Starting phenix.real_space_refine on Tue Jun 17 23:45:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgi_43201/06_2025/8vgi_43201.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgi_43201/06_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_43201/06_2025/8vgi_43201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgi_43201/06_2025/8vgi_43201.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgi_43201/06_2025/8vgi_43201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgi_43201/06_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-5710/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: 14.05, per 1000 atoms: 0.69 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: 5.02 Conformation dependent library (CDL) restraints added in 3.2 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: 4.18 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: 10.33 Time building geometry restraints manager: 6.10 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: 123.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 56.120 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 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:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.108 21032 Z= 0.479 Angle : 1.167 8.770 28724 Z= 0.643 Chirality : 0.074 0.286 3220 Planarity : 0.010 0.072 3660 Dihedral : 13.302 89.992 7496 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.48 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 Details of bonding type rmsd hydrogen bonds : bond 0.24367 ( 707) hydrogen bonds : angle 9.68060 ( 1935) SS BOND : bond 0.01102 ( 40) SS BOND : angle 2.31785 ( 80) covalent geometry : bond 0.01141 (20992) covalent geometry : angle 1.16179 (28644) *********************** 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 : 2.345 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: 1.2124 time to fit residues: 960.2228 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 : 2.245 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 165 ASN B 165 ASN B 192 GLN C 146 ASN C 165 ASN D 20 GLN D 165 ASN D 192 GLN E 147 GLN E 158 ASN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN G 147 GLN G 158 ASN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3508 r_free = 0.3508 target = 0.099019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.060099 restraints weight = 42083.753| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.40 r_work: 0.2539 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 21032 Z= 0.246 Angle : 0.850 9.705 28724 Z= 0.444 Chirality : 0.051 0.166 3220 Planarity : 0.006 0.070 3660 Dihedral : 8.292 119.418 2884 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.88 % Allowed : 15.71 % Favored : 81.41 % 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: -1.31 (0.44), residues: 124 sheet: 0.23 (0.16), residues: 848 loop : -0.23 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 215 HIS 0.005 0.001 HIS G 189 PHE 0.022 0.003 PHE F 126 TYR 0.017 0.002 TYR L 29 ARG 0.008 0.001 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 707) hydrogen bonds : angle 6.89631 ( 1935) SS BOND : bond 0.00542 ( 40) SS BOND : angle 1.68770 ( 80) covalent geometry : bond 0.00564 (20992) covalent geometry : angle 0.84617 (28644) *********************** 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 589 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 523 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8990 (t0) cc_final: 0.8489 (t0) REVERT: A 149 GLU cc_start: 0.8636 (mp0) cc_final: 0.8191 (mp0) REVERT: A 150 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8852 (mmt-90) REVERT: A 164 GLU cc_start: 0.8241 (tp30) cc_final: 0.7917 (tm-30) REVERT: B 145 ASP cc_start: 0.9052 (t0) cc_final: 0.8577 (t0) REVERT: B 149 GLU cc_start: 0.8693 (mp0) cc_final: 0.8116 (mp0) REVERT: B 164 GLU cc_start: 0.8245 (tp30) cc_final: 0.7950 (tm-30) REVERT: C 145 ASP cc_start: 0.9059 (t0) cc_final: 0.8496 (t0) REVERT: C 149 GLU cc_start: 0.8656 (mp0) cc_final: 0.7949 (mp0) REVERT: C 164 GLU cc_start: 0.8280 (tp30) cc_final: 0.7976 (tm-30) REVERT: C 171 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8975 (mttt) REVERT: D 75 TYR cc_start: 0.8932 (t80) cc_final: 0.8729 (t80) REVERT: D 145 ASP cc_start: 0.9008 (t0) cc_final: 0.8435 (t0) REVERT: D 149 GLU cc_start: 0.8641 (mp0) cc_final: 0.7933 (mp0) REVERT: D 164 GLU cc_start: 0.8176 (tp30) cc_final: 0.7882 (tm-30) REVERT: E 30 ASN cc_start: 0.9214 (t0) cc_final: 0.8693 (t0) REVERT: E 50 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8737 (mp0) REVERT: E 142 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8058 (ttm-80) REVERT: E 145 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8211 (pptt) REVERT: E 192 TYR cc_start: 0.7565 (m-80) cc_final: 0.7208 (m-80) REVERT: E 210 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8121 (t0) REVERT: E 211 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7326 (ttm-80) REVERT: F 6 GLU cc_start: 0.7176 (mp0) cc_final: 0.6606 (mp0) REVERT: F 51 ILE cc_start: 0.9615 (tt) cc_final: 0.9392 (tp) REVERT: F 72 ASP cc_start: 0.8480 (t0) cc_final: 0.8055 (t0) REVERT: F 75 LYS cc_start: 0.9568 (mttt) cc_final: 0.9254 (mttt) REVERT: F 76 ASN cc_start: 0.8904 (t0) cc_final: 0.8188 (t0) REVERT: F 105 GLN cc_start: 0.7792 (pm20) cc_final: 0.7462 (pm20) REVERT: F 148 ASP cc_start: 0.8359 (p0) cc_final: 0.8096 (p0) REVERT: F 152 GLU cc_start: 0.8725 (pm20) cc_final: 0.8181 (pm20) REVERT: F 170 PHE cc_start: 0.8924 (m-80) cc_final: 0.8593 (m-80) REVERT: F 205 LYS cc_start: 0.9641 (tppt) cc_final: 0.9315 (mmmt) REVERT: G 30 ASN cc_start: 0.9228 (t0) cc_final: 0.8711 (t0) REVERT: G 50 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8709 (mp0) REVERT: G 142 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: G 145 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8223 (pptt) REVERT: G 192 TYR cc_start: 0.7562 (m-80) cc_final: 0.7345 (m-80) REVERT: G 210 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8135 (t0) REVERT: G 211 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7405 (ttm-80) REVERT: H 6 GLU cc_start: 0.7187 (mp0) cc_final: 0.6535 (mp0) REVERT: H 51 ILE cc_start: 0.9624 (tt) cc_final: 0.9401 (tp) REVERT: H 72 ASP cc_start: 0.8471 (t0) cc_final: 0.8052 (t0) REVERT: H 75 LYS cc_start: 0.9566 (mttt) cc_final: 0.9251 (mttt) REVERT: H 76 ASN cc_start: 0.8899 (t0) cc_final: 0.8188 (t0) REVERT: H 105 GLN cc_start: 0.7812 (pm20) cc_final: 0.7358 (pm20) REVERT: H 148 ASP cc_start: 0.8365 (p0) cc_final: 0.8104 (p0) REVERT: H 152 GLU cc_start: 0.8722 (pm20) cc_final: 0.8184 (pm20) REVERT: H 170 PHE cc_start: 0.8990 (m-80) cc_final: 0.8368 (m-80) REVERT: H 205 LYS cc_start: 0.9648 (tppt) cc_final: 0.9323 (mmmt) REVERT: I 18 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7967 (mmm-85) REVERT: I 30 ASN cc_start: 0.9200 (t0) cc_final: 0.8673 (t0) REVERT: I 50 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8735 (mp0) REVERT: I 53 ILE cc_start: 0.8848 (mp) cc_final: 0.8595 (mp) REVERT: I 210 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8100 (t0) REVERT: J 6 GLU cc_start: 0.7083 (mp0) cc_final: 0.6579 (mp0) REVERT: J 51 ILE cc_start: 0.9619 (tt) cc_final: 0.9405 (tp) REVERT: J 72 ASP cc_start: 0.8485 (t0) cc_final: 0.7620 (t0) REVERT: J 75 LYS cc_start: 0.9551 (mttt) cc_final: 0.9323 (mttt) REVERT: J 76 ASN cc_start: 0.8938 (t0) cc_final: 0.8233 (t0) REVERT: J 105 GLN cc_start: 0.7818 (pm20) cc_final: 0.7192 (pm20) REVERT: J 148 ASP cc_start: 0.8340 (p0) cc_final: 0.7243 (p0) REVERT: J 152 GLU cc_start: 0.8804 (pm20) cc_final: 0.8315 (pm20) REVERT: J 170 PHE cc_start: 0.9156 (m-80) cc_final: 0.8614 (m-80) REVERT: J 203 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8034 (t0) REVERT: J 205 LYS cc_start: 0.9671 (tppt) cc_final: 0.9320 (mmmt) REVERT: J 210 LYS cc_start: 0.9015 (mptt) cc_final: 0.8591 (tptt) REVERT: K 6 GLU cc_start: 0.7076 (mp0) cc_final: 0.6576 (mp0) REVERT: K 51 ILE cc_start: 0.9630 (tt) cc_final: 0.9418 (tp) REVERT: K 72 ASP cc_start: 0.8479 (t0) cc_final: 0.7614 (t0) REVERT: K 75 LYS cc_start: 0.9552 (mttt) cc_final: 0.9324 (mttt) REVERT: K 76 ASN cc_start: 0.8930 (t0) cc_final: 0.8228 (t0) REVERT: K 105 GLN cc_start: 0.7801 (pm20) cc_final: 0.7176 (pm20) REVERT: K 148 ASP cc_start: 0.8333 (p0) cc_final: 0.7198 (p0) REVERT: K 152 GLU cc_start: 0.8798 (pm20) cc_final: 0.8297 (pm20) REVERT: K 170 PHE cc_start: 0.9012 (m-80) cc_final: 0.8547 (m-80) REVERT: K 203 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8030 (t0) REVERT: K 205 LYS cc_start: 0.9672 (tppt) cc_final: 0.9316 (mmmt) REVERT: K 210 LYS cc_start: 0.9038 (mptt) cc_final: 0.8618 (tptt) REVERT: L 18 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7967 (mmm-85) REVERT: L 30 ASN cc_start: 0.9202 (t0) cc_final: 0.8670 (t0) REVERT: L 50 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8745 (mp0) REVERT: L 53 ILE cc_start: 0.8844 (mp) cc_final: 0.8592 (mp) REVERT: L 210 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8161 (t0) outliers start: 66 outliers final: 22 residues processed: 549 average time/residue: 1.1486 time to fit residues: 723.7986 Evaluate side-chains 439 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 407 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 151 CYS Chi-restraints excluded: chain G residue 23 CYS 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 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 210 