Starting phenix.real_space_refine on Sat Sep 12 17:44:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ub2_26434/09_2026/7ub2_26434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ub2_26434/09_2026/7ub2_26434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ub2_26434/09_2026/7ub2_26434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ub2_26434/09_2026/7ub2_26434.map" model { file = "/net/cci-nas-00/data/ceres_data/7ub2_26434/09_2026/7ub2_26434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ub2_26434/09_2026/7ub2_26434.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 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: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 70 5.16 5 C 11050 2.51 5 N 2933 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17579 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1557 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 185} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1029 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "Z" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 980 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Restraints were copied for chains: F, G, H, I, J, K, L, M, N Time building chain proxies: 2.36, per 1000 atoms: 0.13 Number of scatterers: 17579 At special positions: 0 Unit cell: (106.981, 115.072, 166.315, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 98 15.00 O 3428 8.00 N 2933 7.00 C 11050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 580.2 milliseconds 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 30 sheets defined 48.7% alpha, 21.5% beta 39 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'E' and resid 34 through 48 removed outlier: 3.580A pdb=" N LYS E 48 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS E 198 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET E 203 " --> pdb=" O ASP E 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 48 removed outlier: 3.580A pdb=" N LYS F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS F 198 " --> pdb=" O PHE F 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 217 removed outlier: 4.168A pdb=" N MET F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS G 48 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 190 Processing helix chain 'G' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS G 198 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP G 199 " --> pdb=" O GLY G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET G 203 " --> pdb=" O ASP G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE H 52 " --> pdb=" O LYS H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 190 Processing helix chain 'H' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS H 198 " --> pdb=" O PHE H 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP H 199 " --> pdb=" O GLY H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 217 removed outlier: 4.170A pdb=" N MET H 203 " --> pdb=" O ASP H 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS I 48 " --> pdb=" O VAL I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 121 removed outlier: 3.619A pdb=" N GLY I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 190 Processing helix chain 'I' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS I 198 " --> pdb=" O PHE I 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 199 " --> pdb=" O GLY I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET I 203 " --> pdb=" O ASP I 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 48 removed outlier: 3.580A pdb=" N LYS J 48 " --> pdb=" O VAL J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE J 52 " --> pdb=" O LYS J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 190 Processing helix chain 'J' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS J 198 " --> pdb=" O PHE J 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP J 199 " --> pdb=" O GLY J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET J 203 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE K 52 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 121 removed outlier: 3.619A pdb=" N GLY K 121 " --> pdb=" O ALA K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 190 Processing helix chain 'K' and resid 193 through 199 removed outlier: 4.016A pdb=" N LYS K 198 " --> pdb=" O PHE K 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET K 203 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 62 removed outlier: 3.681A pdb=" N PHE L 52 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY L 121 " --> pdb=" O ALA L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 190 Processing helix chain 'L' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS L 198 " --> pdb=" O PHE L 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP L 199 " --> pdb=" O GLY L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET L 203 " --> pdb=" O ASP L 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 48 removed outlier: 3.581A pdb=" N LYS M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 84 removed outlier: 3.513A pdb=" N VAL M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 121 removed outlier: 3.618A pdb=" N GLY M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 190 Processing helix chain 'M' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS M 198 " --> pdb=" O PHE M 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP M 199 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET M 203 " --> pdb=" O ASP M 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 48 removed outlier: 3.580A pdb=" N LYS N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 62 removed outlier: 3.682A pdb=" N PHE N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 84 removed outlier: 3.514A pdb=" N VAL N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 121 removed outlier: 3.619A pdb=" N GLY N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 190 Processing helix chain 'N' and resid 193 through 199 removed outlier: 4.015A pdb=" N LYS N 198 " --> pdb=" O PHE N 194 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP N 199 " --> pdb=" O GLY N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 217 removed outlier: 4.169A pdb=" N MET N 203 " --> pdb=" O ASP N 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 