Starting phenix.real_space_refine on Sat Jul 4 01:06:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ub2_26434/07_2026/7ub2_26434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ub2_26434/07_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_26434/07_2026/7ub2_26434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ub2_26434/07_2026/7ub2_26434.map" model { file = "/net/cci-nas-00/data/ceres_data/7ub2_26434/07_2026/7ub2_26434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ub2_26434/07_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-dev-6108/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: 2.53, per 1000 atoms: 0.14 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: 1.57 Conformation dependent library (CDL) restraints added in 841.0 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: 1.93 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: 3.08 Time building geometry restraints manager: 2.07 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.410 Find NCS groups from input model: 0.280 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- 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 : 0.609 9.129 24901 Z= 0.465 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 0.60870 / 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 : 0.633 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: 0.1465 time to fit residues: 84.9070 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 : 0.653 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.148420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.104363 restraints weight = 21950.223| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.32 r_work: 0.2759 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 18152 Z= 0.212 Angle : 0.625 6.964 24901 Z= 0.363 Chirality : 0.043 0.183 2722 Planarity : 0.004 0.032 2758 Dihedral : 19.724 89.140 3258 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.77 % Allowed : 25.87 % Favored : 70.36 % 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: 0.60 (0.19), residues: 1890 helix: 2.58 (0.17), residues: 850 sheet: -0.46 (0.26), residues: 350 loop : -2.06 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 210 TYR 0.017 0.002 TYR K 200 PHE 0.029 0.002 PHE K 165 TRP 0.013 0.002 TRP F 196 HIS 0.006 0.003 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (18152) covalent geometry : angle 0.62524 / 0.36 (24901) hydrogen bonds : bond 0.06291 / 4.11 ( 869) hydrogen bonds : angle 4.79125 / 4.03 ( 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 389 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.6131 (mmm) cc_final: 0.5409 (mmt) REVERT: E 209 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6824 (tt) REVERT: F 72 MET cc_start: 0.6796 (mmp) cc_final: 0.6414 (mmp) REVERT: F 124 LYS cc_start: 0.8477 (tttm) cc_final: 0.8244 (tttp) REVERT: F 159 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8160 (m) REVERT: F 183 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7100 (tm-30) REVERT: F 187 GLN cc_start: 0.7500 (tp40) cc_final: 0.7095 (mm-40) REVERT: F 188 LYS cc_start: 0.8395 (tptm) cc_final: 0.8116 (ttmt) REVERT: G 47 LYS cc_start: 0.8509 (tppp) cc_final: 0.8208 (tptt) REVERT: G 188 LYS cc_start: 0.8900 (tttt) cc_final: 0.8633 (ttpt) REVERT: H 72 MET cc_start: 0.6933 (tpp) cc_final: 0.6724 (tpp) REVERT: H 197 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8102 (tttm) REVERT: J 124 LYS cc_start: 0.8627 (tttm) cc_final: 0.8325 (ttpp) REVERT: K 40 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7627 (mttt) REVERT: K 68 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8162 (mmmt) REVERT: K 124 LYS cc_start: 0.8311 (tttp) cc_final: 0.8087 (ttpt) REVERT: K 142 LEU cc_start: 0.9416 (tp) cc_final: 0.9146 (tp) REVERT: K 187 GLN cc_start: 0.8937 (tp40) cc_final: 0.8733 (mm110) REVERT: L 40 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7767 (mttp) REVERT: L 68 LYS cc_start: 0.8617 (mmmm) cc_final: 0.8295 (mmtm) REVERT: L 197 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8491 (mttt) REVERT: M 152 ASN cc_start: 0.7223 (t0) cc_final: 0.7019 (p0) REVERT: M 187 GLN cc_start: 0.8434 (tp40) cc_final: 0.8001 (mm-40) REVERT: M 197 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7699 (mttt) REVERT: M 198 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8125 (mtmt) outliers start: 63 outliers final: 34 residues processed: 365 average time/residue: 0.1400 time to fit residues: 76.2524 Evaluate side-chains 349 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 0.8980 chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 61 ASN I 61 ASN N 