 ASN cc_start: 0.9216 (t0) cc_final: 0.8791 (t0) REVERT: G 50 GLU cc_start: 0.9252 (mt-10) cc_final: 0.9030 (mt-10) REVERT: G 105 GLU cc_start: 0.8715 (tp30) cc_final: 0.8143 (mp0) REVERT: G 125 LEU cc_start: 0.9520 (pp) cc_final: 0.9243 (mm) REVERT: G 142 ARG cc_start: 0.8851 (ttm-80) cc_final: 0.8549 (tpp80) REVERT: G 148 TRP cc_start: 0.8150 (m100) cc_final: 0.7495 (m100) REVERT: G 158 ASN cc_start: 0.9239 (m110) cc_final: 0.8680 (t0) REVERT: G 211 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6552 (ptm160) REVERT: H 3 GLN cc_start: 0.8957 (pm20) cc_final: 0.8538 (pm20) REVERT: H 26 ARG cc_start: 0.8994 (ttm110) cc_final: 0.8673 (ptp-110) REVERT: H 51 ILE cc_start: 0.9725 (OUTLIER) cc_final: 0.9486 (tp) REVERT: H 72 ASP cc_start: 0.8997 (t0) cc_final: 0.8633 (t0) REVERT: H 76 ASN cc_start: 0.9040 (t0) cc_final: 0.8638 (t0) REVERT: H 77 GLN cc_start: 0.8989 (tt0) cc_final: 0.8654 (tp40) REVERT: H 152 GLU cc_start: 0.9064 (pm20) cc_final: 0.8716 (pm20) REVERT: H 170 PHE cc_start: 0.8924 (m-80) cc_final: 0.8598 (m-80) REVERT: H 195 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7705 (p) REVERT: I 18 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7379 (mmt90) REVERT: I 30 ASN cc_start: 0.9212 (t0) cc_final: 0.8814 (t0) REVERT: I 50 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8877 (mp0) REVERT: I 105 GLU cc_start: 0.8638 (tp30) cc_final: 0.8294 (mp0) REVERT: I 125 LEU cc_start: 0.9530 (pp) cc_final: 0.9273 (mm) REVERT: I 142 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8447 (ttm-80) REVERT: I 148 TRP cc_start: 0.8091 (m100) cc_final: 0.7126 (m100) REVERT: I 158 ASN cc_start: 0.9243 (m110) cc_final: 0.8680 (t0) REVERT: I 211 ARG cc_start: 0.7602 (ttp-170) cc_final: 0.6903 (ptm160) REVERT: J 6 GLU cc_start: 0.7173 (mp0) cc_final: 0.6452 (mp0) REVERT: J 51 ILE cc_start: 0.9706 (OUTLIER) cc_final: 0.9456 (tp) REVERT: J 76 ASN cc_start: 0.9019 (t0) cc_final: 0.8637 (t0) REVERT: J 105 GLN cc_start: 0.7946 (pm20) cc_final: 0.7320 (pm20) REVERT: J 195 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7690 (p) REVERT: J 201 ASN cc_start: 0.9051 (t0) cc_final: 0.8387 (m110) REVERT: K 51 ILE cc_start: 0.9727 (OUTLIER) cc_final: 0.9487 (tp) REVERT: K 76 ASN cc_start: 0.9020 (t0) cc_final: 0.8675 (t0) REVERT: K 105 GLN cc_start: 0.8230 (pm20) cc_final: 0.8003 (pm20) REVERT: K 152 GLU cc_start: 0.9097 (pm20) cc_final: 0.8738 (pm20) REVERT: K 170 PHE cc_start: 0.9015 (m-80) cc_final: 0.8739 (m-80) REVERT: K 195 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7677 (p) REVERT: K 201 ASN cc_start: 0.9146 (t0) cc_final: 0.8454 (m110) REVERT: L 18 ARG cc_start: 0.8253 (ttm110) cc_final: 0.7356 (mmt90) REVERT: L 30 ASN cc_start: 0.9220 (t0) cc_final: 0.8797 (t0) REVERT: L 50 GLU cc_start: 0.9243 (mt-10) cc_final: 0.9038 (mt-10) REVERT: L 105 GLU cc_start: 0.8633 (tp30) cc_final: 0.8310 (mp0) REVERT: L 125 LEU cc_start: 0.9530 (pp) cc_final: 0.9274 (mm) REVERT: L 148 TRP cc_start: 0.8059 (m100) cc_final: 0.7134 (m100) REVERT: L 158 ASN cc_start: 0.9245 (m110) cc_final: 0.8684 (t0) REVERT: L 211 ARG cc_start: 0.7248 (ttp-170) cc_final: 0.6689 (ptm160) outliers start: 61 outliers final: 43 residues processed: 468 average time/residue: 1.1176 time to fit residues: 606.1613 Evaluate side-chains 480 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 426 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 88 ILE 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 C residue 190 SER 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 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 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 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 11 CYS 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 148 ASP 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 11 CYS 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 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 174 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.098775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.060123 restraints weight = 42451.441| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.40 r_work: 0.2552 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20992 Z= 0.322 Angle : 0.784 10.657 28644 Z= 0.405 Chirality : 0.048 0.218 3220 Planarity : 0.006 0.065 3660 Dihedral : 5.197 29.713 2860 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.66 % Allowed : 25.22 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2636 helix: 0.10 (0.49), residues: 128 sheet: 0.67 (0.16), residues: 892 loop : -0.17 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 51 HIS 0.005 0.001 HIS A 166 PHE 0.030 0.002 PHE E 139 TYR 0.029 0.002 TYR E 140 ARG 0.017 0.001 ARG E 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15969.91 seconds wall clock time: 282 minutes 59.59 seconds (16979.59 seconds total)