95 through 100 Processing sheet with id=AA2, first strand: chain 'E' and resid 123 through 132 Processing sheet with id=AA3, first strand: chain 'E' and resid 136 through 140 removed outlier: 7.189A pdb=" N GLU E 147 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP E 139 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU E 145 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 95 through 100 Processing sheet with id=AA5, first strand: chain 'F' and resid 123 through 132 Processing sheet with id=AA6, first strand: chain 'F' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU F 147 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP F 139 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU F 145 " --> pdb=" O TRP F 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 95 through 100 Processing sheet with id=AA8, first strand: chain 'G' and resid 123 through 132 Processing sheet with id=AA9, first strand: chain 'G' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU G 147 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP G 139 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU G 145 " --> pdb=" O TRP G 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 95 through 100 Processing sheet with id=AB2, first strand: chain 'H' and resid 123 through 132 Processing sheet with id=AB3, first strand: chain 'H' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU H 147 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP H 139 " --> pdb=" O GLU H 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU H 145 " --> pdb=" O TRP H 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 95 through 100 Processing sheet with id=AB5, first strand: chain 'I' and resid 123 through 132 Processing sheet with id=AB6, first strand: chain 'I' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU I 147 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP I 139 " --> pdb=" O GLU I 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU I 145 " --> pdb=" O TRP I 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 95 through 100 Processing sheet with id=AB8, first strand: chain 'J' and resid 123 through 132 Processing sheet with id=AB9, first strand: chain 'J' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU J 147 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP J 139 " --> pdb=" O GLU J 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU J 145 " --> pdb=" O TRP J 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 95 through 100 Processing sheet with id=AC2, first strand: chain 'K' and resid 123 through 132 Processing sheet with id=AC3, first strand: chain 'K' and resid 136 through 140 removed outlier: 7.188A pdb=" N GLU K 147 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP K 139 " --> pdb=" O GLU K 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU K 145 " --> pdb=" O TRP K 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 95 through 100 Processing sheet with id=AC5, first strand: chain 'L' and resid 123 through 132 Processing sheet with id=AC6, first strand: chain 'L' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU L 147 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP L 139 " --> pdb=" O GLU L 145 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU L 145 " --> pdb=" O TRP L 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 95 through 100 Processing sheet with id=AC8, first strand: chain 'M' and resid 123 through 132 Processing sheet with id=AC9, first strand: chain 'M' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU M 147 " --> pdb=" O LEU M 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP M 139 " --> pdb=" O GLU M 145 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU M 145 " --> pdb=" O TRP M 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 95 through 100 Processing sheet with id=AD2, first strand: chain 'N' and resid 123 through 132 Processing sheet with id=AD3, first strand: chain 'N' and resid 136 through 140 removed outlier: 7.187A pdb=" N GLU N 147 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP N 139 " --> pdb=" O GLU N 145 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLU N 145 " --> pdb=" O TRP N 139 " (cutoff:3.500A) 791 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4337 1.33 - 1.45: 3840 1.45 - 1.57: 9651 1.57 - 1.69: 194 1.69 - 1.81: 130 Bond restraints: 18152 Sorted by residual: bond pdb=" C3' DT Z 18 " pdb=" C2' DT Z 18 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.04e+00 bond pdb=" C3' DA Y 62 " pdb=" C2' DA Y 62 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.03e+00 bond pdb=" C3' DA Y 47 " pdb=" C2' DA Y 47 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.83e+00 bond pdb=" C3' DT Z 15 " pdb=" C2' DT Z 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.81e+00 bond pdb=" C3' DA Y 52 " pdb=" C2' DA Y 52 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.80e+00 ... (remaining 18147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 24262 1.83 - 3.65: 555 3.65 - 5.48: 69 5.48 - 7.30: 5 7.30 - 9.13: 10 Bond angle restraints: 24901 Sorted by residual: angle pdb=" N3 DT Z 27 " pdb=" C4 DT Z 27 " pdb=" O4 DT Z 27 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT Z 52 " pdb=" C4 DT Z 52 " pdb=" O4 DT Z 52 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT Z 22 " pdb=" C4 DT Z 22 " pdb=" O4 DT Z 22 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT Z 32 " pdb=" C4 DT Z 32 " pdb=" O4 DT Z 32 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT Z 42 " pdb=" C4 DT Z 42 " pdb=" O4 DT Z 42 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 24896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8314 17.99 - 35.97: 1745 35.97 - 53.96: 452 53.96 - 71.95: 192 71.95 - 89.94: 27 Dihedral angle restraints: 10730 sinusoidal: 5140 harmonic: 5590 Sorted by residual: dihedral pdb=" CA ASP F 201 " pdb=" CB ASP F 201 " pdb=" CG ASP F 201 " pdb=" OD1 ASP F 201 " ideal model delta sinusoidal sigma weight residual -30.00 -86.59 56.59 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP N 201 " pdb=" CB ASP N 201 " pdb=" CG ASP N 201 " pdb=" OD1 ASP N 201 " ideal model delta sinusoidal sigma weight residual -30.00 -86.56 56.56 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP L 201 " pdb=" CB ASP L 201 " pdb=" CG ASP L 201 " pdb=" OD1 ASP L 201 " ideal model delta sinusoidal sigma weight residual -30.00 -86.55 56.55 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 10727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1661 0.029 - 0.057: 662 0.057 - 0.086: 260 0.086 - 0.115: 114 0.115 - 0.143: 25 Chirality restraints: 2722 Sorted by residual: chirality pdb=" CA ILE H 126 " pdb=" N ILE H 126 " pdb=" C ILE H 126 " pdb=" CB ILE H 126 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE K 126 " pdb=" N ILE K 126 " pdb=" C ILE K 126 " pdb=" CB ILE K 126 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE F 126 " pdb=" N ILE F 126 " pdb=" C ILE F 126 " pdb=" CB ILE F 126 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 2719 not shown) Planarity restraints: 2758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE N 88 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ILE N 88 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE N 88 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP N 89 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 88 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.48e+00 pdb=" C ILE J 88 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE J 88 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP J 89 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 88 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C ILE G 88 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE G 88 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP G 89 " -0.011 2.00e-02 2.50e+03 ... (remaining 2755 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 443 2.69 - 3.24: 15014 3.24 - 3.79: 24873 3.79 - 4.35: 32653 4.35 - 4.90: 56899 Nonbonded interactions: 129882 Sorted by model distance: nonbonded pdb=" NE2 GLN N 107 " pdb=" N7 DA Y 67 " model vdw 2.134 3.200 nonbonded pdb=" NE2 GLN H 107 " pdb=" N7 DA Y 37 " model vdw 2.145 3.200 nonbonded pdb=" NE2 GLN I 107 " pdb=" N7 DA Y 42 " model vdw 2.173 3.200 nonbonded pdb=" NE2 GLN M 107 " pdb=" N7 DA Y 62 " model vdw 2.181 3.200 nonbonded pdb=" NE2 GLN J 107 " pdb=" N7 DA Y 47 " model vdw 2.211 3.200 ... (remaining 129877 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: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 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 : 0.004 0.043 18152 Z= 0.292 Angle : 0.610 9.129 24901 Z= 0.467 Chirality : 0.040 0.143 2722 Planarity : 0.002 0.019 2758 Dihedral : 21.081 89.936 7150 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.60 % Allowed : 29.40 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1890 helix: 2.71 (0.18), residues: 850 sheet: -0.50 (0.25), residues: 350 loop : -2.13 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 132 TYR 0.019 0.001 TYR E 60 PHE 0.013 0.001 PHE E 165 TRP 0.003 0.000 TRP J 96 HIS 0.002 0.001 HIS L 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.29 (18152) covalent geometry : angle 0.61024 / 0.47 (24901) hydrogen bonds : bond 0.13212 / 8.41 ( 869) hydrogen bonds : angle 5.85394 / 4.63 ( 2499) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 384 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.7914 (ttmt) cc_final: 0.7631 (tmtt) REVERT: E 203 MET cc_start: 0.4755 (mmm) cc_final: 0.4410 (mmt) REVERT: E 215 LYS cc_start: 0.5444 (mttm) cc_final: 0.5053 (mmtp) REVERT: F 79 MET cc_start: 0.8080 (ttt) cc_final: 0.7876 (tpt) REVERT: F 124 LYS cc_start: 0.7804 (tttm) cc_final: 0.7085 (ttpp) REVERT: F 187 GLN cc_start: 0.6991 (tp40) cc_final: 0.6522 (mm-40) REVERT: G 47 LYS cc_start: 0.8293 (tppp) cc_final: 0.7972 (tptt) REVERT: G 124 LYS cc_start: 0.8060 (tttm) cc_final: 0.7850 (tptt) REVERT: G 166 GLN cc_start: 0.8751 (tt0) cc_final: 0.8529 (tt0) REVERT: G 188 LYS cc_start: 0.8487 (tttt) cc_final: 0.8132 (ttpt) REVERT: H 124 LYS cc_start: 0.8160 (tttm) cc_final: 0.7951 (tttm) REVERT: H 137 LEU cc_start: 0.8124 (mt) cc_final: 0.7917 (mt) REVERT: H 197 LYS cc_start: 0.8567 (ttmm) cc_final: 0.7973 (tttm) REVERT: I 222 ASP cc_start: 0.8287 (m-30) cc_final: 0.7992 (m-30) REVERT: K 40 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7404 (mttt) REVERT: K 68 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7877 (mmmt) REVERT: K 142 LEU cc_start: 0.9381 (tp) cc_final: 0.9154 (tp) REVERT: K 187 GLN cc_start: 0.8565 (tp40) cc_final: 0.8280 (mm-40) REVERT: L 40 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7650 (mttp) REVERT: L 68 LYS cc_start: 0.8328 (mmmm) cc_final: 0.7952 (mmtm) REVERT: L 194 PHE cc_start: 0.9251 (t80) cc_final: 0.9042 (t80) REVERT: L 197 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8426 (mttt) REVERT: M 124 LYS cc_start: 0.7928 (tttm) cc_final: 0.7637 (tttp) REVERT: M 152 ASN cc_start: 0.6673 (t0) cc_final: 0.6416 (p0) REVERT: M 187 GLN cc_start: 0.8140 (tp40) cc_final: 0.7622 (mm-40) REVERT: M 198 LYS cc_start: 0.8424 (mtmt) cc_final: 0.8056 (mtmt) REVERT: N 124 LYS cc_start: 0.7630 (tttm) cc_final: 0.7403 (ttmt) REVERT: N 187 GLN cc_start: 0.7401 (tp40) cc_final: 0.7164 (mm110) outliers start: 10 outliers final: 4 residues processed: 390 average time/residue: 0.1343 time to fit residues: 78.3619 Evaluate side-chains 344 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 340 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain M residue 199 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN I 61 ASN I 169 ASN L 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.149337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.105281 restraints weight = 21936.298| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.32 r_work: 0.2758 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18152 Z= 0.215 Angle : 0.635 7.169 24901 Z= 0.367 Chirality : 0.044 0.184 2722 Planarity : 0.004 0.032 2758 Dihedral : 19.732 88.792 3258 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.01 % Allowed : 25.45 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1890 helix: 2.53 (0.17), residues: 850 sheet: -0.46 (0.26), residues: 350 loop : -2.07 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 210 TYR 0.017 0.002 TYR K 200 PHE 0.029 0.002 PHE K 165 TRP 0.012 0.002 TRP F 196 HIS 0.006 0.003 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (18152) covalent geometry : angle 