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.154120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.110221 restraints weight = 22154.348| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.38 r_work: 0.2854 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18152 Z= 0.129 Angle : 0.532 6.613 24901 Z= 0.317 Chirality : 0.040 0.183 2722 Planarity : 0.003 0.023 2758 Dihedral : 19.811 88.648 3258 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.35 % Allowed : 25.75 % 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: 0.82 (0.19), residues: 1890 helix: 2.81 (0.17), residues: 850 sheet: -0.42 (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 0.011 0.001 TYR I 110 PHE 0.016 0.001 PHE K 165 TRP 0.006 0.001 TRP I 96 HIS 0.003 0.002 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (18152) covalent geometry : angle 0.53206 / 0.32 (24901) hydrogen bonds : bond 0.04547 / 2.91 ( 869) hydrogen bonds : angle 4.52720 / 3.81 ( 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 372 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 316 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8010 (tmtt) REVERT: E 173 LYS cc_start: 0.7943 (tppt) cc_final: 0.7740 (tptt) REVERT: E 203 MET cc_start: 0.5954 (mmm) cc_final: 0.5230 (mmt) REVERT: E 209 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6820 (tt) REVERT: F 72 MET cc_start: 0.6745 (mmp) cc_final: 0.6362 (mmp) REVERT: F 124 LYS cc_start: 0.8348 (tttm) cc_final: 0.7858 (ttpp) REVERT: F 187 GLN cc_start: 0.7514 (tp40) cc_final: 0.7125 (mm-40) REVERT: F 188 LYS cc_start: 0.8391 (tptm) cc_final: 0.8007 (ttmt) REVERT: G 47 LYS cc_start: 0.8530 (tppp) cc_final: 0.8225 (tptt) REVERT: G 188 LYS cc_start: 0.8854 (tttt) cc_final: 0.8640 (ttpt) REVERT: H 197 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8101 (tptp) REVERT: K 40 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7532 (mttt) REVERT: K 68 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8171 (mmmt) REVERT: K 124 LYS cc_start: 0.8091 (tttp) cc_final: 0.7889 (ttpt) REVERT: K 142 LEU cc_start: 0.9380 (tp) cc_final: 0.9149 (tp) REVERT: K 187 GLN cc_start: 0.8916 (tp40) cc_final: 0.8664 (mm-40) REVERT: L 40 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7813 (mttp) REVERT: L 65 TYR cc_start: 0.8988 (p90) cc_final: 0.8675 (p90) REVERT: L 68 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8317 (mmtm) REVERT: L 197 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8461 (mttt) REVERT: L 206 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8588 (tttp) REVERT: M 136 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8079 (pt) REVERT: M 152 ASN cc_start: 0.7116 (t0) cc_final: 0.6767 (p0) REVERT: M 187 GLN cc_start: 0.8459 (tp40) cc_final: 0.8038 (mm-40) REVERT: M 197 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7696 (mttt) REVERT: M 198 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8111 (mtmt) outliers start: 56 outliers final: 38 residues processed: 345 average time/residue: 0.1276 time to fit residues: 65.5436 Evaluate side-chains 347 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 306 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 223 MET 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: 5.9990 chunk 132 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 107 GLN L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.154373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.110470 restraints weight = 21933.477| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.29 r_work: 0.2841 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18152 Z= 0.119 Angle : 0.510 7.756 24901 Z= 0.303 Chirality : 0.040 0.167 2722 Planarity : 0.003 0.023 2758 Dihedral : 19.790 87.921 3258 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.19 % Allowed : 25.69 % Favored : 70.12 % 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: 0.81 (0.19), residues: 1890 helix: 2.78 (0.17), residues: 860 sheet: -0.41 (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 0.018 0.001 TYR J 60 PHE 0.016 0.001 PHE K 165 TRP 0.005 0.001 TRP E 177 HIS 0.003 0.002 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.12 (18152) covalent geometry : angle 0.51009 / 0.30 (24901) hydrogen bonds : bond 0.04041 / 2.57 ( 869) hydrogen bonds : angle 4.40023 / 3.69 ( 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 389 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8058 (tmtt) REVERT: E 173 LYS cc_start: 0.7884 (tppt) cc_final: 0.7611 (tptt) REVERT: E 203 MET cc_start: 0.5960 (mmm) cc_final: 0.4859 (mmt) REVERT: E 206 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.5927 (ptmm) REVERT: E 209 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6759 (tt) REVERT: F 72 MET cc_start: 0.6653 (mmp) cc_final: 0.6276 (mmp) REVERT: F 187 GLN cc_start: 0.7473 (tp40) cc_final: 0.7071 (mm-40) REVERT: F 188 LYS cc_start: 0.8386 (tptm) cc_final: 0.7960 (ttmt) REVERT: F 198 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6308 (mtmt) REVERT: G 47 LYS cc_start: 0.8519 (tppp) cc_final: 0.8271 (tptt) REVERT: G 188 LYS cc_start: 0.8827 (tttt) cc_final: 0.8587 (ttpt) REVERT: H 197 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8330 (tptt) REVERT: J 182 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8693 (mt) REVERT: K 40 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7512 (mttt) REVERT: K 64 ASP cc_start: 0.8136 (p0) cc_final: 0.7909 (p0) REVERT: K 68 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8189 (mmmt) REVERT: K 124 LYS cc_start: 0.8038 (tttp) cc_final: 0.7828 (ttpt) REVERT: K 142 LEU cc_start: 0.9404 (tp) cc_final: 0.9161 (tp) REVERT: L 40 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7808 (mttp) REVERT: L 68 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8307 (mmtm) REVERT: L 197 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8408 (mttt) REVERT: M 136 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7986 (pt) REVERT: M 152 ASN cc_start: 0.7053 (t0) cc_final: 0.6693 (p0) REVERT: M 187 GLN cc_start: 0.8430 (tp40) cc_final: 0.8003 (mm-40) REVERT: M 197 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7658 (mttt) REVERT: M 198 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8035 (mtmt) outliers start: 70 outliers final: 43 residues processed: 360 average time/residue: 0.1373 time to fit residues: 73.9366 Evaluate side-chains 360 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 197 LYS 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 174 THR 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 J residue 206 LYS 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 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 198 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 0.0370 chunk 16 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN H 107 GLN I 61 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 = 0.3608 r_free = 0.3608 target = 0.151451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.108635 restraints weight = 21901.058| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.20 r_work: 0.2784 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18152 Z= 0.149 Angle : 0.539 8.140 24901 Z= 0.318 Chirality : 0.041 0.209 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.803 88.198 3258 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.89 % Allowed : 25.87 % Favored : 70.24 % 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: 2.73 (0.17), residues: 860 sheet: -0.42 (0.26), residues: 350 loop : -2.15 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 210 TYR 0.017 0.001 TYR J 60 PHE 0.023 0.002 PHE K 165 TRP 0.009 0.001 TRP M 177 HIS 0.004 0.002 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (18152) covalent geometry : angle 0.53859 / 0.32 (24901) hydrogen bonds : bond 0.04786 / 3.10 ( 869) hydrogen bonds : angle 4.35898 / 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 374 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 309 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8196 (tmtt) REVERT: E 173 LYS cc_start: 0.7927 (tppt) cc_final: 0.7660 (tptt) REVERT: E 203 MET cc_start: 0.5946 (mmm) cc_final: 0.4805 (mmt) REVERT: E 206 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.5989 (ptmm) REVERT: E 209 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6773 (tt) REVERT: F 72 MET cc_start: 0.6599 (mmp) cc_final: 0.6236 (mmp) REVERT: F 183 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7385 (tm-30) REVERT: F 187 GLN cc_start: 0.7489 (tp40) cc_final: 0.7090 (mm-40) REVERT: F 188 LYS cc_start: 0.8349 (tptm) cc_final: 0.7881 (ttmt) REVERT: F 198 LYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6352 (mtmt) REVERT: G 68 LYS cc_start: 0.8306 (mmmt) cc_final: 0.8100 (mmtt) REVERT: G 133 GLU cc_start: 0.7293 (tp30) cc_final: 0.6949 (tp30) REVERT: G 188 LYS cc_start: 0.8847 (tttt) cc_final: 0.8612 (ttpt) REVERT: H 197 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8364 (tptt) REVERT: H 210 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8937 (ttt180) REVERT: J 124 LYS cc_start: 0.8604 (tttm) cc_final: 0.8282 (ttpp) REVERT: K 40 LYS cc_start: 0.7828 (mtpt) cc_final: 0.7531 (mttt) REVERT: K 68 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8212 (mmmt) REVERT: K 124 LYS cc_start: 0.8219 (tttp) cc_final: 0.8015 (ttpt) REVERT: L 40 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7850 (mttp) REVERT: L 68 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8337 (mmtm) REVERT: L 197 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8421 (mttt) REVERT: L 206 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8547 (tttp) REVERT: M 136 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8099 (pt) REVERT: M 152 ASN cc_start: 0.7198 (t0) cc_final: 0.6852 (p0) REVERT: M 187 GLN cc_start: 0.8377 (tp40) cc_final: 0.7930 (mm-40) REVERT: M 197 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7670 (mttt) REVERT: M 198 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7996 (mtmt) outliers start: 65 outliers final: 47 residues processed: 346 average time/residue: 0.1377 time to fit residues: 70.7460 Evaluate side-chains 363 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 309 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 201 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 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 174 THR 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 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 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 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 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: 5.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 61 ASN I 61 ASN I 187 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 = 0.3611 r_free = 0.3611 target = 0.151740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.107926 restraints weight = 21868.897| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.28 r_work: 0.2806 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18152 Z= 0.128 Angle : 0.519 8.604 24901 Z= 0.309 Chirality : 0.040 0.183 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.815 88.069 3258 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.13 % Allowed : 25.39 % 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: 0.73 (0.19), residues: 1890 helix: 2.77 (0.17), residues: 860 sheet: -0.41 (0.26), residues: 350 loop : -2.19 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 132 TYR 0.018 0.001 TYR J 60 PHE 0.018 0.002 PHE K 165 TRP 0.006 0.001 TRP E 177 HIS 0.003 0.002 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (18152) covalent geometry : angle 0.51886 / 0.31 (24901) hydrogen bonds : bond 0.04374 / 2.81 ( 869) hydrogen bonds : angle 4.31744 / 3.65 ( 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 383 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 314 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8204 (tmtt) REVERT: E 173 LYS cc_start: 0.7949 (tppt) cc_final: 0.7711 (tptt) REVERT: E 203 MET cc_start: 0.5922 (mmm) cc_final: 0.4773 (mmt) REVERT: E 205 LYS cc_start: 0.6271 (mtpt) cc_final: 0.5624 (mtmm) REVERT: E 206 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.5995 (ptmm) REVERT: E 209 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6743 (tt) REVERT: F 72 MET cc_start: 0.6443 (mmp) cc_final: 0.6079 (mmp) REVERT: F 183 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 187 GLN cc_start: 0.7488 (tp40) cc_final: 0.7074 (mm-40) REVERT: F 188 LYS cc_start: 0.8351 (tptm) cc_final: 0.7873 (ttmt) REVERT: G 133 GLU cc_start: 0.7240 (tp30) cc_final: 0.6899 (tp30) REVERT: G 188 LYS cc_start: 0.8815 (tttt) cc_final: 0.8573 (ttpt) REVERT: H 197 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8343 (tptt) REVERT: H 210 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8937 (ttt180) REVERT: J 124 LYS cc_start: 0.8555 (tttm) cc_final: 0.8237 (ttpp) REVERT: J 182 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8709 (mt) REVERT: K 40 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7464 (mttt) REVERT: K 68 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8204 (mmmt) REVERT: L 40 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7848 (mttp) REVERT: L 68 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8341 (mmtm) REVERT: L 197 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8413 (mttt) REVERT: L 206 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8491 (tttp) REVERT: L 210 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8898 (ttt180) REVERT: M 136 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8087 (pt) REVERT: M 152 ASN cc_start: 0.7137 (t0) cc_final: 0.6689 (p0) REVERT: M 187 GLN cc_start: 0.8338 (tp40) cc_final: 0.7898 (mm-40) REVERT: M 197 LYS cc_start: 0.8037 (ttmm) cc_final: 0.7649 (mttt) REVERT: M 198 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7961 (mtmt) outliers start: 69 outliers final: 51 residues processed: 354 average time/residue: 0.1406 time to fit residues: 73.3613 Evaluate side-chains 369 