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 64 optimal weight: 0.2980 chunk 226 optimal weight: 2.9990 chunk 118 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 238 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 192 GLN B 20 GLN B 36 HIS C 20 GLN C 192 GLN D 20 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.060738 restraints weight = 41569.409| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.43 r_work: 0.2554 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21032 Z= 0.173 Angle : 0.760 7.443 28724 Z= 0.390 Chirality : 0.048 0.152 3220 Planarity : 0.006 0.065 3660 Dihedral : 5.750 21.607 2860 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.71 % Allowed : 17.50 % Favored : 79.80 % 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: 0.06 (0.16), residues: 2636 helix: -1.13 (0.44), residues: 148 sheet: 0.66 (0.17), residues: 776 loop : -0.09 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 148 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 0.011 0.001 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 707) hydrogen bonds : angle 6.33710 ( 1935) SS BOND : bond 0.00538 ( 40) SS BOND : angle 1.53953 ( 80) covalent geometry : bond 0.00405 (20992) covalent geometry : angle 0.75694 (28644) *********************** 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 518 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 456 time to evaluate : 2.552 Fit side-chains REVERT: A 145 ASP cc_start: 0.8946 (t0) cc_final: 0.8283 (t0) REVERT: A 149 GLU cc_start: 0.8741 (mp0) cc_final: 0.8185 (mp0) REVERT: A 164 GLU cc_start: 0.8254 (tp30) cc_final: 0.7923 (tm-30) REVERT: B 109 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 145 ASP cc_start: 0.8967 (t0) cc_final: 0.8399 (t0) REVERT: B 149 GLU cc_start: 0.8851 (mp0) cc_final: 0.8278 (mp0) REVERT: B 164 GLU cc_start: 0.8248 (tp30) cc_final: 0.7861 (tm-30) REVERT: C 128 GLU cc_start: 0.9407 (tp30) cc_final: 0.9047 (tp30) REVERT: C 145 ASP cc_start: 0.8971 (t0) cc_final: 0.8439 (t0) REVERT: C 149 GLU cc_start: 0.8787 (mp0) cc_final: 0.8215 (mp0) REVERT: C 164 GLU cc_start: 0.8268 (tp30) cc_final: 0.7886 (tm-30) REVERT: C 171 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8914 (mttt) REVERT: D 109 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8681 (mm-30) REVERT: D 145 ASP cc_start: 0.8912 (t0) cc_final: 0.8373 (t0) REVERT: D 149 GLU cc_start: 0.8810 (mp0) cc_final: 0.8247 (mp0) REVERT: D 164 GLU cc_start: 0.8199 (tp30) cc_final: 0.7856 (tm-30) REVERT: E 18 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8052 (mmt90) REVERT: E 30 ASN cc_start: 0.9190 (t0) cc_final: 0.8671 (t0) REVERT: E 50 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8746 (mp0) REVERT: E 53 ILE cc_start: 0.8991 (mp) cc_final: 0.8688 (mp) REVERT: E 117 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7144 (mp) REVERT: E 139 PHE cc_start: 0.8829 (p90) cc_final: 0.8621 (p90) REVERT: E 142 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.8136 (ttm-80) REVERT: E 148 TRP cc_start: 0.8237 (m100) cc_final: 0.7177 (m100) REVERT: E 158 ASN cc_start: 0.9269 (m110) cc_final: 0.8751 (t0) REVERT: E 210 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8173 (t0) REVERT: F 3 GLN cc_start: 0.8876 (pm20) cc_final: 0.8567 (pm20) REVERT: F 6 GLU cc_start: 0.7091 (mp0) cc_final: 0.6398 (mp0) REVERT: F 51 ILE cc_start: 0.9641 (tt) cc_final: 0.9406 (tp) REVERT: F 72 ASP cc_start: 0.8759 (t0) cc_final: 0.8260 (t0) REVERT: F 76 ASN cc_start: 0.8926 (t0) cc_final: 0.8238 (t0) REVERT: F 105 GLN cc_start: 0.7864 (pm20) cc_final: 0.7235 (pm20) REVERT: F 152 GLU cc_start: 0.8814 (pm20) cc_final: 0.8481 (pm20) REVERT: F 170 PHE cc_start: 0.8828 (m-80) cc_final: 0.8150 (m-80) REVERT: G 18 ARG cc_start: 0.8393 (mmm-85) cc_final: 0.8056 (mmt90) REVERT: G 30 ASN cc_start: 0.9189 (t0) cc_final: 0.8665 (t0) REVERT: G 50 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8733 (mp0) REVERT: G 53 ILE cc_start: 0.8977 (mp) cc_final: 0.8673 (mp) REVERT: G 117 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7291 (mp) REVERT: G 139 PHE cc_start: 0.8806 (p90) cc_final: 0.8586 (p90) REVERT: G 142 ARG cc_start: 0.8667 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: G 148 TRP cc_start: 0.8205 (m100) cc_final: 0.7182 (m100) REVERT: G 158 ASN cc_start: 0.9271 (m110) cc_final: 0.8819 (t0) REVERT: G 210 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8177 (t0) REVERT: H 3 GLN cc_start: 0.8873 (pm20) cc_final: 0.8563 (pm20) REVERT: H 6 GLU cc_start: 0.7194 (mp0) cc_final: 0.6386 (mp0) REVERT: H 51 ILE cc_start: 0.9647 (tt) cc_final: 0.9403 (tp) REVERT: H 72 ASP cc_start: 0.8766 (t0) cc_final: 0.8267 (t0) REVERT: H 76 ASN cc_start: 0.8916 (t0) cc_final: 0.8234 (t0) REVERT: H 105 GLN cc_start: 0.7812 (pm20) cc_final: 0.7297 (pm20) REVERT: H 152 GLU cc_start: 0.8811 (pm20) cc_final: 0.8479 (pm20) REVERT: H 170 PHE cc_start: 0.8961 (m-80) cc_final: 0.8291 (m-80) REVERT: I 30 ASN cc_start: 0.9201 (t0) cc_final: 0.8685 (t0) REVERT: I 50 GLU cc_start: 0.9289 (mt-10) cc_final: 0.8743 (mp0) REVERT: I 53 ILE cc_start: 0.8860 (mp) cc_final: 0.8548 (mp) REVERT: I 117 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7281 (mp) REVERT: I 142 ARG cc_start: 0.9036 (ttm-80) cc_final: 0.8550 (ttm-80) REVERT: I 148 TRP cc_start: 0.8180 (m100) cc_final: 0.7141 (m100) REVERT: I 158 ASN cc_start: 0.9271 (m110) cc_final: 0.8757 (t0) REVERT: I 210 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8241 (t0) REVERT: J 6 GLU cc_start: 0.6968 (mp0) cc_final: 0.6412 (mp0) REVERT: J 51 ILE cc_start: 0.9630 (tt) cc_final: 0.9396 (tp) REVERT: J 72 ASP cc_start: 0.8619 (t0) cc_final: 0.7938 (t0) REVERT: J 76 ASN cc_start: 0.8960 (t0) cc_final: 0.8257 (t0) REVERT: J 105 GLN cc_start: 0.7834 (pm20) cc_final: 0.7194 (pm20) REVERT: J 152 GLU cc_start: 0.8915 (pm20) cc_final: 0.8618 (pm20) REVERT: J 170 PHE cc_start: 0.9121 (m-80) cc_final: 0.8535 (m-80) REVERT: J 180 TYR cc_start: 0.9242 (m-80) cc_final: 0.9011 (m-10) REVERT: K 6 GLU cc_start: 0.6967 (mp0) cc_final: 0.6408 (mp0) REVERT: K 51 ILE cc_start: 0.9640 (tt) cc_final: 0.9404 (tp) REVERT: K 72 ASP cc_start: 0.8633 (t0) cc_final: 0.7926 (t0) REVERT: K 76 ASN cc_start: 0.8948 (t0) cc_final: 0.8240 (t0) REVERT: K 105 GLN cc_start: 0.7826 (pm20) cc_final: 0.7187 (pm20) REVERT: K 152 GLU cc_start: 0.8909 (pm20) cc_final: 0.8605 (pm20) REVERT: K 170 PHE cc_start: 0.9137 (m-80) cc_final: 0.8521 (m-80) REVERT: K 180 TYR cc_start: 0.9245 (m-80) cc_final: 0.9010 (m-10) REVERT: L 30 ASN cc_start: 0.9195 (t0) cc_final: 0.8674 (t0) REVERT: L 50 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8736 (mp0) REVERT: L 53 ILE cc_start: 0.8863 (mp) cc_final: 0.8551 (mp) REVERT: L 117 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7266 (mp) REVERT: L 142 ARG cc_start: 0.8906 (ttm-80) cc_final: 0.8596 (ttm-80) REVERT: L 148 TRP cc_start: 0.8164 (m100) cc_final: 0.7113 (m100) REVERT: L 158 ASN cc_start: 0.9264 (m110) cc_final: 0.8792 (t0) REVERT: L 210 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8236 (t0) outliers start: 62 outliers final: 21 residues processed: 473 average time/residue: 1.0789 time to fit residues: 592.7280 Evaluate side-chains 444 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 414 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 117 ILE Chi-restraints excluded: chain I residue 167 ASP 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 117 ILE Chi-restraints excluded: chain L residue 167 ASP 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: 0.8980 chunk 168 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 82 optimal weight: 0.0980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 221AGLN ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.061458 restraints weight = 42167.041| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.45 r_work: 0.2575 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21032 Z= 0.146 Angle : 0.720 7.894 28724 Z= 0.368 Chirality : 0.047 0.164 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.408 20.342 2860 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.75 % Allowed : 19.02 % Favored : 78.23 % 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: 0.15 (0.16), residues: 2636 helix: -0.24 (0.50), residues: 124 sheet: 0.78 (0.16), residues: 808 loop : -0.17 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 137 HIS 0.006 0.001 HIS B 166 PHE 0.016 0.002 PHE E 139 TYR 0.023 0.002 TYR L 140 ARG 0.006 0.000 ARG L 142 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 707) hydrogen bonds : angle 5.95608 ( 1935) SS BOND : bond 0.00490 ( 40) SS BOND : angle 1.36724 ( 80) covalent geometry : bond 0.00336 (20992) covalent geometry : angle 0.71734 (28644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 476 time to evaluate : 2.815 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: A 145 ASP cc_start: 0.8844 (t0) cc_final: 0.8355 (t0) REVERT: A 149 GLU cc_start: 0.8884 (mp0) cc_final: 0.8478 (mp0) REVERT: A 164 GLU cc_start: 0.8264 (tp30) cc_final: 0.7861 (tm-30) REVERT: A 189 ASP cc_start: 0.9056 (t0) cc_final: 0.8720 (t0) REVERT: A 204 ASN cc_start: 0.9490 (OUTLIER) cc_final: 0.9205 (t160) REVERT: B 109 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8584 (mm-30) REVERT: B 145 ASP cc_start: 0.8800 (t0) cc_final: 0.8254 (t0) REVERT: B 149 GLU cc_start: 0.8925 (mp0) cc_final: 0.8365 (mp0) REVERT: B 164 GLU cc_start: 0.8258 (tp30) cc_final: 0.7901 (tm-30) REVERT: B 204 ASN cc_start: 0.9493 (OUTLIER) cc_final: 0.9210 (t160) REVERT: B 228 TYR cc_start: 0.9588 (m-80) cc_final: 0.9370 (m-80) REVERT: C 128 GLU cc_start: 0.9435 (tp30) cc_final: 0.9050 (tp30) REVERT: C 145 ASP cc_start: 0.8806 (t0) cc_final: 0.8254 (t0) REVERT: C 149 GLU cc_start: 0.8904 (mp0) cc_final: 0.8348 (mp0) REVERT: C 164 GLU cc_start: 0.8316 (tp30) cc_final: 0.7946 (tm-30) REVERT: C 171 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8875 (mttt) REVERT: C 204 ASN cc_start: 0.9486 (OUTLIER) cc_final: 0.9192 (t160) REVERT: D 109 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8665 (mm-30) REVERT: D 145 ASP cc_start: 0.8785 (t0) cc_final: 0.8174 (t0) REVERT: D 149 GLU cc_start: 0.8895 (mp0) cc_final: 0.8280 (mp0) REVERT: D 164 GLU cc_start: 0.8209 (tp30) cc_final: 0.7816 (tm-30) REVERT: D 204 ASN cc_start: 0.9495 (OUTLIER) cc_final: 0.9213 (t160) REVERT: E 18 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8151 (mmt90) REVERT: E 30 ASN cc_start: 0.9163 (t0) cc_final: 0.8693 (t0) REVERT: E 50 GLU cc_start: 0.9270 (mt-10) cc_final: 0.9037 (mp0) REVERT: E 148 TRP cc_start: 0.8182 (m100) cc_final: 0.7178 (m100) REVERT: E 158 ASN cc_start: 0.9235 (m110) cc_final: 0.8604 (t0) REVERT: E 161 GLU cc_start: 0.8796 (mp0) cc_final: 0.8548 (mp0) REVERT: E 210 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8235 (t0) REVERT: F 3 GLN cc_start: 0.8928 (pm20) cc_final: 0.8682 (pm20) REVERT: F 6 GLU cc_start: 0.7128 (mp0) cc_final: 0.6307 (mp0) REVERT: F 51 ILE cc_start: 0.9657 (tt) cc_final: 0.9421 (tp) REVERT: F 72 ASP cc_start: 0.8848 (t0) cc_final: 0.8399 (t0) REVERT: F 76 ASN cc_start: 0.8889 (t0) cc_final: 0.8288 (t0) REVERT: F 105 GLN cc_start: 0.7867 (pm20) cc_final: 0.7260 (pm20) REVERT: F 152 GLU cc_start: 0.8811 (pm20) cc_final: 0.8546 (pm20) REVERT: F 170 PHE cc_start: 0.8808 (m-80) cc_final: 0.8169 (m-80) REVERT: G 18 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8150 (mmt90) REVERT: G 30 ASN cc_start: 0.9163 (t0) cc_final: 0.8694 (t0) REVERT: G 50 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9021 (mp0) REVERT: G 148 TRP cc_start: 0.8142 (m100) cc_final: 0.7181 (m100) REVERT: G 158 ASN cc_start: 0.9228 (m110) cc_final: 0.8585 (t0) REVERT: G 161 GLU cc_start: 0.8830 (mp0) cc_final: 0.8616 (mp0) REVERT: G 210 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8243 (t0) REVERT: H 3 GLN cc_start: 0.8926 (pm20) cc_final: 0.8679 (pm20) REVERT: H 6 GLU cc_start: 0.7213 (mp0) cc_final: 0.6215 (mp0) REVERT: H 51 ILE cc_start: 0.9660 (tt) cc_final: 0.9417 (tp) REVERT: H 72 ASP cc_start: 0.8852 (t0) cc_final: 0.8401 (t0) REVERT: H 76 ASN cc_start: 0.8884 (t0) cc_final: 0.8280 (t0) REVERT: H 105 GLN cc_start: 0.7773 (pm20) cc_final: 0.7215 (pm20) REVERT: H 152 GLU cc_start: 0.8817 (pm20) cc_final: 0.8554 (pm20) REVERT: H 170 PHE cc_start: 0.8974 (m-80) cc_final: 0.8288 (m-80) REVERT: I 18 ARG cc_start: 0.8205 (mmm-85) cc_final: 0.7878 (mmt90) REVERT: I 30 ASN cc_start: 0.9206 (t0) cc_final: 0.8755 (t0) REVERT: I 50 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8730 (mp0) REVERT: I 53 ILE cc_start: 0.8902 (mp) cc_final: 0.8632 (mp) REVERT: I 142 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8254 (ttm-80) REVERT: I 148 TRP cc_start: 0.8180 (m100) cc_final: 0.7212 (m100) REVERT: I 158 ASN cc_start: 0.9222 (m110) cc_final: 0.8650 (t0) REVERT: I 161 GLU cc_start: 0.8861 (mp0) cc_final: 0.8614 (mp0) REVERT: I 210 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8397 (t0) REVERT: J 6 GLU cc_start: 0.6975 (mp0) cc_final: 0.6246 (mp0) REVERT: J 51 ILE cc_start: 0.9657 (tt) cc_final: 0.9418 (tp) REVERT: J 72 ASP cc_start: 0.8714 (t0) cc_final: 0.8062 (t0) REVERT: J 76 ASN cc_start: 0.8945 (t0) cc_final: 0.8354 (t0) REVERT: J 105 GLN cc_start: 0.7884 (pm20) cc_final: 0.7286 (pm20) REVERT: J 152 GLU cc_start: 0.8830 (pm20) cc_final: 0.8358 (pm20) REVERT: J 170 PHE cc_start: 0.9131 (m-80) cc_final: 0.8561 (m-80) REVERT: J 201 ASN cc_start: 0.8846 (t0) cc_final: 0.8037 (m110) REVERT: K 6 GLU cc_start: 0.6974 (mp0) cc_final: 0.6198 (mp0) REVERT: K 51 ILE cc_start: 0.9663 (tt) cc_final: 0.9421 (tp) REVERT: K 72 ASP cc_start: 0.8703 (t0) cc_final: 0.8045 (t0) REVERT: K 76 ASN cc_start: 0.8945 (t0) cc_final: 0.8354 (t0) REVERT: K 105 GLN cc_start: 0.7879 (pm20) cc_final: 0.7222 (pm20) REVERT: K 152 GLU cc_start: 0.8839 (pm20) cc_final: 0.8387 (pm20) REVERT: K 170 PHE cc_start: 0.9155 (m-80) cc_final: 0.8559 (m-80) REVERT: K 201 ASN cc_start: 0.8808 (t0) cc_final: 0.8011 (m110) REVERT: L 18 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7903 (mmt90) REVERT: L 30 ASN cc_start: 0.9193 (t0) cc_final: 0.8731 (t0) REVERT: L 50 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8722 (mp0) REVERT: L 53 ILE cc_start: 0.8900 (mp) cc_final: 0.8634 (mp) REVERT: L 142 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8340 (tpp80) REVERT: L 148 TRP cc_start: 0.8108 (m100) cc_final: 0.7092 (m100) REVERT: L 158 ASN cc_start: 0.9229 (m110) cc_final: 0.8619 (t0) REVERT: L 161 GLU cc_start: 0.8847 (mp0) cc_final: 0.8637 (mp0) REVERT: L 210 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8399 (t0) outliers start: 63 outliers final: 27 residues processed: 504 average time/residue: 1.1574 time to fit residues: 686.6376 Evaluate side-chains 478 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 442 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 210 ASN Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain 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: 4.9990 chunk 2 optimal weight: 1.9990 chunk 259 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3527 r_free = 0.3527 target = 0.100364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.060803 restraints weight = 42145.044| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.45 r_work: 0.2564 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21032 Z= 0.162 Angle : 0.695 8.036 28724 Z= 0.357 Chirality : 0.046 0.165 3220 Planarity : 0.006 0.063 3660 Dihedral : 5.211 19.621 2860 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.01 % Allowed : 20.29 % Favored : 76.70 % 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: 0.11 (0.16), residues: 2636 helix: -0.05 (0.50), residues: 124 sheet: 0.76 (0.16), residues: 836 loop : -0.24 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.005 0.001 HIS D 166 PHE 0.022 0.002 PHE I 139 TYR 0.025 0.002 TYR L 140 ARG 0.006 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 707) hydrogen bonds : angle 5.83266 ( 1935) SS BOND : bond 0.00485 ( 40) SS BOND : angle 1.20873 ( 80) covalent geometry : bond 0.00377 (20992) covalent geometry : angle 0.69257 (28644) *********************** 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 521 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 452 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8941 (mp0) cc_final: 0.8732 (mp0) REVERT: A 164 GLU cc_start: 0.8361 (tp30) cc_final: 0.7948 (tm-30) REVERT: A 204 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.9199 (t160) REVERT: B 109 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8569 (mm-30) REVERT: B 145 ASP cc_start: 0.8773 (t0) cc_final: 0.8209 (t0) REVERT: B 149 GLU cc_start: 0.8968 (mp0) cc_final: 0.8352 (mp0) REVERT: B 164 GLU cc_start: 0.8319 (tp30) cc_final: 0.7946 (tm-30) REVERT: B 204 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.9204 (t160) REVERT: C 128 GLU cc_start: 0.9425 (tp30) cc_final: 0.9060 (tp30) REVERT: C 145 ASP cc_start: 0.8776 (t0) cc_final: 0.8359 (t0) REVERT: C 149 GLU cc_start: 0.8934 (mp0) cc_final: 0.8635 (mm-30) REVERT: C 164 GLU cc_start: 0.8375 (tp30) cc_final: 0.7930 (tm-30) REVERT: C 171 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8915 (mttt) REVERT: C 204 ASN cc_start: 0.9497 (OUTLIER) cc_final: 0.9188 (t160) REVERT: D 109 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8653 (mm-30) REVERT: D 145 ASP cc_start: 0.8738 (t0) cc_final: 0.8141 (t0) REVERT: D 149 GLU cc_start: 0.8939 (mp0) cc_final: 0.8278 (mp0) REVERT: D 164 GLU cc_start: 0.8312 (tp30) cc_final: 0.7973 (tm-30) REVERT: D 204 ASN cc_start: 0.9506 (OUTLIER) cc_final: 0.9206 (t160) REVERT: E 18 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8167 (mmt90) REVERT: E 30 ASN cc_start: 0.9185 (t0) cc_final: 0.8750 (t0) REVERT: E 50 GLU cc_start: 0.9248 (mt-10) cc_final: 0.9017 (mp0) REVERT: E 148 TRP cc_start: 0.8135 (m100) cc_final: 0.7207 (m100) REVERT: E 158 ASN cc_start: 0.9249 (m110) cc_final: 0.8659 (t0) REVERT: E 210 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8337 (t0) REVERT: F 3 GLN cc_start: 0.9013 (pm20) cc_final: 0.8522 (pm20) REVERT: F 6 GLU cc_start: 0.7150 (mp0) cc_final: 0.6254 (mp0) REVERT: F 51 ILE cc_start: 0.9686 (tt) cc_final: 0.9434 (tp) REVERT: F 72 ASP cc_start: 0.8876 (t0) cc_final: 0.8439 (t0) REVERT: F 76 ASN cc_start: 0.8911 (t0) cc_final: 0.8345 (t0) REVERT: F 105 GLN cc_start: 0.7891 (pm20) cc_final: 0.7258 (pm20) REVERT: F 152 GLU cc_start: 0.8908 (pm20) cc_final: 0.8619 (pm20) REVERT: F 170 PHE cc_start: 0.8834 (m-80) cc_final: 0.8219 (m-80) REVERT: G 18 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8174 (mmt90) REVERT: G 30 ASN cc_start: 0.9189 (t0) cc_final: 0.8754 (t0) REVERT: G 50 GLU cc_start: 0.9250 (mt-10) cc_final: 0.9019 (mp0) REVERT: G 148 TRP cc_start: 0.8111 (m100) cc_final: 0.7209 (m100) REVERT: G 158 ASN cc_start: 0.9237 (m110) cc_final: 0.8653 (t0) REVERT: G 210 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8365 (t0) REVERT: H 3 GLN cc_start: 0.9015 (pm20) cc_final: 0.8533 (pm20) REVERT: H 6 GLU cc_start: 0.7228 (mp0) cc_final: 0.6021 (mp0) REVERT: H 51 ILE cc_start: 0.9688 (tt) cc_final: 0.9431 (tp) REVERT: H 72 ASP cc_start: 0.8879 (t0) cc_final: 0.8438 (t0) REVERT: H 76 ASN cc_start: 0.8912 (t0) cc_final: 0.8334 (t0) REVERT: H 105 GLN cc_start: 0.7775 (pm20) cc_final: 0.7232 (pm20) REVERT: H 152 GLU cc_start: 0.8910 (pm20) cc_final: 0.8612 (pm20) REVERT: H 170 PHE cc_start: 0.9013 (m-80) cc_final: 0.8343 (m-80) REVERT: I 18 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7937 (mmt90) REVERT: I 30 ASN cc_start: 0.9203 (t0) cc_final: 0.8777 (t0) REVERT: I 50 GLU cc_start: 0.9251 (mt-10) cc_final: 0.9011 (mp0) REVERT: I 142 ARG cc_start: 0.8900 (ttm-80) cc_final: 0.8494 (ttm-80) REVERT: I 148 TRP cc_start: 0.8119 (m100) cc_final: 0.7251 (m100) REVERT: I 158 ASN cc_start: 0.9230 (m110) cc_final: 0.8624 (t0) REVERT: I 210 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8492 (t0) REVERT: J 6 GLU cc_start: 0.6984 (mp0) cc_final: 0.6375 (mp0) REVERT: J 27 PHE cc_start: 0.8418 (m-80) cc_final: 0.6628 (m-80) REVERT: J 51 ILE cc_start: 0.9681 (tt) cc_final: 0.9447 (tp) REVERT: J 76 ASN cc_start: 0.8935 (t0) cc_final: 0.8388 (t0) REVERT: J 105 GLN cc_start: 0.7917 (pm20) cc_final: 0.7214 (pm20) REVERT: J 152 GLU cc_start: 0.8971 (pm20) cc_final: 0.8593 (pm20) REVERT: J 170 PHE cc_start: 0.9160 (m-80) cc_final: 0.8625 (m-80) REVERT: J 201 ASN cc_start: 0.9027 (t0) cc_final: 0.8260 (m110) REVERT: K 6 GLU cc_start: 0.6968 (mp0) cc_final: 0.6281 (mp0) REVERT: K 27 PHE cc_start: 0.8417 (m-80) cc_final: 0.6643 (m-80) REVERT: K 51 ILE cc_start: 0.9690 (tt) cc_final: 0.9458 (tp) REVERT: K 76 ASN cc_start: 0.8940 (t0) cc_final: 0.8397 (t0) REVERT: K 105 GLN cc_start: 0.7897 (pm20) cc_final: 0.7232 (pm20) REVERT: K 152 GLU cc_start: 0.8967 (pm20) cc_final: 0.8575 (pm20) REVERT: K 170 PHE cc_start: 0.9165 (m-80) cc_final: 0.8597 (m-80) REVERT: K 201 ASN cc_start: 0.8989 (t0) cc_final: 0.8233 (m110) REVERT: L 18 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8027 (mmt90) REVERT: L 30 ASN cc_start: 0.9198 (t0) cc_final: 0.8767 (t0) REVERT: L 50 GLU cc_start: 0.9260 (mt-10) cc_final: 0.9022 (mp0) REVERT: L 142 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8345 (ttm-80) REVERT: L 148 TRP cc_start: 0.8187 (m100) cc_final: 0.7294 (m100) REVERT: L 158 ASN cc_start: 0.9218 (m110) cc_final: 0.8612 (t0) outliers start: 69 outliers final: 31 residues processed: 486 average time/residue: 1.5609 time to fit residues: 883.4317 Evaluate side-chains 468 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 429 time to evaluate : 3.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 134 MET 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 171 LYS Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 204 ASN 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 178 THR Chi-restraints excluded: chain E residue 210 ASN 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 G residue 210 ASN 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 75 ILE Chi-restraints excluded: chain I residue 210 ASN Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 20 LEU 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 2 VAL Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 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: 0.9990 chunk 71 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 143 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.100949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.061631 restraints weight = 41843.184| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.40 r_work: 0.2579 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21032 Z= 0.142 Angle : 0.702 8.877 28724 Z= 0.360 Chirality : 0.046 0.171 3220 Planarity : 0.005 0.063 3660 Dihedral : 5.074 17.914 2860 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.53 % Allowed : 21.38 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.50), residues: 128 sheet: 0.84 (0.16), residues: 816 loop : -0.15 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 137 HIS 0.005 0.001 HIS A 166 PHE 0.022 0.002 PHE L 139 TYR 0.025 0.002 TYR I 140 ARG 0.016 0.001 ARG J 26 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 707) hydrogen bonds : angle 5.66564 ( 1935) SS BOND : bond 0.00434 ( 40) SS BOND : angle 1.09933 ( 80) covalent geometry : bond 0.00335 (20992) covalent geometry : angle 0.70086 (28644) *********************** 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 561 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 480 time to evaluate : 3.442 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: A 149 GLU cc_start: 0.8954 (mp0) cc_final: 0.8737 (mp0) REVERT: A 164 GLU cc_start: 0.8381 (tp30) cc_final: 0.7945 (tm-30) REVERT: A 189 ASP cc_start: 0.8989 (t0) cc_final: 0.8706 (t0) REVERT: A 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9167 (t160) REVERT: B 109 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8607 (mm-30) REVERT: B 145 ASP cc_start: 0.8726 (t0) cc_final: 0.8151 (t0) REVERT: B 149 GLU cc_start: 0.8983 (mp0) cc_final: 0.8350 (mp0) REVERT: B 164 GLU cc_start: 0.8322 (tp30) cc_final: 0.7942 (tm-30) REVERT: B 204 ASN cc_start: 0.9484 (OUTLIER) cc_final: 0.9170 (t160) REVERT: C 145 ASP cc_start: 0.8725 (t0) cc_final: 0.8126 (t0) REVERT: C 149 GLU cc_start: 0.8941 (mp0) cc_final: 0.8263 (mp0) REVERT: C 164 GLU cc_start: 0.8406 (tp30) cc_final: 0.7982 (tm-30) REVERT: C 171 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8918 (mttt) REVERT: C 204 ASN cc_start: 0.9493 (OUTLIER) cc_final: 0.9171 (t160) REVERT: D 70 GLU cc_start: 0.8545 (pt0) cc_final: 0.8326 (pp20) REVERT: D 109 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8697 (mm-30) REVERT: D 145 ASP cc_start: 0.8693 (t0) cc_final: 0.8081 (t0) REVERT: D 149 GLU cc_start: 0.8968 (mp0) cc_final: 0.8278 (mp0) REVERT: D 164 GLU cc_start: 0.8305 (tp30) cc_final: 0.7917 (tm-30) REVERT: D 204 ASN cc_start: 0.9481 (OUTLIER) cc_final: 0.9166 (t160) REVERT: E 18 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8173 (mmt90) REVERT: E 30 ASN cc_start: 0.9164 (t0) cc_final: 0.8765 (t0) REVERT: E 50 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9030 (mp0) REVERT: E 125 LEU cc_start: 0.9557 (pp) cc_final: 0.9236 (mm) REVERT: E 140 TYR cc_start: 0.8522 (t80) cc_final: 0.8282 (t80) REVERT: E 142 ARG cc_start: 0.8963 (ttm-80) cc_final: 0.8385 (ttm-80) REVERT: E 148 TRP cc_start: 0.8128 (m100) cc_final: 0.7074 (m100) REVERT: E 158 ASN cc_start: 0.9235 (m110) cc_final: 0.8638 (t0) REVERT: E 161 GLU cc_start: 0.8753 (mp0) cc_final: 0.8455 (mp0) REVERT: E 211 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7092 (ptm160) REVERT: F 3 GLN cc_start: 0.8907 (pm20) cc_final: 0.8270 (pm20) REVERT: F 6 GLU cc_start: 0.7072 (mp0) cc_final: 0.6157 (mp0) REVERT: F 27 PHE cc_start: 0.8355 (m-80) cc_final: 0.6897 (m-80) REVERT: F 35 THR cc_start: 0.9575 (OUTLIER) cc_final: 0.9312 (t) REVERT: F 51 ILE cc_start: 0.9689 (tt) cc_final: 0.9460 (tp) REVERT: F 72 ASP cc_start: 0.8897 (t0) cc_final: 0.8458 (t0) REVERT: F 76 ASN cc_start: 0.8920 (t0) cc_final: 0.8366 (t0) REVERT: F 105 GLN cc_start: 0.7854 (pm20) cc_final: 0.7221 (pm20) REVERT: F 152 GLU cc_start: 0.8896 (pm20) cc_final: 0.8603 (pm20) REVERT: F 170 PHE cc_start: 0.8832 (m-80) cc_final: 0.8256 (m-80) REVERT: F 216 GLU cc_start: 0.8688 (pp20) cc_final: 0.7688 (pm20) REVERT: G 18 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8175 (mmt90) REVERT: G 30 ASN cc_start: 0.9168 (t0) cc_final: 0.8769 (t0) REVERT: G 50 GLU cc_start: 0.9275 (mt-10) cc_final: 0.9028 (mp0) REVERT: G 125 LEU cc_start: 0.9558 (pp) cc_final: 0.9237 (mm) REVERT: G 148 TRP cc_start: 0.8127 (m100) cc_final: 0.7143 (m100) REVERT: G 158 ASN cc_start: 0.9250 (m110) cc_final: 0.8692 (t0) REVERT: G 161 GLU cc_start: 0.8817 (mp0) cc_final: 0.8549 (mp0) REVERT: H 3 GLN cc_start: 0.9007 (pm20) cc_final: 0.8239 (pm20) REVERT: H 27 PHE cc_start: 0.8354 (m-80) cc_final: 0.7492 (m-80) REVERT: H 35 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9311 (t) REVERT: H 51 ILE cc_start: 0.9691 (OUTLIER) cc_final: 0.9461 (tp) REVERT: H 72 ASP cc_start: 0.8893 (t0) cc_final: 0.8450 (t0) REVERT: H 76 ASN cc_start: 0.8922 (t0) cc_final: 0.8373 (t0) REVERT: H 152 GLU cc_start: 0.8910 (pm20) cc_final: 0.8595 (pm20) REVERT: H 170 PHE cc_start: 0.9033 (m-80) cc_final: 0.8392 (m-80) REVERT: I 18 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8167 (mmt90) REVERT: I 30 ASN cc_start: 0.9178 (t0) cc_final: 0.8789 (t0) REVERT: I 50 GLU cc_start: 0.9260 (mt-10) cc_final: 0.9027 (mp0) REVERT: I 125 LEU cc_start: 0.9557 (pp) cc_final: 0.9234 (mm) REVERT: I 142 ARG cc_start: 0.8884 (ttm-80) cc_final: 0.8677 (ttm-80) REVERT: I 148 TRP cc_start: 0.8096 (m100) cc_final: 0.7193 (m100) REVERT: I 158 ASN cc_start: 0.9222 (m110) cc_final: 0.8569 (t0) REVERT: I 161 GLU cc_start: 0.8763 (mp0) cc_final: 0.8476 (mp0) REVERT: J 6 GLU cc_start: 0.6967 (mp0) cc_final: 0.6267 (mp0) REVERT: J 51 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9444 (tp) REVERT: J 76 ASN cc_start: 0.8906 (t0) cc_final: 0.8406 (t0) REVERT: J 105 GLN cc_start: 0.7927 (pm20) cc_final: 0.7290 (pm20) REVERT: J 152 GLU cc_start: 0.8991 (pm20) cc_final: 0.8666 (pm20) REVERT: J 170 PHE cc_start: 0.9147 (m-80) cc_final: 0.8647 (m-80) REVERT: J 201 ASN cc_start: 0.9085 (t0) cc_final: 0.8354 (m110) REVERT: K 6 GLU cc_start: 0.6959 (mp0) cc_final: 0.6278 (mp0) REVERT: K 51 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9467 (tp) REVERT: K 76 ASN cc_start: 0.8890 (t0) cc_final: 0.8400 (t0) REVERT: K 105 GLN cc_start: 0.7885 (pm20) cc_final: 0.7250 (pm20) REVERT: K 152 GLU cc_start: 0.8986 (pm20) cc_final: 0.8674 (pm20) REVERT: K 170 PHE cc_start: 0.9160 (m-80) cc_final: 0.8632 (m-80) REVERT: K 201 ASN cc_start: 0.9084 (t0) cc_final: 0.8357 (m110) REVERT: L 18 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8156 (mmt90) REVERT: L 30 ASN cc_start: 0.9182 (t0) cc_final: 0.8787 (t0) REVERT: L 50 GLU cc_start: 0.9257 (mt-10) cc_final: 0.9027 (mp0) REVERT: L 125 LEU cc_start: 0.9557 (pp) cc_final: 0.9233 (mm) REVERT: L 142 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8304 (tpp80) REVERT: L 148 TRP cc_start: 0.8112 (m100) cc_final: 0.7161 (m100) REVERT: L 158 ASN cc_start: 0.9212 (m110) cc_final: 0.8606 (t0) REVERT: L 161 GLU cc_start: 0.8757 (mp0) cc_final: 0.8480 (mp0) outliers start: 81 outliers final: 50 residues processed: 527 average time/residue: 1.6787 time to fit residues: 1036.0905 Evaluate side-chains 492 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 432 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain C residue 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 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 12 VAL Chi-restraints excluded: chain F residue 35 THR 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 12 VAL Chi-restraints excluded: chain H residue 35 THR 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 I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 20 LEU 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 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 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 117 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 2 optimal weight: 0.8980 chunk 255 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 259 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN ** H 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.100083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.060997 restraints weight = 41825.375| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.39 r_work: 0.2564 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21032 Z= 0.172 Angle : 0.725 9.154 28724 Z= 0.371 Chirality : 0.047 0.243 3220 Planarity : 0.006 0.067 3660 Dihedral : 5.031 18.224 2860 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.40 % Allowed : 23.04 % Favored : 73.56 % 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: 0.18 (0.16), residues: 2636 helix: -0.11 (0.50), residues: 128 sheet: 0.86 (0.16), residues: 832 loop : -0.21 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 141 HIS 0.005 0.001 HIS C 166 PHE 0.024 0.002 PHE E 139 TYR 0.024 0.002 TYR L 140 ARG 0.020 0.001 ARG H 26 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 707) hydrogen bonds : angle 5.66729 ( 1935) SS BOND : bond 0.00477 ( 40) SS BOND : angle 1.08782 ( 80) covalent geometry : bond 0.00405 (20992) covalent geometry : angle 0.72393 (28644) *********************** 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 522 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 444 time to evaluate : 2.467 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: A 128 GLU cc_start: 0.9400 (tp30) cc_final: 0.9058 (tp30) REVERT: A 145 ASP cc_start: 0.8760 (t0) cc_final: 0.8278 (t0) REVERT: A 149 GLU cc_start: 0.8952 (mp0) cc_final: 0.8511 (mp0) REVERT: A 164 GLU cc_start: 0.8418 (tp30) cc_final: 0.8010 (tm-30) REVERT: A 204 ASN cc_start: 0.9489 (OUTLIER) cc_final: 0.9172 (t160) REVERT: B 109 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8590 (mm-30) REVERT: B 128 GLU cc_start: 0.9421 (tp30) cc_final: 0.9081 (tp30) REVERT: B 145 ASP cc_start: 0.8743 (t0) cc_final: 0.8180 (t0) REVERT: B 149 GLU cc_start: 0.8981 (mp0) cc_final: 0.8363 (mp0) REVERT: B 164 GLU cc_start: 0.8365 (tp30) cc_final: 0.7961 (tm-30) REVERT: B 204 ASN cc_start: 0.9495 (OUTLIER) cc_final: 0.9181 (t160) REVERT: C 128 GLU cc_start: 0.9392 (tp30) cc_final: 0.9096 (tp30) REVERT: C 145 ASP cc_start: 0.8728 (t0) cc_final: 0.8145 (t0) REVERT: C 149 GLU cc_start: 0.8953 (mp0) cc_final: 0.8302 (mp0) REVERT: C 164 GLU cc_start: 0.8442 (tp30) cc_final: 0.8014 (tm-30) REVERT: C 171 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8954 (mttt) REVERT: C 204 ASN cc_start: 0.9509 (OUTLIER) cc_final: 0.9189 (t160) REVERT: D 109 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8693 (mm-30) REVERT: D 128 GLU cc_start: 0.9401 (tp30) cc_final: 0.9062 (tp30) REVERT: D 145 ASP cc_start: 0.8707 (t0) cc_final: 0.8112 (t0) REVERT: D 149 GLU cc_start: 0.8965 (mp0) cc_final: 0.8289 (mp0) REVERT: D 164 GLU cc_start: 0.8333 (tp30) cc_final: 0.7901 (tm-30) REVERT: D 204 ASN cc_start: 0.9499 (OUTLIER) cc_final: 0.9186 (t160) REVERT: E 18 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8214 (mmt90) REVERT: E 30 ASN cc_start: 0.9176 (t0) cc_final: 0.8768 (t0) REVERT: E 50 GLU cc_start: 0.9292 (mt-10) cc_final: 0.9061 (mp0) REVERT: E 108 ARG cc_start: 0.5466 (OUTLIER) cc_final: 0.5232 (tmm-80) REVERT: E 142 ARG cc_start: 0.8918 (ttm-80) cc_final: 0.8559 (ttm110) REVERT: E 148 TRP cc_start: 0.8142 (m100) cc_final: 0.7134 (m100) REVERT: E 158 ASN cc_start: 0.9226 (m110) cc_final: 0.8649 (t0) REVERT: E 161 GLU cc_start: 0.8720 (mp0) cc_final: 0.8503 (mp0) REVERT: E 211 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.6971 (ptm160) REVERT: F 3 GLN cc_start: 0.8903 (pm20) cc_final: 0.8330 (pm20) REVERT: F 6 GLU cc_start: 0.7131 (mp0) cc_final: 0.6209 (mp0) REVERT: F 51 ILE cc_start: 0.9704 (OUTLIER) cc_final: 0.9477 (tp) REVERT: F 72 ASP cc_start: 0.8906 (t0) cc_final: 0.8488 (t0) REVERT: F 76 ASN cc_start: 0.8914 (t0) cc_final: 0.8403 (t0) REVERT: F 105 GLN cc_start: 0.7862 (pm20) cc_final: 0.7213 (pm20) REVERT: F 152 GLU cc_start: 0.8952 (pm20) cc_final: 0.8653 (pm20) REVERT: F 170 PHE cc_start: 0.8806 (m-80) cc_final: 0.8488 (m-80) REVERT: G 18 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8187 (mmt90) REVERT: G 30 ASN cc_start: 0.9184 (t0) cc_final: 0.8776 (t0) REVERT: G 50 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9059 (mp0) REVERT: G 105 GLU cc_start: 0.8679 (tp30) cc_final: 0.8056 (mp0) REVERT: G 142 ARG cc_start: 0.8826 (ttm110) cc_final: 0.8205 (tpp80) REVERT: G 148 TRP cc_start: 0.8112 (m100) cc_final: 0.7167 (m100) REVERT: G 158 ASN cc_start: 0.9227 (m110) cc_final: 0.8616 (t0) REVERT: G 161 GLU cc_start: 0.8763 (mp0) cc_final: 0.8550 (mp0) REVERT: G 211 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7000 (ptm160) REVERT: H 3 GLN cc_start: 0.8841 (pm20) cc_final: 0.7948 (pm20) REVERT: H 6 GLU cc_start: 0.7521 (mp0) cc_final: 0.6374 (mp0) REVERT: H 26 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8579 (ptp-110) REVERT: H 51 ILE cc_start: 0.9698 (tt) cc_final: 0.9465 (tp) REVERT: H 72 ASP cc_start: 0.8920 (t0) cc_final: 0.8481 (t0) REVERT: H 76 ASN cc_start: 0.8942 (t0) cc_final: 0.8378 (t0) REVERT: H 152 GLU cc_start: 0.8963 (pm20) cc_final: 0.8657 (pm20) REVERT: H 170 PHE cc_start: 0.8961 (m-80) cc_final: 0.8334 (m-80) REVERT: I 18 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8226 (mmt90) REVERT: I 30 ASN cc_start: 0.9179 (t0) cc_final: 0.8787 (t0) REVERT: I 50 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9064 (mp0) REVERT: I 125 LEU cc_start: 0.9525 (pp) cc_final: 0.9238 (mm) REVERT: I 148 TRP cc_start: 0.8123 (m100) cc_final: 0.7251 (m100) REVERT: I 158 ASN cc_start: 0.9207 (m110) cc_final: 0.8637 (t0) REVERT: I 161 GLU cc_start: 0.8748 (mp0) cc_final: 0.8541 (mp0) REVERT: J 6 GLU cc_start: 0.7062 (mp0) cc_final: 0.6341 (mp0) REVERT: J 51 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9462 (tp) REVERT: J 76 ASN cc_start: 0.8923 (t0) cc_final: 0.8475 (t0) REVERT: J 77 GLN cc_start: 0.9014 (pt0) cc_final: 0.8126 (pp30) REVERT: J 105 GLN cc_start: 0.7896 (pm20) cc_final: 0.7289 (pm20) REVERT: J 152 GLU cc_start: 0.9021 (pm20) cc_final: 0.8675 (pm20) REVERT: J 170 PHE cc_start: 0.9126 (m-80) cc_final: 0.8615 (m-80) REVERT: J 201 ASN cc_start: 0.9123 (t0) cc_final: 0.8418 (m110) REVERT: K 6 GLU cc_start: 0.7055 (mp0) cc_final: 0.6319 (mp0) REVERT: K 51 ILE cc_start: 0.9703 (OUTLIER) cc_final: 0.9470 (tp) REVERT: K 76 ASN cc_start: 0.8920 (t0) cc_final: 0.8475 (t0) REVERT: K 77 GLN cc_start: 0.9000 (pt0) cc_final: 0.8098 (pp30) REVERT: K 105 GLN cc_start: 0.7866 (pm20) cc_final: 0.7217 (pm20) REVERT: K 152 GLU cc_start: 0.9051 (pm20) cc_final: 0.8657 (pm20) REVERT: K 170 PHE cc_start: 0.9144 (m-80) cc_final: 0.8592 (m-80) REVERT: K 201 ASN cc_start: 0.9123 (t0) cc_final: 0.8421 (m110) REVERT: L 18 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8224 (mmt90) REVERT: L 30 ASN cc_start: 0.9191 (t0) cc_final: 0.8791 (t0) REVERT: L 50 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9069 (mp0) REVERT: L 125 LEU cc_start: 0.9525 (pp) cc_final: 0.9237 (mm) REVERT: L 142 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8388 (tpp80) REVERT: L 148 TRP cc_start: 0.8122 (m100) cc_final: 0.7191 (m100) REVERT: L 158 ASN cc_start: 0.9214 (m110) cc_final: 0.8639 (t0) REVERT: L 161 GLU cc_start: 0.8751 (mp0) cc_final: 0.8548 (mp0) REVERT: L 211 ARG cc_start: 0.7251 (ttp-170) cc_final: 0.6493 (ptm160) outliers start: 78 outliers final: 52 residues processed: 484 average time/residue: 1.2180 time to fit residues: 