0.63451 / 0.37 (24901) hydrogen bonds : bond 0.06345 / 4.15 ( 869) hydrogen bonds : angle 4.77703 / 4.02 ( 2499) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 328 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.6039 (mmm) cc_final: 0.5252 (mmt) REVERT: E 209 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6778 (tt) REVERT: F 72 MET cc_start: 0.6783 (mmp) cc_final: 0.6401 (mmp) REVERT: F 124 LYS cc_start: 0.8464 (tttm) cc_final: 0.8227 (tttp) REVERT: F 159 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8137 (m) REVERT: F 164 TYR cc_start: 0.8453 (t80) cc_final: 0.8171 (t80) REVERT: F 183 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7071 (tm-30) REVERT: F 187 GLN cc_start: 0.7476 (tp40) cc_final: 0.7063 (mm-40) REVERT: F 188 LYS cc_start: 0.8370 (tptm) cc_final: 0.8086 (ttmt) REVERT: G 47 LYS cc_start: 0.8509 (tppp) cc_final: 0.8196 (tptt) REVERT: G 188 LYS cc_start: 0.8888 (tttt) cc_final: 0.8622 (ttpt) REVERT: H 72 MET cc_start: 0.6965 (tpp) cc_final: 0.6749 (tpp) REVERT: H 197 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8098 (tttm) REVERT: I 187 GLN cc_start: 0.8971 (tp40) cc_final: 0.8581 (mm110) REVERT: J 124 LYS cc_start: 0.8631 (tttm) cc_final: 0.8317 (ttpp) REVERT: K 40 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7617 (mttt) REVERT: K 68 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8164 (mmmt) REVERT: K 124 LYS cc_start: 0.8316 (tttp) cc_final: 0.8081 (ttpt) REVERT: K 142 LEU cc_start: 0.9432 (tp) cc_final: 0.9173 (tp) REVERT: K 187 GLN cc_start: 0.8934 (tp40) cc_final: 0.8722 (mm110) REVERT: L 40 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7762 (mttp) REVERT: L 68 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8299 (mmtm) REVERT: L 197 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8459 (mttt) REVERT: M 152 ASN cc_start: 0.7226 (t0) cc_final: 0.7006 (p0) REVERT: M 187 GLN cc_start: 0.8419 (tp40) cc_final: 0.7977 (mm-40) REVERT: M 197 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7653 (mttt) REVERT: M 198 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8100 (mtmt) outliers start: 67 outliers final: 34 residues processed: 370 average time/residue: 0.1318 time to fit residues: 72.8918 Evaluate side-chains 351 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 40 LYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 128 optimal weight: 1.9990 chunk 127 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 61 ASN N 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.152721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.108824 restraints weight = 22142.066| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.30 r_work: 0.2826 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18152 Z= 0.128 Angle : 0.537 6.704 24901 Z= 0.319 Chirality : 0.040 0.183 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.802 88.981 3258 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.99 % Allowed : 25.93 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1890 helix: 2.78 (0.17), residues: 850 sheet: -0.43 (0.26), residues: 350 loop : -1.97 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 210 TYR 0.015 0.001 TYR I 60 PHE 0.015 0.001 PHE K 165 TRP 0.006 0.001 TRP I 96 HIS 0.003 0.001 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (18152) covalent geometry : angle 0.53671 / 0.32 (24901) hydrogen bonds : bond 0.04581 / 2.94 ( 869) hydrogen bonds : angle 4.54897 / 3.83 ( 2499) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7960 (tmtt) REVERT: E 173 LYS cc_start: 0.7860 (tppt) cc_final: 0.7582 (tptt) REVERT: E 203 MET cc_start: 0.5909 (mmm) cc_final: 0.5229 (mmt) REVERT: E 209 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6731 (tt) REVERT: F 72 MET cc_start: 0.6736 (mmp) cc_final: 0.6358 (mmp) REVERT: F 124 LYS cc_start: 0.8339 (tttm) cc_final: 0.7814 (ttpp) REVERT: F 159 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8099 (m) REVERT: F 187 GLN cc_start: 0.7464 (tp40) cc_final: 0.7075 (mm-40) REVERT: F 188 LYS cc_start: 0.8349 (tptm) cc_final: 0.7948 (ttmt) REVERT: G 47 LYS cc_start: 0.8497 (tppp) cc_final: 0.8183 (tptt) REVERT: G 188 LYS cc_start: 0.8839 (tttt) cc_final: 0.8613 (ttpt) REVERT: H 197 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8074 (tptp) REVERT: K 40 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7518 (mttt) REVERT: K 68 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8160 (mmmt) REVERT: K 124 LYS cc_start: 0.8074 (tttp) cc_final: 0.7853 (ttpt) REVERT: K 142 LEU cc_start: 0.9402 (tp) cc_final: 0.9168 (tp) REVERT: K 187 GLN cc_start: 0.8919 (tp40) cc_final: 0.8690 (mm-40) REVERT: L 40 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7732 (mttp) REVERT: L 65 TYR cc_start: 0.8957 (p90) cc_final: 0.8646 (p90) REVERT: L 68 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8298 (mmtm) REVERT: L 197 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8427 (mttt) REVERT: L 206 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8552 (tttp) REVERT: M 136 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8018 (pt) REVERT: M 152 ASN cc_start: 0.7076 (t0) cc_final: 0.6697 (p0) REVERT: M 187 GLN cc_start: 0.8426 (tp40) cc_final: 0.7997 (mm-40) REVERT: M 197 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7669 (mttt) REVERT: M 198 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8094 (mtmt) outliers start: 50 outliers final: 35 residues processed: 340 average time/residue: 0.1440 time to fit residues: 73.0946 Evaluate side-chains 345 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 306 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 181 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 107 GLN H 107 GLN I 61 ASN L 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.152712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.108630 restraints weight = 21925.711| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.45 r_work: 0.2834 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18152 Z= 0.122 Angle : 0.514 6.055 24901 Z= 0.307 Chirality : 0.040 0.179 2722 Planarity : 0.003 0.023 2758 Dihedral : 19.789 87.897 3258 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.77 % Allowed : 25.21 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1890 helix: 