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 310 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 197 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 37 MET 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 174 THR 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 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 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 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 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: 5.9990 chunk 86 optimal weight: 0.0470 chunk 177 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN G 61 ASN I 107 GLN I 187 GLN J 107 GLN L 187 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.152093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.108638 restraints weight = 22054.151| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.26 r_work: 0.2802 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18152 Z= 0.125 Angle : 0.517 8.712 24901 Z= 0.307 Chirality : 0.040 0.236 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.786 87.948 3258 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.01 % Allowed : 25.51 % 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: 0.74 (0.19), residues: 1890 helix: 2.78 (0.17), residues: 860 sheet: -0.41 (0.26), residues: 350 loop : -2.19 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 132 TYR 0.019 0.001 TYR J 60 PHE 0.018 0.002 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 0.00234 / 0.12 (18152) covalent geometry : angle 0.51719 / 0.31 (24901) hydrogen bonds : bond 0.04226 / 2.72 ( 869) hydrogen bonds : angle 4.28683 / 3.62 ( 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 378 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 311 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8200 (tmtt) REVERT: E 173 LYS cc_start: 0.7990 (tppt) cc_final: 0.7738 (tptt) REVERT: E 203 MET cc_start: 0.5913 (mmm) cc_final: 0.4731 (mmt) REVERT: E 205 LYS cc_start: 0.6279 (mtpt) cc_final: 0.5620 (mtmm) REVERT: E 206 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.5962 (ptmm) REVERT: E 209 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6730 (tt) REVERT: F 72 MET cc_start: 0.6457 (mmp) cc_final: 0.6095 (mmp) REVERT: F 183 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7430 (tm-30) REVERT: F 187 GLN cc_start: 0.7541 (tp40) cc_final: 0.7116 (mm-40) REVERT: F 188 LYS cc_start: 0.8340 (tptm) cc_final: 0.7882 (ttmt) REVERT: G 68 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8103 (mmmt) REVERT: G 133 GLU cc_start: 0.7192 (tp30) cc_final: 0.6849 (tp30) REVERT: G 188 LYS cc_start: 0.8823 (tttt) cc_final: 0.8583 (ttpt) REVERT: H 197 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8292 (tptt) REVERT: H 210 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8937 (ttt180) REVERT: J 124 LYS cc_start: 0.8554 (tttm) cc_final: 0.8233 (ttpp) REVERT: J 182 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8714 (mt) REVERT: K 40 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7457 (mttt) REVERT: K 64 ASP cc_start: 0.8130 (p0) cc_final: 0.7891 (p0) REVERT: K 68 LYS cc_start: 0.8522 (mmmm) cc_final: 0.8208 (mmmt) REVERT: L 40 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7805 (mttp) REVERT: L 68 LYS cc_start: 0.8574 (mmmm) cc_final: 0.8338 (mmtm) REVERT: L 197 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8415 (mttt) REVERT: L 206 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8457 (tttp) REVERT: L 210 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8908 (ttt180) REVERT: M 136 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8070 (pt) REVERT: M 152 ASN cc_start: 0.7115 (t0) cc_final: 0.6670 (p0) REVERT: M 187 GLN cc_start: 0.8349 (tp40) cc_final: 0.7903 (mm-40) REVERT: M 197 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7657 (mttt) REVERT: M 198 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7955 (mtmt) REVERT: N 159 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7477 (m) outliers start: 67 outliers final: 50 residues processed: 352 average time/residue: 0.1423 time to fit residues: 73.8557 Evaluate side-chains 367 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 308 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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 197 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 37 MET 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 157 LYS Chi-restraints excluded: chain H residue 174 THR 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 130 GLU Chi-restraints excluded: chain J residue 159 VAL 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 47 LYS 