681.7639 Evaluate side-chains 490 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 2.603 ------------------------------------------------------------------------------- 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 134 MET 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 C residue 204 ASN 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 108 ARG 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 110 THR Chi-restraints excluded: chain H residue 148 ASP Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 20 LEU 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 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 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 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: 0.5980 chunk 52 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 50 GLN F 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.100774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.061559 restraints weight = 42034.995| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.47 r_work: 0.2579 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21032 Z= 0.147 Angle : 0.720 8.967 28724 Z= 0.368 Chirality : 0.047 0.175 3220 Planarity : 0.006 0.063 3660 Dihedral : 4.933 19.027 2860 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.49 % Allowed : 23.12 % Favored : 73.39 % 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: 0.24 (0.16), residues: 2636 helix: -0.07 (0.50), residues: 128 sheet: 0.98 (0.17), residues: 832 loop : -0.22 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.005 0.001 HIS C 166 PHE 0.024 0.001 PHE L 139 TYR 0.027 0.002 TYR D 75 ARG 0.018 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 707) hydrogen bonds : angle 5.58016 ( 1935) SS BOND : bond 0.00445 ( 40) SS BOND : angle 1.21394 ( 80) covalent geometry : bond 0.00348 (20992) covalent geometry : angle 0.71834 (28644) *********************** 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 525 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 445 time to evaluate : 2.793 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: 0.8722 (t0) cc_final: 0.8188 (t0) REVERT: A 149 GLU cc_start: 0.8969 (mp0) cc_final: 0.8443 (mp0) REVERT: A 164 GLU cc_start: 0.8413 (tp30) cc_final: 0.8011 (tm-30) REVERT: A 204 ASN cc_start: 0.9488 (OUTLIER) cc_final: 0.9176 (t160) REVERT: B 70 GLU cc_start: 0.8322 (pp20) cc_final: 0.8052 (pp20) REVERT: B 109 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8604 (mm-30) REVERT: B 145 ASP cc_start: 0.8697 (t0) cc_final: 0.8112 (t0) REVERT: B 149 GLU cc_start: 0.8971 (mp0) cc_final: 0.8352 (mp0) REVERT: B 164 GLU cc_start: 0.8316 (tp30) cc_final: 0.7894 (tm-30) REVERT: B 204 ASN cc_start: 0.9491 (OUTLIER) cc_final: 0.9182 (t160) REVERT: C 128 GLU cc_start: 0.9420 (tp30) cc_final: 0.9110 (tp30) REVERT: C 145 ASP cc_start: 0.8692 (t0) cc_final: 0.8086 (t0) REVERT: C 149 GLU cc_start: 0.8956 (mp0) cc_final: 0.8298 (mp0) REVERT: C 164 GLU cc_start: 0.8437 (tp30) cc_final: 0.8015 (tm-30) REVERT: C 171 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8934 (mttt) REVERT: C 204 ASN cc_start: 0.9496 (OUTLIER) cc_final: 0.9166 (t160) REVERT: D 109 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8712 (mm-30) REVERT: D 145 ASP cc_start: 0.8684 (t0) cc_final: 0.8051 (t0) REVERT: D 149 GLU cc_start: 0.8947 (mp0) cc_final: 0.8282 (mp0) REVERT: D 164 GLU cc_start: 0.8337 (tp30) cc_final: 0.7876 (tm-30) REVERT: D 204 ASN cc_start: 0.9493 (OUTLIER) cc_final: 0.9185 (t160) REVERT: E 11 LEU cc_start: 0.9309 (pp) cc_final: 0.8716 (pp) REVERT: E 18 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8216 (mmt90) REVERT: E 30 ASN cc_start: 0.9167 (t0) cc_final: 0.8781 (t0) REVERT: E 50 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9095 (mt-10) REVERT: E 105 GLU cc_start: 0.8571 (tp30) cc_final: 0.8076 (mp0) REVERT: E 108 ARG cc_start: 0.5543 (OUTLIER) cc_final: 0.5342 (tmm-80) REVERT: E 125 LEU cc_start: 0.9558 (pp) cc_final: 0.9229 (mm) REVERT: E 142 ARG cc_start: 0.8907 (ttm-80) cc_final: 0.8372 (tpp80) REVERT: E 148 TRP cc_start: 0.8099 (m100) cc_final: 0.7153 (m100) REVERT: E 158 ASN cc_start: 0.9226 (m110) cc_final: 0.8640 (t0) REVERT: E 211 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.6901 (ptm160) REVERT: F 3 GLN cc_start: 0.8902 (pm20) cc_final: 0.8310 (pm20) REVERT: F 6 GLU cc_start: 0.7072 (mp0) cc_final: 0.6185 (mp0) REVERT: F 51 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9464 (tp) REVERT: F 72 ASP cc_start: 0.8913 (t0) cc_final: 0.8509 (t0) REVERT: F 76 ASN cc_start: 0.8895 (t0) cc_final: 0.8464 (t0) REVERT: F 105 GLN cc_start: 0.7835 (pm20) cc_final: 0.7167 (pm20) REVERT: F 152 GLU cc_start: 0.8949 (pm20) cc_final: 0.8638 (pm20) REVERT: F 170 PHE cc_start: 0.8769 (m-80) cc_final: 0.8443 (m-80) REVERT: G 18 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8177 (mmt90) REVERT: G 30 ASN cc_start: 0.9178 (t0) cc_final: 0.8792 (t0) REVERT: G 50 GLU cc_start: 0.9300 (mt-10) cc_final: 0.9085 (mt-10) REVERT: G 79 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7912 (mp-120) REVERT: G 125 LEU cc_start: 0.9559 (pp) cc_final: 0.9227 (mm) REVERT: G 142 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8522 (ttm-80) REVERT: G 148 TRP cc_start: 0.8068 (m100) cc_final: 0.7079 (m100) REVERT: G 158 ASN cc_start: 0.9232 (m110) cc_final: 0.8614 (t0) REVERT: G 161 GLU cc_start: 0.8769 (mp0) cc_final: 0.8543 (mp0) REVERT: G 211 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.6904 (ptm160) REVERT: H 3 GLN cc_start: 0.8872 (pm20) cc_final: 0.8005 (pm20) REVERT: H 26 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8624 (ptp-110) REVERT: H 51 ILE cc_start: 0.9693 (OUTLIER) cc_final: 0.9468 (tp) REVERT: H 72 ASP cc_start: 0.8924 (t0) cc_final: 0.8523 (t0) REVERT: H 76 ASN cc_start: 0.8915 (t0) cc_final: 0.8446 (t0) REVERT: H 152 GLU cc_start: 0.8959 (pm20) cc_final: 0.8655 (pm20) REVERT: H 170 PHE cc_start: 0.8942 (m-80) cc_final: 0.8364 (m-80) REVERT: I 18 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8227 (mmt90) REVERT: I 30 ASN cc_start: 0.9172 (t0) cc_final: 0.8806 (t0) REVERT: I 50 GLU cc_start: 0.9279 (mt-10) cc_final: 0.9072 (mt-10) REVERT: I 105 GLU cc_start: 0.8600 (tp30) cc_final: 0.8109 (mp0) REVERT: I 125 LEU cc_start: 0.9514 (pp) cc_final: 0.9248 (mm) REVERT: I 148 TRP cc_start: 0.8040 (m100) cc_final: 0.7110 (m100) REVERT: I 158 ASN cc_start: 0.9224 (m110) cc_final: 0.8669 (t0) REVERT: I 161 GLU cc_start: 0.8747 (mp0) cc_final: 0.8530 (mp0) REVERT: J 6 GLU cc_start: 0.7002 (mp0) cc_final: 0.6117 (mp0) REVERT: J 26 ARG cc_start: 0.8858 (mtp-110) cc_final: 0.8491 (ptm160) REVERT: J 51 ILE cc_start: 0.9690 (OUTLIER) cc_final: 0.9456 (tp) REVERT: J 76 ASN cc_start: 0.8934 (t0) cc_final: 0.8500 (t0) REVERT: J 77 GLN cc_start: 0.8996 (pt0) cc_final: 0.8093 (pp30) REVERT: J 105 GLN cc_start: 0.7894 (pm20) cc_final: 0.7278 (pm20) REVERT: J 152 GLU cc_start: 0.9006 (pm20) cc_final: 0.8630 (pm20) REVERT: J 170 PHE cc_start: 0.9092 (m-80) cc_final: 0.8560 (m-80) REVERT: J 201 ASN cc_start: 0.9130 (t0) cc_final: 0.8436 (m110) REVERT: K 6 GLU cc_start: 0.7023 (mp0) cc_final: 0.6178 (mp0) REVERT: K 26 ARG cc_start: 0.8847 (mtp-110) cc_final: 0.8477 (ptm160) REVERT: K 51 ILE cc_start: 0.9702 (OUTLIER) cc_final: 0.9475 (tp) REVERT: K 76 ASN cc_start: 0.8928 (t0) cc_final: 0.8493 (t0) REVERT: K 77 GLN cc_start: 0.8994 (pt0) cc_final: 0.8087 (pp30) REVERT: K 105 GLN cc_start: 0.7875 (pm20) cc_final: 0.7253 (pm20) REVERT: K 152 GLU cc_start: 0.9026 (pm20) cc_final: 0.8667 (pm20) REVERT: K 170 PHE cc_start: 0.9125 (m-80) cc_final: 0.8567 (m-80) REVERT: K 201 ASN cc_start: 0.9129 (t0) cc_final: 0.8429 (m110) REVERT: L 18 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.8185 (mmt90) REVERT: L 30 ASN cc_start: 0.9181 (t0) cc_final: 0.8803 (t0) REVERT: L 50 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9075 (mt-10) REVERT: L 105 GLU cc_start: 0.8644 (tp30) cc_final: 0.8099 (mp0) REVERT: L 125 LEU cc_start: 0.9513 (pp) cc_final: 0.9249 (mm) REVERT: L 148 TRP cc_start: 0.8054 (m100) cc_final: 0.7151 (m100) REVERT: L 158 ASN cc_start: 0.9230 (m110) cc_final: 0.8676 (t0) REVERT: L 161 GLU cc_start: 0.8769 (mp0) cc_final: 0.8557 (mp0) REVERT: L 211 ARG cc_start: 0.7188 (ttp-170) cc_final: 0.6551 (ptm160) outliers start: 80 outliers final: 53 residues processed: 485 average time/residue: 1.3458 time to fit residues: 755.3264 Evaluate side-chains 487 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 424 time to evaluate : 3.229 ------------------------------------------------------------------------------- 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 134 MET 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 134 MET 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 108 ARG 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 29 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 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 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 20 LEU 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 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 144 CYS Chi-restraints excluded: chain K residue 156 VAL Chi-restraints excluded: chain K residue 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 117 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 201 optimal weight: 8.9990 chunk 245 optimal weight: 0.0570 chunk 140 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 