2.73 (0.17), residues: 860 sheet: -0.43 (0.26), residues: 350 loop : -2.04 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 132 TYR 0.016 0.001 TYR J 60 PHE 0.017 0.001 PHE K 165 TRP 0.006 0.001 TRP E 177 HIS 0.004 0.002 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (18152) covalent geometry : angle 0.51369 / 0.31 (24901) hydrogen bonds : bond 0.04228 / 2.70 ( 869) hydrogen bonds : angle 4.41279 / 3.71 ( 2499) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8077 (tmtt) REVERT: E 173 LYS cc_start: 0.7904 (tppt) cc_final: 0.7627 (tptt) REVERT: E 203 MET cc_start: 0.5947 (mmm) cc_final: 0.5200 (mmt) REVERT: E 206 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.5953 (ttpp) REVERT: E 209 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6763 (tt) REVERT: F 72 MET cc_start: 0.6656 (mmp) cc_final: 0.6280 (mmp) REVERT: F 124 LYS cc_start: 0.8308 (tttm) cc_final: 0.7837 (ttpp) REVERT: F 187 GLN cc_start: 0.7476 (tp40) cc_final: 0.7079 (mm-40) REVERT: F 188 LYS cc_start: 0.8374 (tptm) cc_final: 0.7973 (ttmt) REVERT: F 198 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6320 (mtmt) REVERT: G 47 LYS cc_start: 0.8522 (tppp) cc_final: 0.8282 (tptt) REVERT: G 188 LYS cc_start: 0.8843 (tttt) cc_final: 0.8609 (ttpt) REVERT: H 197 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8334 (tptt) REVERT: J 182 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8690 (mt) REVERT: K 40 LYS cc_start: 0.7796 (mtpt) cc_final: 0.7531 (mttt) REVERT: K 64 ASP cc_start: 0.8146 (p0) cc_final: 0.7898 (p0) REVERT: K 68 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8194 (mmmt) REVERT: K 142 LEU cc_start: 0.9399 (tp) cc_final: 0.9156 (tp) REVERT: L 40 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7818 (mttp) REVERT: L 68 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8312 (mmtm) REVERT: L 197 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8432 (mttt) REVERT: L 206 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8466 (tttp) REVERT: M 136 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8030 (pt) REVERT: M 152 ASN cc_start: 0.7073 (t0) cc_final: 0.6741 (p0) REVERT: M 187 GLN cc_start: 0.8422 (tp40) cc_final: 0.8000 (mm-40) REVERT: M 197 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7657 (mttt) REVERT: M 198 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8053 (mtmt) REVERT: N 72 MET cc_start: 0.4892 (ttm) cc_final: 0.4560 (tpp) outliers start: 63 outliers final: 41 residues processed: 356 average time/residue: 0.1416 time to fit residues: 75.0339 Evaluate side-chains 355 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 61 ASN L 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.151366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107492 restraints weight = 21897.216| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.27 r_work: 0.2804 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18152 Z= 0.138 Angle : 0.531 7.827 24901 Z= 0.314 Chirality : 0.040 0.208 2722 Planarity : 0.003 0.026 2758 Dihedral : 19.822 88.152 3258 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.95 % Allowed : 25.57 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1890 helix: 2.71 (0.17), residues: 860 sheet: -0.42 (0.26), residues: 350 loop : -2.14 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 210 TYR 0.018 0.001 TYR J 60 PHE 0.021 0.002 PHE K 165 TRP 0.008 0.001 TRP E 177 HIS 0.004 0.002 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (18152) covalent geometry : angle 0.53061 / 0.31 (24901) hydrogen bonds : bond 0.04630 / 2.99 ( 869) hydrogen bonds : angle 4.36239 / 3.69 ( 2499) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 315 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8186 (tmtt) REVERT: E 173 LYS cc_start: 0.7916 (tppt) cc_final: 0.7648 (tptt) REVERT: E 203 MET cc_start: 0.5950 (mmm) cc_final: 0.5163 (mmt) REVERT: E 206 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6029 (ttpp) REVERT: E 209 LEU cc_start: 0.7121 (OUTLIER) cc_final: 0.6743 (tt) REVERT: F 72 MET cc_start: 0.6593 (mmp) cc_final: 0.6231 (mmp) REVERT: F 124 LYS cc_start: 0.8366 (tttm) cc_final: 0.7914 (ttpp) REVERT: F 183 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7390 (tm-30) REVERT: F 187 GLN cc_start: 0.7473 (tp40) cc_final: 0.7074 (mm-40) REVERT: F 188 LYS cc_start: 0.8348 (tptm) cc_final: 0.7894 (ttmt) REVERT: F 198 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6339 (mtmt) REVERT: G 133 GLU cc_start: 0.7252 (tp30) cc_final: 0.6913 (tp30) REVERT: G 188 LYS cc_start: 0.8850 (tttt) cc_final: 0.8615 (ttpt) REVERT: H 197 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8355 (tptt) REVERT: H 210 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8935 (ttt180) REVERT: K 40 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7520 (mttt) REVERT: K 64 ASP cc_start: 0.8123 (p0) cc_final: 0.7892 (p0) REVERT: K 68 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8208 (mmmt) REVERT: K 142 LEU cc_start: 0.9453 (tp) cc_final: 0.9240 (tp) REVERT: L 40 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7843 (mttp) REVERT: L 68 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8334 (mmtm) REVERT: L 197 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8420 (mttt) REVERT: L 206 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8520 (tttp) REVERT: M 136 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8091 (pt) REVERT: M 152 ASN cc_start: 0.7134 (t0) cc_final: 0.6698 (p0) REVERT: M 187 GLN cc_start: 0.8430 (tp40) cc_final: 0.7991 (mm-40) REVERT: M 197 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7677 (mttt) REVERT: M 198 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8010 (mtmt) outliers start: 66 outliers final: 49 residues processed: 353 average time/residue: 0.1383 time to fit residues: 72.7989 Evaluate side-chains 368 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 76 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 61 ASN I 61 ASN I 107 GLN J 107 GLN L 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.150906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107076 restraints weight = 21869.006| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.26 r_work: 0.2789 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18152 Z= 