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 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 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: 4.9990 chunk 69 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN I 187 GLN L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.150020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.106168 restraints weight = 21893.374| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.26 r_work: 0.2775 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18152 Z= 0.157 Angle : 0.551 9.037 24901 Z= 0.324 Chirality : 0.041 0.200 2722 Planarity : 0.003 0.026 2758 Dihedral : 19.749 88.590 3258 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.13 % Allowed : 25.27 % Favored : 70.60 % 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: 0.64 (0.19), residues: 1890 helix: 2.70 (0.17), residues: 860 sheet: -0.43 (0.26), residues: 350 loop : -2.27 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 210 TYR 0.021 0.001 TYR J 60 PHE 0.025 0.002 PHE K 165 TRP 0.009 0.001 TRP E 177 HIS 0.004 0.002 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (18152) covalent geometry : angle 0.55101 / 0.32 (24901) hydrogen bonds : bond 0.05050 / 3.28 ( 869) hydrogen bonds : angle 4.31660 / 3.66 ( 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 382 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 313 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8308 (tmtt) REVERT: E 173 LYS cc_start: 0.8019 (tppt) cc_final: 0.7794 (tptt) REVERT: E 203 MET cc_start: 0.5990 (mmm) cc_final: 0.4728 (mmt) REVERT: E 205 LYS cc_start: 0.6309 (mtpt) cc_final: 0.5665 (mtmm) REVERT: E 206 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6057 (ptmm) REVERT: E 209 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6765 (tt) REVERT: F 72 MET cc_start: 0.6563 (mmp) cc_final: 0.6216 (mmp) REVERT: F 135 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8346 (mt-10) REVERT: F 183 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7435 (tm-30) REVERT: F 187 GLN cc_start: 0.7498 (tp40) cc_final: 0.7175 (mm-40) REVERT: F 188 LYS cc_start: 0.8326 (tptm) cc_final: 0.7859 (ttmt) REVERT: F 198 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6510 (mtmt) REVERT: G 68 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8086 (mmtm) REVERT: G 133 GLU cc_start: 0.7296 (tp30) cc_final: 0.6949 (tp30) REVERT: G 188 LYS cc_start: 0.8876 (tttt) cc_final: 0.8641 (ttpt) REVERT: H 140 ASN cc_start: 0.8401 (p0) cc_final: 0.8072 (p0) REVERT: H 197 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8160 (tttt) REVERT: H 210 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8964 (ttt180) REVERT: J 124 LYS cc_start: 0.8608 (tttm) cc_final: 0.8309 (ttpp) REVERT: K 40 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7507 (mttt) REVERT: K 64 ASP cc_start: 0.8119 (p0) cc_final: 0.7900 (p0) REVERT: K 68 LYS cc_start: 0.8540 (mmmm) cc_final: 0.8246 (mmmt) REVERT: L 40 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7872 (mttp) REVERT: L 68 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8372 (mmtm) REVERT: L 197 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8431 (mttt) REVERT: L 206 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8513 (tttp) REVERT: L 210 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8856 (ttt180) REVERT: M 136 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8176 (pt) REVERT: M 152 ASN cc_start: 0.7301 (t0) cc_final: 0.6991 (p0) REVERT: M 187 GLN cc_start: 0.8341 (tp40) cc_final: 0.7906 (mm-40) REVERT: M 197 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7662 (mttt) REVERT: M 198 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7967 (mtmt) REVERT: N 159 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7472 (m) outliers start: 69 outliers final: 50 residues processed: 349 average time/residue: 0.1340 time to fit residues: 68.7867 Evaluate side-chains 369 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 310 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 197 LYS 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 37 MET 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 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 174 THR 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 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 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 40 LYS 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 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: 0.8980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN I 187 GLN L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.151514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.108231 