249 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 182 optimal weight: 0.0050 overall best weight: 0.5914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 159 ASN K 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.101669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.062462 restraints weight = 42117.423| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.43 r_work: 0.2596 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21032 Z= 0.132 Angle : 0.723 9.370 28724 Z= 0.367 Chirality : 0.047 0.176 3220 Planarity : 0.006 0.063 3660 Dihedral : 4.822 20.533 2860 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.10 % Allowed : 23.73 % Favored : 73.17 % 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: 0.29 (0.16), residues: 2636 helix: -0.01 (0.50), residues: 128 sheet: 1.05 (0.17), residues: 840 loop : -0.22 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 51 HIS 0.005 0.001 HIS C 166 PHE 0.026 0.002 PHE I 139 TYR 0.043 0.002 TYR I 173 ARG 0.020 0.001 ARG I 142 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 707) hydrogen bonds : angle 5.48472 ( 1935) SS BOND : bond 0.00400 ( 40) SS BOND : angle 1.14671 ( 80) covalent geometry : bond 0.00310 (20992) covalent geometry : angle 0.72140 (28644) *********************** 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 529 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 458 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8708 (t0) cc_final: 0.8168 (t0) REVERT: A 149 GLU cc_start: 0.8976 (mp0) cc_final: 0.8446 (mp0) REVERT: A 164 GLU cc_start: 0.8395 (tp30) cc_final: 0.7931 (tm-30) REVERT: A 204 ASN cc_start: 0.9486 (OUTLIER) cc_final: 0.9162 (t160) REVERT: A 228 TYR cc_start: 0.9507 (m-80) cc_final: 0.9303 (m-80) REVERT: B 70 GLU cc_start: 0.8340 (pp20) cc_final: 0.8066 (pp20) REVERT: B 109 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8737 (mm-30) REVERT: B 145 ASP cc_start: 0.8680 (t0) cc_final: 0.8103 (t0) REVERT: B 149 GLU cc_start: 0.8979 (mp0) cc_final: 0.8339 (mp0) REVERT: B 164 GLU cc_start: 0.8327 (tp30) cc_final: 0.7874 (tm-30) REVERT: B 204 ASN cc_start: 0.9489 (OUTLIER) cc_final: 0.9171 (t160) REVERT: C 128 GLU cc_start: 0.9431 (tp30) cc_final: 0.9192 (tp30) REVERT: C 145 ASP cc_start: 0.8677 (t0) cc_final: 0.8117 (t0) REVERT: C 149 GLU cc_start: 0.8959 (mp0) cc_final: 0.8378 (mp0) REVERT: C 164 GLU cc_start: 0.8435 (tp30) cc_final: 0.8014 (tm-30) REVERT: C 204 ASN cc_start: 0.9497 (OUTLIER) cc_final: 0.9182 (t160) REVERT: C 228 TYR cc_start: 0.9490 (m-80) cc_final: 0.9262 (m-80) REVERT: D 109 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8735 (mm-30) REVERT: D 145 ASP cc_start: 0.8680 (t0) cc_final: 0.8057 (t0) REVERT: D 149 GLU cc_start: 0.8962 (mp0) cc_final: 0.8333 (mp0) REVERT: D 164 GLU cc_start: 0.8334 (tp30) cc_final: 0.7951 (tm-30) REVERT: D 204 ASN cc_start: 0.9494 (OUTLIER) cc_final: 0.9176 (t160) REVERT: D 228 TYR cc_start: 0.9490 (m-80) cc_final: 0.9273 (m-80) REVERT: E 11 LEU cc_start: 0.9291 (pp) cc_final: 0.8669 (pp) REVERT: E 18 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8216 (mmt90) REVERT: E 30 ASN cc_start: 0.9177 (t0) cc_final: 0.8814 (t0) REVERT: E 50 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9098 (mt-10) REVERT: E 105 GLU cc_start: 0.8651 (tp30) cc_final: 0.8169 (mp0) REVERT: E 125 LEU cc_start: 0.9558 (pp) cc_final: 0.9213 (mm) REVERT: E 158 ASN cc_start: 0.9251 (m110) cc_final: 0.8698 (t0) REVERT: E 211 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7031 (ptm160) REVERT: F 3 GLN cc_start: 0.8841 (pm20) cc_final: 0.8224 (pm20) REVERT: F 6 GLU cc_start: 0.7113 (mp0) cc_final: 0.5999 (mp0) REVERT: F 26 ARG cc_start: 0.8871 (mtp-110) cc_final: 0.8451 (ptm160) REVERT: F 51 ILE cc_start: 0.9689 (OUTLIER) cc_final: 0.9474 (tp) REVERT: F 72 ASP cc_start: 0.8951 (t0) cc_final: 0.8604 (OUTLIER) REVERT: F 76 ASN cc_start: 0.8852 (t0) cc_final: 0.8498 (t0) REVERT: F 77 GLN cc_start: 0.8963 (tt0) cc_final: 0.8418 (tp40) REVERT: F 105 GLN cc_start: 0.7836 (pm20) cc_final: 0.7194 (pm20) REVERT: F 170 PHE cc_start: 0.8764 (m-80) cc_final: 0.8485 (m-80) REVERT: G 18 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8173 (mmt90) REVERT: G 30 ASN cc_start: 0.9186 (t0) cc_final: 0.8827 (t0) REVERT: G 50 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9094 (mt-10) REVERT: G 105 GLU cc_start: 0.8591 (tp30) cc_final: 0.8097 (mp0) REVERT: G 125 LEU cc_start: 0.9559 (pp) cc_final: 0.9211 (mm) REVERT: G 148 TRP cc_start: 0.8075 (m100) cc_final: 0.7143 (m100) REVERT: G 158 ASN cc_start: 0.9262 (m110) cc_final: 0.8734 (t0) REVERT: G 211 ARG cc_start: 0.7881 (ttp-170) cc_final: 0.7063 (ptm160) REVERT: H 3 GLN cc_start: 0.8897 (pm20) cc_final: 0.8066 (pm20) REVERT: H 26 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8658 (ptp-110) REVERT: H 35 THR cc_start: 0.9571 (p) cc_final: 0.9295 (t) REVERT: H 51 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9481 (tp) REVERT: H 72 ASP cc_start: 0.8967 (t0) cc_final: 0.8618 (OUTLIER) REVERT: H 76 ASN cc_start: 0.8873 (t0) cc_final: 0.8484 (t0) REVERT: H 77 GLN cc_start: 0.8926 (tt0) cc_final: 0.8574 (tp40) REVERT: H 170 PHE cc_start: 0.8961 (m-80) cc_final: 0.8477 (m-80) REVERT: I 18 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.8198 (mmt90) REVERT: I 30 ASN cc_start: 0.9172 (t0) cc_final: 0.8830 (t0) REVERT: I 105 GLU cc_start: 0.8632 (tp30) cc_final: 0.8042 (mp0) REVERT: I 125 LEU cc_start: 0.9510 (pp) cc_final: 0.9279 (mm) REVERT: I 142 ARG cc_start: 0.9011 (ttm-80) cc_final: 0.8335 (tpp80) REVERT: I 148 TRP cc_start: 0.8096 (m100) cc_final: 0.7108 (m100) REVERT: I 158 ASN cc_start: 0.9249 (m110) cc_final: 0.8728 (t0) REVERT: I 161 GLU cc_start: 0.8767 (mp0) cc_final: 0.8551 (mp0) REVERT: I 211 ARG cc_start: 0.7221 (ttp-170) cc_final: 0.6688 (ptm160) REVERT: J 26 ARG cc_start: 0.8869 (mtp-110) cc_final: 0.8459 (ptm160) REVERT: J 51 ILE cc_start: 0.9688 (OUTLIER) cc_final: 0.9459 (tp) REVERT: J 76 ASN cc_start: 0.8940 (t0) cc_final: 0.8529 (t0) REVERT: J 77 GLN cc_start: 0.8960 (pt0) cc_final: 0.8045 (pp30) REVERT: J 152 GLU cc_start: 0.9006 (pm20) cc_final: 0.8705 (pm20) REVERT: J 170 PHE cc_start: 0.9122 (m-80) cc_final: 0.8586 (m-80) REVERT: J 201 ASN cc_start: 0.9072 (t0) cc_final: 0.8414 (m110) REVERT: K 6 GLU cc_start: 0.7016 (mp0) cc_final: 0.6096 (mp0) REVERT: K 26 ARG cc_start: 0.8867 (mtp-110) cc_final: 0.8454 (ptm160) REVERT: K 51 ILE cc_start: 0.9701 (OUTLIER) cc_final: 0.9479 (tp) REVERT: K 76 ASN cc_start: 0.8932 (t0) cc_final: 0.8528 (t0) REVERT: K 77 GLN cc_start: 0.8960 (pt0) cc_final: 0.8040 (pp30) REVERT: K 105 GLN cc_start: 0.7844 (pm20) cc_final: 0.7266 (pm20) REVERT: K 152 GLU cc_start: 0.9003 (pm20) cc_final: 0.8693 (pm20) REVERT: K 170 PHE cc_start: 0.9139 (m-80) cc_final: 0.8634 (m-80) REVERT: K 201 ASN cc_start: 0.9036 (t0) cc_final: 0.8367 (m110) REVERT: L 18 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8188 (mmt90) REVERT: L 30 ASN cc_start: 0.9186 (t0) cc_final: 0.8828 (t0) REVERT: L 105 GLU cc_start: 0.8643 (tp30) cc_final: 0.8442 (tp30) REVERT: L 125 LEU cc_start: 0.9508 (pp) cc_final: 0.9277 (mm) REVERT: L 142 ARG cc_start: 0.9037 (tpp80) cc_final: 0.8592 (ttm-80) REVERT: L 148 TRP cc_start: 0.8114 (m100) cc_final: 0.7145 (m100) REVERT: L 158 ASN cc_start: 0.9258 (m110) cc_final: 0.8734 (t0) REVERT: L 161 GLU cc_start: 0.8784 (mp0) cc_final: 0.8547 (mp0) REVERT: L 211 ARG cc_start: 0.7219 (ttp-170) cc_final: 0.6521 (ptm160) outliers start: 71 outliers final: 54 residues processed: 493 average time/residue: 1.1350 time to fit residues: 657.2103 Evaluate side-chains 496 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 436 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 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 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 29 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 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 199 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 16 GLU 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 159 ASN Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain K residue 11 CYS Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 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 159 ASN 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 117 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 151 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 210 optimal weight: 0.4980 chunk 164 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 169 optimal weight: 0.9990 chunk 260 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN ** I 79 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.060825 restraints weight = 42212.181| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.40 r_work: 0.2561 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21032 Z= 0.229 Angle : 0.754 8.593 28724 Z= 0.388 Chirality : 0.048 0.176 3220 Planarity : 0.006 0.064 3660 Dihedral : 4.937 20.273 2860 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.92 % Allowed : 24.91 % Favored : 72.16 % 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: 0.23 (0.16), residues: 2636 helix: 0.01 (0.49), residues: 128 sheet: 1.03 (0.17), residues: 840 loop : -0.28 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 51 HIS 0.010 0.001 HIS B 166 PHE 0.026 0.002 PHE L 139 TYR 0.037 0.002 TYR G 173 ARG 0.017 0.001 ARG G 142 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 