0.146 Angle : 0.533 7.036 24901 Z= 0.317 Chirality : 0.041 0.189 2722 Planarity : 0.003 0.026 2758 Dihedral : 19.813 88.772 3258 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.13 % Allowed : 25.09 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 1890 helix: 2.72 (0.17), residues: 860 sheet: -0.41 (0.26), residues: 350 loop : -2.21 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 210 TYR 0.020 0.001 TYR J 60 PHE 0.022 0.002 PHE K 165 TRP 0.009 0.001 TRP E 177 HIS 0.004 0.002 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (18152) covalent geometry : angle 0.53321 / 0.32 (24901) hydrogen bonds : bond 0.04819 / 3.12 ( 869) hydrogen bonds : angle 4.34157 / 3.68 ( 2499) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 311 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8219 (tmtt) REVERT: E 173 LYS cc_start: 0.7995 (tppt) cc_final: 0.7733 (tptt) REVERT: E 203 MET cc_start: 0.5949 (mmm) cc_final: 0.5112 (mmt) REVERT: E 205 LYS cc_start: 0.6278 (mtpt) cc_final: 0.5650 (mtmm) REVERT: E 206 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6073 (ttpp) REVERT: E 209 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6748 (tt) REVERT: F 72 MET cc_start: 0.6443 (mmp) cc_final: 0.6091 (mmp) REVERT: F 124 LYS cc_start: 0.8372 (tttm) cc_final: 0.7937 (ttpp) REVERT: F 183 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7419 (tm-30) REVERT: F 187 GLN cc_start: 0.7521 (tp40) cc_final: 0.7105 (mm-40) REVERT: F 188 LYS cc_start: 0.8350 (tptm) cc_final: 0.7887 (ttmt) REVERT: F 198 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6433 (mtmt) REVERT: G 68 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8167 (mmmt) REVERT: G 133 GLU cc_start: 0.7333 (tp30) cc_final: 0.6980 (tp30) REVERT: G 188 LYS cc_start: 0.8836 (tttt) cc_final: 0.8594 (ttpt) REVERT: H 197 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8377 (tptt) REVERT: H 210 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8983 (ttt180) REVERT: K 40 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7473 (mttt) REVERT: K 64 ASP cc_start: 0.8105 (p0) cc_final: 0.7887 (p0) REVERT: K 68 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8228 (mmmt) REVERT: L 40 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7844 (mttp) REVERT: L 68 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8354 (mmtm) REVERT: L 197 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8433 (mttt) REVERT: L 206 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8553 (tttp) REVERT: M 136 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8132 (pt) REVERT: M 152 ASN cc_start: 0.7284 (t0) cc_final: 0.6985 (p0) REVERT: M 187 GLN cc_start: 0.8352 (tp40) cc_final: 0.7914 (mm-40) REVERT: M 197 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7670 (mttt) REVERT: M 198 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8007 (mtmt) REVERT: N 159 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7456 (m) outliers start: 69 outliers final: 53 residues processed: 351 average time/residue: 0.1372 time to fit residues: 71.6098 Evaluate side-chains 370 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 309 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 chunk 189 optimal weight: 0.0980 chunk 54 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 61 ASN I 61 ASN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.151306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107410 restraints weight = 22014.154| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.28 r_work: 0.2800 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18152 Z= 0.129 Angle : 0.522 8.631 24901 Z= 0.311 Chirality : 0.040 0.220 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.755 88.275 3258 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.07 % Allowed : 25.15 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.19), residues: 1890 helix: 2.73 (0.17), residues: 860 sheet: -0.43 (0.26), residues: 350 loop : -2.20 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 132 TYR 0.020 0.001 TYR J 60 PHE 0.018 0.002 PHE K 165 TRP 0.007 0.001 TRP E 177 HIS 0.003 0.002 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (18152) covalent geometry : angle 0.52243 / 0.31 (24901) hydrogen bonds : bond 0.04458 / 2.87 ( 869) hydrogen bonds : angle 4.31489 / 3.65 ( 2499) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 315 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8323 (tmtt) REVERT: E 203 MET cc_start: 0.5976 (mmm) cc_final: 0.5147 (mmt) REVERT: E 205 LYS cc_start: 0.6289 (mtpt) cc_final: 0.5633 (mtmm) REVERT: E 206 LYS cc_start: 0.6840 (OUTLIER) cc_final: 0.6064 (ttpp) REVERT: E 209 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6719 (tt) REVERT: F 72 MET cc_start: 0.6457 (mmp) cc_final: 0.6109 (mmp) REVERT: F 124 LYS cc_start: 0.8337 (tttm) cc_final: 0.7897 (ttpp) REVERT: F 183 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7435 (tm-30) REVERT: F 187 GLN cc_start: 0.7535 (tp40) cc_final: 0.7117 (mm-40) REVERT: F 188 LYS cc_start: 0.8367 (tptm) cc_final: 0.7897 (ttmt) REVERT: G 68 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8132 (mmtm) REVERT: G 133 GLU cc_start: 0.7234 (tp30) cc_final: 0.6954 (tp30) REVERT: G 188 LYS cc_start: 0.8828 (tttt) cc_final: 0.8593 (ttpt) REVERT: H 197 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8305 (tptt) REVERT: H 210 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8940 (ttt180) REVERT: J 124 LYS cc_start: 0.8589 (tttm) cc_final: 0.8270 (ttpp) REVERT: K 40 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7459 (mttt) REVERT: K 64 ASP cc_start: 0.8090 (p0) cc_final: 0.7883 (p0) REVERT: K 68 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8221 (mmmt) REVERT: L 40 LYS cc_start: 0.8118 (mtpt) cc_final: 0.7859 (mttp) REVERT: L 68 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8349 (mmtm) REVERT: L 197 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8418 (mttt) REVERT: L 206 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8538 (tttp) REVERT: L 210 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8916 (ttt180) REVERT: M 43 LYS cc_start: 0.7755 (ttmm) cc_final: 0.7497 (ptmm) REVERT: M 136 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8134 (pt) REVERT: M 152 ASN cc_start: 