restraints weight = 22013.474| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.26 r_work: 0.2797 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18152 Z= 0.124 Angle : 0.532 9.822 24901 Z= 0.313 Chirality : 0.040 0.232 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.771 88.259 3258 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.77 % Allowed : 26.17 % Favored : 70.06 % 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: 2.78 (0.17), residues: 860 sheet: -0.40 (0.26), residues: 350 loop : -2.23 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 210 TYR 0.022 0.001 TYR J 60 PHE 0.016 0.001 PHE K 165 TRP 0.008 0.001 TRP F 177 HIS 0.003 0.002 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (18152) covalent geometry : angle 0.53191 / 0.31 (24901) hydrogen bonds : bond 0.04290 / 2.75 ( 869) hydrogen bonds : angle 4.28673 / 3.63 ( 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 370 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 307 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.5981 (mmm) cc_final: 0.4714 (mmt) REVERT: E 205 LYS cc_start: 0.6287 (mtpt) cc_final: 0.5646 (mtmm) REVERT: E 206 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6112 (ptmm) REVERT: E 209 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6719 (tt) REVERT: F 72 MET cc_start: 0.6501 (mmp) cc_final: 0.6154 (mmp) REVERT: F 135 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8339 (mt-10) REVERT: F 183 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7499 (tm-30) REVERT: F 187 GLN cc_start: 0.7525 (tp40) cc_final: 0.7189 (mm-40) REVERT: F 188 LYS cc_start: 0.8322 (tptm) cc_final: 0.7822 (ttmt) REVERT: G 68 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8105 (mmtm) REVERT: G 133 GLU cc_start: 0.7260 (tp30) cc_final: 0.6923 (tp30) REVERT: G 188 LYS cc_start: 0.8842 (tttt) cc_final: 0.8611 (ttpt) REVERT: H 72 MET cc_start: 0.6807 (tpp) cc_final: 0.6486 (tpp) REVERT: H 197 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8309 (tptt) REVERT: H 210 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8955 (ttt180) REVERT: J 124 LYS cc_start: 0.8563 (tttm) cc_final: 0.8237 (ttpp) REVERT: K 40 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7463 (mttt) REVERT: K 64 ASP cc_start: 0.8112 (p0) cc_final: 0.7892 (p0) REVERT: K 68 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8234 (mmmt) REVERT: L 40 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7868 (mttp) REVERT: L 68 LYS cc_start: 0.8593 (mmmm) cc_final: 0.8366 (mmtm) REVERT: L 197 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8411 (mttt) REVERT: L 206 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8491 (tttp) REVERT: L 210 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8894 (ttt180) REVERT: M 136 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8109 (pt) REVERT: M 152 ASN cc_start: 0.7110 (t0) cc_final: 0.6673 (p0) REVERT: M 187 GLN cc_start: 0.8341 (tp40) cc_final: 0.7880 (mm-40) REVERT: M 197 LYS cc_start: 0.8056 (ttmm) cc_final: 0.7675 (mttt) REVERT: M 198 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7974 (mtmt) REVERT: N 159 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7381 (m) outliers start: 63 outliers final: 50 residues processed: 343 average time/residue: 0.1505 time to fit residues: 76.2085 Evaluate side-chains 361 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 197 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 37 MET 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 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 174 THR 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 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 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 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: 0.0000 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.0980 chunk 88 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 30 optimal weight: 10.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN I 187 GLN J 107 GLN L 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.152795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.110356 restraints weight = 21923.367| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.32 r_work: 0.2839 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1915 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= 0.117 Angle : 0.519 10.672 24901 Z= 0.304 Chirality : 0.040 0.240 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.723 88.477 3258 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.41 % Allowed : 26.11 % 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: 0.75 (0.19), residues: 1890 helix: 