707) hydrogen bonds : angle 5.60623 ( 1935) SS BOND : bond 0.00485 ( 40) SS BOND : angle 1.27897 ( 80) covalent geometry : bond 0.00536 (20992) covalent geometry : angle 0.75160 (28644) ********************** 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 496 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 429 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8769 (t0) cc_final: 0.8246 (t0) REVERT: A 149 GLU cc_start: 0.8986 (mp0) cc_final: 0.8499 (mp0) REVERT: A 164 GLU cc_start: 0.8452 (tp30) cc_final: 0.8016 (tm-30) REVERT: A 204 ASN cc_start: 0.9500 (OUTLIER) cc_final: 0.9186 (t160) REVERT: B 70 GLU cc_start: 0.8394 (pp20) cc_final: 0.8126 (pp20) REVERT: B 109 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8685 (mm-30) REVERT: B 145 ASP cc_start: 0.8743 (t0) cc_final: 0.8205 (t0) REVERT: B 149 GLU cc_start: 0.8981 (mp0) cc_final: 0.8418 (mp0) REVERT: B 164 GLU cc_start: 0.8407 (tp30) cc_final: 0.7957 (tm-30) REVERT: B 204 ASN cc_start: 0.9499 (OUTLIER) cc_final: 0.9185 (t160) REVERT: C 128 GLU cc_start: 0.9440 (tp30) cc_final: 0.9050 (tp30) REVERT: C 145 ASP cc_start: 0.8726 (t0) cc_final: 0.8206 (t0) REVERT: C 149 GLU cc_start: 0.8961 (mp0) cc_final: 0.8414 (mp0) REVERT: C 164 GLU cc_start: 0.8481 (tp30) cc_final: 0.8010 (tm-30) REVERT: C 204 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.9192 (t160) REVERT: D 109 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8750 (mm-30) REVERT: D 145 ASP cc_start: 0.8733 (t0) cc_final: 0.8145 (t0) REVERT: D 149 GLU cc_start: 0.8973 (mp0) cc_final: 0.8337 (mp0) REVERT: D 164 GLU cc_start: 0.8400 (tp30) cc_final: 0.7993 (tm-30) REVERT: D 204 ASN cc_start: 0.9499 (OUTLIER) cc_final: 0.9187 (t160) REVERT: E 11 LEU cc_start: 0.9320 (pp) cc_final: 0.8687 (pp) REVERT: E 18 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8264 (mmt90) REVERT: E 30 ASN cc_start: 0.9194 (t0) cc_final: 0.8804 (t0) REVERT: E 50 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9106 (mt-10) REVERT: E 105 GLU cc_start: 0.8721 (tp30) cc_final: 0.8168 (mp0) REVERT: E 125 LEU cc_start: 0.9579 (pp) cc_final: 0.9238 (mm) REVERT: E 142 ARG cc_start: 0.8914 (ttm110) cc_final: 0.8613 (tpp80) REVERT: E 148 TRP cc_start: 0.8045 (m100) cc_final: 0.7167 (m100) REVERT: E 158 ASN cc_start: 0.9238 (m110) cc_final: 0.8677 (t0) REVERT: E 211 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7033 (ptm160) REVERT: F 3 GLN cc_start: 0.8894 (pm20) cc_final: 0.8632 (pm20) REVERT: F 6 GLU cc_start: 0.7115 (mp0) cc_final: 0.6061 (mp0) REVERT: F 26 ARG cc_start: 0.8897 (mtp-110) cc_final: 0.8546 (ptm160) REVERT: F 27 PHE cc_start: 0.7910 (m-80) cc_final: 0.6400 (m-80) REVERT: F 51 ILE cc_start: 0.9706 (OUTLIER) cc_final: 0.9482 (tp) REVERT: F 72 ASP cc_start: 0.8981 (t0) cc_final: 0.8626 (t0) REVERT: F 76 ASN cc_start: 0.8889 (t0) cc_final: 0.8552 (t0) REVERT: F 77 GLN cc_start: 0.8959 (tt0) cc_final: 0.8449 (tp40) REVERT: F 105 GLN cc_start: 0.7845 (pm20) cc_final: 0.7189 (pm20) REVERT: F 170 PHE cc_start: 0.8760 (m-80) cc_final: 0.8486 (m-80) REVERT: F 180 TYR cc_start: 0.9061 (m-10) cc_final: 0.8846 (m-10) REVERT: F 216 GLU cc_start: 0.8795 (pp20) cc_final: 0.7745 (pm20) REVERT: G 18 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8229 (mmt90) REVERT: G 30 ASN cc_start: 0.9208 (t0) cc_final: 0.8822 (t0) REVERT: G 50 GLU cc_start: 0.9297 (mt-10) cc_final: 0.9089 (mt-10) REVERT: G 105 GLU cc_start: 0.8691 (tp30) cc_final: 0.8182 (mp0) REVERT: G 125 LEU cc_start: 0.9581 (pp) cc_final: 0.9237 (mm) REVERT: G 158 ASN cc_start: 0.9248 (m110) cc_final: 0.8710 (t0) REVERT: G 173 TYR cc_start: 0.7849 (m-10) cc_final: 0.7403 (m-10) REVERT: G 211 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.6924 (ptm160) REVERT: H 3 GLN cc_start: 0.8958 (pm20) cc_final: 0.8424 (pm20) REVERT: H 26 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8716 (ptp-110) REVERT: H 51 ILE cc_start: 0.9713 (OUTLIER) cc_final: 0.9483 (tp) REVERT: H 72 ASP cc_start: 0.9011 (t0) cc_final: 0.8653 (t0) REVERT: H 76 ASN cc_start: 0.8937 (t0) cc_final: 0.8522 (t0) REVERT: H 77 GLN cc_start: 0.8955 (tt0) cc_final: 0.8654 (tp40) REVERT: H 170 PHE cc_start: 0.8932 (m-80) cc_final: 0.8557 (m-80) REVERT: H 195 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7686 (p) REVERT: I 18 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8274 (mmt90) REVERT: I 30 ASN cc_start: 0.9198 (t0) cc_final: 0.8828 (t0) REVERT: I 50 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8880 (mp0) REVERT: I 105 GLU cc_start: 0.8693 (tp30) cc_final: 0.8074 (mp0) REVERT: I 148 TRP cc_start: 0.8126 (m100) cc_final: 0.7233 (m100) REVERT: I 158 ASN cc_start: 0.9245 (m110) cc_final: 0.8717 (t0) REVERT: I 161 GLU cc_start: 0.8787 (mp0) cc_final: 0.8576 (mp0) REVERT: I 173 TYR cc_start: 0.7388 (m-10) cc_final: 0.7155 (m-10) REVERT: I 199 GLN cc_start: 0.9405 (tp40) cc_final: 0.9195 (tp-100) REVERT: I 211 ARG cc_start: 0.7231 (ttp-170) cc_final: 0.6760 (ptm160) REVERT: J 6 GLU cc_start: 0.7347 (mp0) cc_final: 0.6517 (pm20) REVERT: J 26 ARG cc_start: 0.8845 (mtp-110) cc_final: 0.8383 (ptm160) REVERT: J 51 ILE cc_start: 0.9702 (OUTLIER) cc_final: 0.9462 (tp) REVERT: J 76 ASN cc_start: 0.9002 (t0) cc_final: 0.8630 (t0) REVERT: J 77 GLN cc_start: 0.9044 (pt0) cc_final: 0.8151 (pp30) REVERT: J 105 GLN cc_start: 0.8153 (pm20) cc_final: 0.7856 (pm20) REVERT: J 152 GLU cc_start: 0.9020 (pm20) cc_final: 0.8638 (pm20) REVERT: J 170 PHE cc_start: 0.9066 (m-80) cc_final: 0.8690 (m-80) REVERT: J 195 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7604 (p) REVERT: J 201 ASN cc_start: 0.9078 (t0) cc_final: 0.8438 (m110) REVERT: K 6 GLU cc_start: 0.7046 (mp0) cc_final: 0.6122 (mp0) REVERT: K 26 ARG cc_start: 0.8852 (mtp-110) cc_final: 0.8398 (ptm160) REVERT: K 51 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9474 (tp) REVERT: K 76 ASN cc_start: 0.8991 (t0) cc_final: 0.8627 (t0) REVERT: K 77 GLN cc_start: 0.9040 (pt0) cc_final: 0.8147 (pp30) REVERT: K 105 GLN cc_start: 0.7863 (pm20) cc_final: 0.7258 (pm20) REVERT: K 152 GLU cc_start: 0.9017 (pm20) cc_final: 0.8620 (pm20) REVERT: K 170 PHE cc_start: 0.9092 (m-80) cc_final: 0.8664 (m-80) REVERT: K 195 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7598 (p) REVERT: K 201 ASN cc_start: 0.9078 (t0) cc_final: 0.8444 (m110) REVERT: L 18 ARG cc_start: 0.8516 (mmm-85) cc_final: 0.8259 (mmt90) REVERT: L 30 ASN cc_start: 0.9206 (t0) cc_final: 0.8821 (t0) REVERT: L 50 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8882 (mp0) REVERT: L 105 GLU cc_start: 0.8674 (tp30) cc_final: 0.8050 (mp0) REVERT: L 142 ARG cc_start: 0.9017 (tpp80) cc_final: 0.8695 (ttm-80) REVERT: L 148 TRP cc_start: 0.8145 (m100) cc_final: 0.7167 (m100) REVERT: L 158 ASN cc_start: 0.9256 (m110) cc_final: 0.8726 (t0) REVERT: L 161 GLU cc_start: 0.8794 (mp0) cc_final: 0.8586 (mp0) REVERT: L 211 ARG cc_start: 0.7216 (ttp-170) cc_final: 0.6618 (ptm160) outliers start: 67 outliers final: 53 residues processed: 464 average time/residue: 1.1178 time to fit residues: 599.0645 Evaluate side-chains 493 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 427 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 134 MET 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 190 SER Chi-restraints excluded: chain C residue 204 ASN Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 11 CYS Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 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 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 45 LYS Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain J residue 11 CYS Chi-restraints excluded: chain J residue 16 GLU Chi-restraints excluded: chain J residue 18 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 159 ASN 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 16 GLU Chi-restraints excluded: chain K residue 20 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 159 ASN 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 45 LYS Chi-restraints excluded: chain L residue 50 GLU Chi-restraints excluded: chain L residue 75 ILE 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: 0.0470 chunk 104 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221AGLN B 221AGLN 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 = 0.3556 r_free = 0.3556 target = 0.101957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.062810 restraints weight = 41904.062| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.42 r_work: 0.2604 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21032 Z= 0.136 Angle : 0.739 9.437 28724 Z= 0.376 Chirality : 0.046 0.175 3220 Planarity : 0.006 0.062 3660 Dihedral : 4.878 26.336 2860 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.75 % Allowed : 25.04 % Favored : 72.21 % 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: 0.35 (0.17), residues: 2636 helix: 0.00 (0.50), residues: 128 sheet: 0.91 (0.16), residues: 928 loop : -0.11 (0.17), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 148 HIS 0.009 0.001 HIS B 166 PHE 0.026 0.002 PHE I 139 TYR 0.030 0.002 TYR H 180 ARG 0.013 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 707) hydrogen bonds : angle 5.46005 ( 1935) SS BOND : bond 0.00416 ( 40) SS BOND : angle 1.30390 ( 80) covalent geometry : bond 0.00318 (20992) covalent geometry : angle 0.73673 (28644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19187.60 seconds wall clock time: 341 minutes 25.72 seconds (20485.72 seconds total)