0.7135 (t0) cc_final: 0.6694 (p0) REVERT: M 187 GLN cc_start: 0.8348 (tp40) cc_final: 0.7900 (mm-40) REVERT: M 197 LYS cc_start: 0.8070 (ttmm) cc_final: 0.7678 (mttt) REVERT: M 198 LYS cc_start: 0.8429 (mtmt) cc_final: 0.7987 (mtmt) REVERT: N 159 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7485 (m) outliers start: 68 outliers final: 51 residues processed: 355 average time/residue: 0.1347 time to fit residues: 70.8064 Evaluate side-chains 369 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 311 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 210 ARG Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 61 ASN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.151632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.108917 restraints weight = 21875.601| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.33 r_work: 0.2809 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18152 Z= 0.126 Angle : 0.513 8.104 24901 Z= 0.306 Chirality : 0.040 0.213 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.729 88.133 3258 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.07 % Allowed : 24.85 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.19), residues: 1890 helix: 2.76 (0.17), residues: 860 sheet: -0.42 (0.26), residues: 350 loop : -2.20 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 210 TYR 0.021 0.001 TYR J 60 PHE 0.019 0.002 PHE K 165 TRP 0.007 0.001 TRP E 177 HIS 0.003 0.002 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (18152) covalent geometry : angle 0.51280 / 0.31 (24901) hydrogen bonds : bond 0.04331 / 2.79 ( 869) hydrogen bonds : angle 4.28983 / 3.62 ( 2499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 311 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8289 (tmtt) REVERT: E 203 MET cc_start: 0.5909 (mmm) cc_final: 0.5076 (mmt) REVERT: E 205 LYS cc_start: 0.6253 (mtpt) cc_final: 0.5599 (mtmm) REVERT: E 206 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6062 (ttpp) REVERT: E 209 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6677 (tt) REVERT: F 72 MET cc_start: 0.6494 (mmp) cc_final: 0.6152 (mmp) REVERT: F 124 LYS cc_start: 0.8312 (tttm) cc_final: 0.7863 (ttpp) REVERT: F 183 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7412 (tm-30) REVERT: F 187 GLN cc_start: 0.7527 (tp40) cc_final: 0.7101 (mm-40) REVERT: F 188 LYS cc_start: 0.8323 (tptm) cc_final: 0.7854 (ttmt) REVERT: G 101 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8290 (mttp) REVERT: G 133 GLU cc_start: 0.7235 (tp30) cc_final: 0.6935 (tp30) REVERT: G 188 LYS cc_start: 0.8838 (tttt) cc_final: 0.8603 (ttpt) REVERT: H 197 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8173 (tptp) REVERT: H 210 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8934 (ttt180) REVERT: K 40 LYS cc_start: 0.7751 (mtpt) cc_final: 0.7451 (mttt) REVERT: K 64 ASP cc_start: 0.8080 (p0) cc_final: 0.7870 (p0) REVERT: K 68 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8224 (mmmt) REVERT: L 40 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7852 (mttp) REVERT: L 68 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8355 (mmtm) REVERT: L 197 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8404 (mttt) REVERT: L 206 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8495 (tttp) REVERT: L 210 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8896 (ttt180) REVERT: M 43 LYS cc_start: 0.7744 (ttmm) cc_final: 0.7483 (ptmm) REVERT: M 136 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8121 (pt) REVERT: M 152 ASN cc_start: 0.7144 (t0) cc_final: 0.6703 (p0) REVERT: M 187 GLN cc_start: 0.8328 (tp40) cc_final: 0.7876 (mm-40) REVERT: M 197 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7671 (mttt) REVERT: M 198 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7967 (mtmt) REVERT: N 159 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7487 (m) outliers start: 68 outliers final: 54 residues processed: 351 average time/residue: 0.1429 time to fit residues: 74.2731 Evaluate side-chains 372 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 210 ARG Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 18 optimal weight: 0.0270 chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 166 GLN I 61 ASN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110152 restraints weight = 21979.784| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.27 r_work: 0.2836 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18152 Z= 0.118 Angle : 0.515 8.980 24901 Z= 0.305 Chirality : 0.040 0.236 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.713 88.196 3258 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.83 % Allowed : 25.27 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 1890 helix: 2.72 (0.17), residues: 870 sheet: -0.39 (0.26), residues: 350 loop : -2.17 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 210 TYR 0.021 0.001 TYR J 60 PHE 0.015 0.001 PHE K 165 TRP 0.006 0.001 TRP F 96 HIS 0.003 0.001 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.12 (18152) covalent geometry : angle 0.51501 / 0.30 (24901) hydrogen bonds : bond 0.03943 / 2.53 ( 869) hydrogen bonds : angle 4.26098 / 3.59 ( 2499) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 315 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8290 (tmtt) REVERT: E 203 MET cc_start: 0.5926 (mmm) cc_final: 0.5225 (mmt) REVERT: E 205 LYS cc_start: 0.6262 (mtpt) cc_final: 0.5606 (mtmm) REVERT: E 206 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6075 (ttpp) REVERT: E 209 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6694 (tt) REVERT: F 72 MET cc_start: 0.6504 (mmp) cc_final: 0.6162 (mmp) REVERT: F 124 LYS cc_start: 0.8325 (tttm) cc_final: 0.7881 (ttpp) REVERT: F 135 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8029 (mt-10) REVERT: F 183 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7474 (tm-30) REVERT: F 187 GLN cc_start: 0.7551 (tp40) cc_final: 0.7210 (mm-40) REVERT: F 188 LYS cc_start: 0.8330 (tptm) cc_final: 0.7857 (ttmt) REVERT: G 101 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8302 (mttp) REVERT: G 133 GLU cc_start: 0.7215 (tp30) cc_final: 0.6920 (tp30) REVERT: G 188 LYS cc_start: 0.8833 (tttt) cc_final: 0.8598 (ttpt) REVERT: H 197 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8185 (tptp) REVERT: H 210 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8945 (ttt180) REVERT: J 124 LYS cc_start: 0.8534 (tttm) cc_final: 0.8212 (ttpp) REVERT: K 40 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7458 (mttt) REVERT: K 64 ASP cc_start: 0.8094 (p0) cc_final: 0.7884 (p0) REVERT: K 68 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8213 (mmmt) REVERT: L 40 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7817 (mttp) REVERT: L 68 LYS cc_start: 0.8580 (mmmm) cc_final: 0.8346 (mmtm) REVERT: L 197 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8409 (mttt) REVERT: L 206 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8441 (tttp) REVERT: L 210 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8905 (ttt180) REVERT: M 136 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8112 (pt) REVERT: M 152 ASN cc_start: 0.7096 (t0) cc_final: 0.6674 (p0) REVERT: M 187 GLN cc_start: 0.8346 (tp40) cc_final: 0.7893 (mm-40) REVERT: M 197 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7693 (mttt) REVERT: M 198 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7968 (mtmt) REVERT: N 72 MET cc_start: 0.4782 (ttm) cc_final: 0.4482 (tpp) REVERT: N 159 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7413 (m) outliers start: 64 outliers final: 50 residues processed: 354 average time/residue: 0.1471 time to fit residues: 77.1496 Evaluate side-chains 366 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 309 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 210 ARG Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.0770 chunk 88 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 133 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 166 GLN I 61 ASN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.152882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.110294 restraints weight = 21851.376| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.47 r_work: 0.2841 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18152 Z= 0.120 Angle : 0.519 10.094 24901 Z= 0.306 Chirality : 0.040 0.247 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.682 88.384 3258 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.35 % Allowed : 25.39 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1890 helix: 2.71 (0.17), residues: 870 sheet: -0.37 (0.26), residues: 350 loop : -2.18 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 210 TYR 0.015 0.001 TYR J 60 PHE 0.017 0.001 PHE K 165 TRP 0.006 0.001 TRP E 177 HIS 0.003 0.001 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (18152) covalent geometry : angle 0.51866 / 0.31 (24901) hydrogen bonds : bond 0.03983 / 2.56 ( 869) hydrogen bonds : angle 4.23635 / 3.56 ( 2499) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8298 (tmtt) REVERT: E 203 MET cc_start: 0.5901 (mmm) cc_final: 0.5088 (mmt) REVERT: E 205 LYS cc_start: 0.6271 (mtpt) cc_final: 0.5610 (mtmm) REVERT: E 206 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6080 (ttpp) REVERT: E 209 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6700 (tt) REVERT: F 72 MET cc_start: 0.6505 (mmp) cc_final: 0.6159 (mmp) REVERT: F 124 LYS cc_start: 0.8305 (tttm) cc_final: 0.7861 (ttpp) REVERT: F 135 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8091 (mt-10) REVERT: F 183 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7505 (tm-30) REVERT: F 187 GLN cc_start: 0.7538 (tp40) cc_final: 0.7201 (mm-40) REVERT: F 188 LYS cc_start: 0.8349 (tptm) cc_final: 0.7873 (ttmt) REVERT: G 101 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8304 (mttp) REVERT: G 133 GLU cc_start: 0.7230 (tp30) cc_final: 0.6897 (tp30) REVERT: G 188 LYS cc_start: 0.8841 (tttt) cc_final: 0.8601 (ttpt) REVERT: H 197 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8184 (tptp) REVERT: H 210 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8941 (ttt180) REVERT: K 40 LYS cc_start: 0.7791 (mtpt) cc_final: 0.7479 (mttt) REVERT: K 64 ASP cc_start: 0.8104 (p0) cc_final: 0.7890 (p0) REVERT: K 68 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8207 (mmmt) REVERT: L 40 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7819 (mttp) REVERT: L 68 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8350 (mmtm) REVERT: L 197 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8401 (mttt) REVERT: L 210 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8902 (ttt180) REVERT: M 152 ASN cc_start: 0.7059 (t0) cc_final: 0.6680 (p0) REVERT: M 187 GLN cc_start: 0.8340 (tp40) cc_final: 0.7893 (mm-40) REVERT: M 197 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7675 (mttt) REVERT: M 198 LYS cc_start: 0.8390 (mtmt) cc_final: 0.7967 (mtmt) REVERT: N 72 MET cc_start: 0.4811 (ttm) cc_final: 0.4509 (tpp) REVERT: N 159 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7378 (m) outliers start: 56 outliers final: 48 residues processed: 341 average time/residue: 0.1453 time to fit residues: 73.3730 Evaluate side-chains 361 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 218 ILE Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 210 ARG Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN I 61 ASN ** J 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.152856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.109669 restraints weight = 22084.515| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.32 r_work: 0.2812 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18152 Z= 0.121 Angle : 0.521 9.217 24901 Z= 0.306 Chirality : 0.040 0.245 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.652 88.501 3258 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.65 % Allowed : 25.27 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1890 helix: 2.71 (0.17), residues: 870 sheet: -0.37 (0.26), residues: 350 loop : -2.19 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 210 TYR 0.012 0.001 TYR J 60 PHE 0.017 0.001 PHE K 165 TRP 0.006 0.001 TRP E 177 HIS 0.003 0.002 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (18152) covalent geometry : angle 0.52083 / 0.31 (24901) hydrogen bonds : bond 0.04019 / 2.59 ( 869) hydrogen bonds : angle 4.22563 / 3.55 ( 2499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3674.19 seconds wall clock time: 63 minutes 43.12 seconds (3823.12 seconds total)