2.73 (0.17), residues: 870 sheet: -0.35 (0.26), residues: 350 loop : -2.20 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 210 TYR 0.021 0.001 TYR J 60 PHE 0.016 0.001 PHE K 165 TRP 0.006 0.001 TRP J 96 HIS 0.003 0.001 HIS H 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.12 (18152) covalent geometry : angle 0.51919 / 0.30 (24901) hydrogen bonds : bond 0.03840 / 2.45 ( 869) hydrogen bonds : angle 4.24733 / 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 365 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 308 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8282 (tmtt) REVERT: E 173 LYS cc_start: 0.7989 (tppt) cc_final: 0.7733 (tptt) REVERT: E 203 MET cc_start: 0.5795 (mmm) cc_final: 0.4551 (mmt) REVERT: E 205 LYS cc_start: 0.6240 (mtpt) cc_final: 0.5588 (mtmm) REVERT: E 206 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.5978 (ptmm) REVERT: E 209 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6675 (tt) REVERT: F 72 MET cc_start: 0.6477 (mmp) cc_final: 0.6145 (mmp) REVERT: F 187 GLN cc_start: 0.7534 (tp40) cc_final: 0.7179 (mm-40) REVERT: F 188 LYS cc_start: 0.8340 (tptm) cc_final: 0.7845 (ttmt) REVERT: G 68 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8108 (mmtm) REVERT: G 133 GLU cc_start: 0.7164 (tp30) cc_final: 0.6847 (tp30) REVERT: G 188 LYS cc_start: 0.8837 (tttt) cc_final: 0.8589 (ttpt) REVERT: H 72 MET cc_start: 0.6834 (tpp) cc_final: 0.6526 (tpp) REVERT: H 197 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8136 (tttt) REVERT: H 210 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8952 (ttt180) REVERT: J 68 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8427 (mmmm) REVERT: K 40 LYS cc_start: 0.7789 (mtpt) cc_final: 0.7472 (mttt) REVERT: K 64 ASP cc_start: 0.8126 (p0) cc_final: 0.7917 (p0) REVERT: K 68 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8209 (mmmt) REVERT: L 40 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7815 (mttp) REVERT: L 68 LYS cc_start: 0.8597 (mmmm) cc_final: 0.8363 (mmtm) REVERT: L 197 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8395 (mttt) REVERT: L 206 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8392 (tttp) REVERT: L 210 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8881 (ttt180) REVERT: M 152 ASN cc_start: 0.7048 (t0) cc_final: 0.6655 (p0) REVERT: M 187 GLN cc_start: 0.8325 (tp40) cc_final: 0.7853 (mm-40) REVERT: M 197 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7631 (mttt) REVERT: M 198 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7967 (mtmt) REVERT: N 159 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7365 (m) outliers start: 57 outliers final: 47 residues processed: 341 average time/residue: 0.1303 time to fit residues: 65.8838 Evaluate side-chains 355 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 301 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 37 MET 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 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 174 THR 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 130 GLU 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 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 130 GLU 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 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: 0.6980 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 0.0060 chunk 61 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 184 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 122 GLN H 61 ASN I 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.153390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110331 restraints weight = 22165.873| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.24 r_work: 0.2832 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18152 Z= 0.115 Angle : 0.510 10.893 24901 Z= 0.299 Chirality : 0.039 0.239 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.646 88.866 3258 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.41 % Allowed : 25.93 % Favored : 70.66 % 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: 0.78 (0.19), residues: 1890 helix: 2.76 (0.17), residues: 870 sheet: -0.34 (0.26), residues: 350 loop : -2.19 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 132 TYR 0.018 0.001 TYR J 60 PHE 0.015 0.001 PHE K 165 TRP 0.005 0.001 TRP F 177 HIS 0.003 0.001 HIS G 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (18152) covalent geometry : angle 0.51017 / 0.30 (24901) hydrogen bonds : bond 0.03747 / 2.40 ( 869) hydrogen bonds : angle 4.20605 / 3.52 ( 2499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.76 seconds wall clock time: 64 minutes 7.13 seconds (3847.13 seconds total)