Starting phenix.real_space_refine on Sun Aug 24 05:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ub2_26434/08_2025/7ub2_26434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ub2_26434/08_2025/7ub2_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ub2_26434/08_2025/7ub2_26434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ub2_26434/08_2025/7ub2_26434.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ub2_26434/08_2025/7ub2_26434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ub2_26434/08_2025/7ub2_26434.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 98 5.49 5 S 70 5.16 5 C 11050 2.51 5 N 2933 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 2.55, per 1000 atoms: 0.15 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: 1.49 Conformation dependent library (CDL) restraints added in 812.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.08 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: 3.27 Time building geometry restraints manager: 1.98 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=" CB LYS K 68 " pdb=" CG LYS K 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB LYS G 68 " pdb=" CG LYS G 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CB LYS F 68 " pdb=" CG LYS F 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB LYS H 68 " pdb=" CG LYS H 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 bond pdb=" CB LYS M 68 " pdb=" CG LYS M 68 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 ... (remaining 18147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 24436 1.83 - 3.65: 380 3.65 - 5.48: 70 5.48 - 7.30: 5 7.30 - 9.13: 10 Bond angle restraints: 24901 Sorted by residual: angle pdb=" N ILE I 88 " pdb=" CA ILE I 88 " pdb=" C ILE I 88 " ideal model delta sigma weight residual 112.17 108.26 3.91 9.50e-01 1.11e+00 1.69e+01 angle pdb=" N ILE N 88 " pdb=" CA ILE N 88 " pdb=" C ILE N 88 " ideal model delta sigma weight residual 112.17 108.27 3.90 9.50e-01 1.11e+00 1.69e+01 angle pdb=" N ILE G 88 " pdb=" CA ILE G 88 " pdb=" C ILE G 88 " ideal model delta sigma weight residual 112.17 108.28 3.89 9.50e-01 1.11e+00 1.68e+01 angle pdb=" N ILE K 88 " pdb=" CA ILE K 88 " pdb=" C ILE K 88 " ideal model delta sigma weight residual 112.17 108.28 3.89 9.50e-01 1.11e+00 1.68e+01 angle pdb=" N ILE M 88 " pdb=" CA ILE M 88 " pdb=" C ILE M 88 " ideal model delta sigma weight residual 112.17 108.28 3.89 9.50e-01 1.11e+00 1.67e+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: 1785 0.029 - 0.057: 634 0.057 - 0.086: 187 0.086 - 0.115: 97 0.115 - 0.143: 19 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.980 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.003 0.043 18152 Z= 0.121 Angle : 0.563 9.129 24901 Z= 0.324 Chirality : 0.037 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 aren 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 covalent geometry : bond 0.00262 (18152) covalent geometry : angle 0.56339 (24901) hydrogen bonds : bond 0.13212 ( 869) hydrogen bonds : angle 5.85394 ( 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 : 0.639 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: 0.1527 time to fit residues: 87.8220 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 : 0.635 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 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: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3548 r_free = 0.3548 target = 0.146277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.102382 restraints weight = 21957.780| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.29 r_work: 0.2717 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 18152 Z= 0.239 Angle : 0.669 8.634 24901 Z= 0.369 Chirality : 0.045 0.212 2722 Planarity : 0.004 0.033 2758 Dihedral : 19.953 89.697 3258 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.83 % Allowed : 25.27 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.19), residues: 1890 helix: 2.55 (0.17), residues: 850 sheet: -0.46 (0.25), residues: 350 loop : -2.16 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 210 TYR 0.017 0.002 TYR K 200 PHE 0.031 0.002 PHE K 165 TRP 0.015 0.002 TRP E 177 HIS 0.007 0.003 HIS I 185 Details of bonding type rmsd covalent geometry : bond 0.00559 (18152) covalent geometry : angle 0.66891 (24901) hydrogen bonds : bond 0.06649 ( 869) hydrogen bonds : angle 4.69607 ( 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 392 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 328 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 209 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6877 (tt) REVERT: F 72 MET cc_start: 0.6566 (mmp) cc_final: 0.6212 (mmp) REVERT: F 79 MET cc_start: 0.8532 (ttt) cc_final: 0.8328 (tpt) REVERT: F 124 LYS cc_start: 0.8496 (tttm) cc_final: 0.8080 (ttpp) REVERT: F 164 TYR cc_start: 0.8506 (t80) cc_final: 0.8274 (t80) REVERT: F 187 GLN cc_start: 0.7426 (tp40) cc_final: 0.6984 (mm-40) REVERT: F 188 LYS cc_start: 0.8317 (tptm) cc_final: 0.7883 (ttmt) REVERT: F 198 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6412 (mtmt) REVERT: G 133 GLU cc_start: 0.7514 (tp30) cc_final: 0.7257 (tp30) REVERT: G 166 GLN cc_start: 0.9047 (tt0) cc_final: 0.8837 (tt0) REVERT: G 188 LYS cc_start: 0.8878 (tttt) cc_final: 0.8601 (ttpt) REVERT: G 199 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8067 (p0) REVERT: H 72 MET cc_start: 0.7077 (tpp) cc_final: 0.6836 (tpp) REVERT: H 197 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8165 (tptp) REVERT: J 124 LYS cc_start: 0.8706 (tttm) cc_final: 0.8447 (ttpp) REVERT: K 68 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8259 (mmmt) REVERT: K 187 GLN cc_start: 0.8974 (tp40) cc_final: 0.8769 (mm110) REVERT: L 40 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7982 (mttp) REVERT: L 68 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8242 (mmtm) REVERT: L 180 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8188 (ttpp) REVERT: L 197 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8385 (mttt) REVERT: M 136 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8248 (pt) REVERT: M 152 ASN cc_start: 0.7389 (t0) cc_final: 0.7042 (p0) REVERT: M 187 GLN cc_start: 0.8361 (tp40) cc_final: 0.7926 (mm-40) REVERT: M 197 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7659 (mttt) REVERT: M 198 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8104 (mtmt) outliers start: 64 outliers final: 39 residues processed: 362 average time/residue: 0.1597 time to fit residues: 84.6524 Evaluate side-chains 349 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain 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 80 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 143 THR 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 40 LYS 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 136 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 128 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 61 ASN G 107 GLN K 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.149783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.106247 restraints weight = 22213.199| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.26 r_work: 0.2816 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18152 Z= 0.136 Angle : 0.545 8.511 24901 Z= 0.308 Chirality : 0.041 0.230 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.968 89.887 3258 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.89 % Allowed : 25.51 % 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 aren not related in a simple way. whole: 0.58 (0.19), residues: 1890 helix: 2.57 (0.17), residues: 860 sheet: -0.42 (0.26), residues: 350 loop : -2.19 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 210 TYR 0.012 0.001 TYR G 110 PHE 0.020 0.002 PHE K 165 TRP 0.007 0.001 TRP E 177 HIS 0.004 0.002 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00294 (18152) covalent geometry : angle 0.54465 (24901) hydrogen bonds : bond 0.04508 ( 869) hydrogen bonds : angle 4.53793 ( 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 379 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.6036 (mmm) cc_final: 0.4711 (mmt) REVERT: E 206 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.5965 (ptmm) REVERT: E 209 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6827 (tt) REVERT: F 72 MET cc_start: 0.6383 (mmp) cc_final: 0.6023 (mmp) REVERT: F 124 LYS cc_start: 0.8408 (tttm) cc_final: 0.8013 (ttpp) REVERT: F 187 GLN cc_start: 0.7482 (tp40) cc_final: 0.7075 (mm-40) REVERT: F 188 LYS cc_start: 0.8352 (tptm) cc_final: 0.7897 (ttmt) REVERT: G 133 GLU cc_start: 0.7330 (tp30) cc_final: 0.7041 (tp30) REVERT: G 188 LYS cc_start: 0.8847 (tttt) cc_final: 0.8634 (ttpt) REVERT: G 206 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8712 (ttpt) REVERT: H 197 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8411 (tptt) REVERT: J 124 LYS cc_start: 0.8569 (tttm) cc_final: 0.8320 (ttpp) REVERT: J 206 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8350 (tttp) REVERT: K 64 ASP cc_start: 0.8049 (p0) cc_final: 0.7667 (p0) REVERT: K 68 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8261 (mmmt) REVERT: L 40 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7887 (mttp) REVERT: L 68 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8385 (mmtm) REVERT: L 197 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8394 (mttt) REVERT: L 206 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8633 (tttp) REVERT: M 152 ASN cc_start: 0.7343 (t0) cc_final: 0.6950 (p0) REVERT: M 187 GLN cc_start: 0.8372 (tp40) cc_final: 0.7905 (mm-40) REVERT: M 197 LYS cc_start: 0.8023 (ttmm) cc_final: 0.7674 (mttt) REVERT: M 198 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8098 (mtmt) REVERT: N 72 MET cc_start: 0.5202 (mmt) cc_final: 0.4985 (ttm) REVERT: N 206 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8391 (pttp) outliers start: 65 outliers final: 37 residues processed: 352 average time/residue: 0.1570 time to fit residues: 81.7343 Evaluate side-chains 345 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 206 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 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 172 GLU Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 37 MET 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 J residue 206 LYS Chi-restraints excluded: chain K residue 47 LYS 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 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 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 Chi-restraints excluded: chain N residue 206 LYS 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: 0.7980 chunk 35 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 119 optimal weight: 0.0770 chunk 41 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 61 ASN I 61 ASN I 107 GLN J 107 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.148817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107521 restraints weight = 22014.204| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.28 r_work: 0.2744 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18152 Z= 0.145 Angle : 0.543 7.449 24901 Z= 0.308 Chirality : 0.041 0.202 2722 Planarity : 0.003 0.026 2758 Dihedral : 19.976 89.150 3258 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.07 % Allowed : 25.51 % Favored : 70.42 % 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 aren not related in a simple way. whole: 0.58 (0.19), residues: 1890 helix: 2.60 (0.17), residues: 860 sheet: -0.37 (0.26), residues: 350 loop : -2.26 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 210 TYR 0.011 0.001 TYR G 110 PHE 0.021 0.002 PHE K 165 TRP 0.007 0.001 TRP E 177 HIS 0.004 0.002 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00322 (18152) covalent geometry : angle 0.54345 (24901) hydrogen bonds : bond 0.04727 ( 869) hydrogen bonds : angle 4.41351 ( 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 374 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 306 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.5899 (mmm) cc_final: 0.5554 (mmt) REVERT: E 206 LYS cc_start: 0.6806 (OUTLIER) cc_final: 0.5877 (ptmm) REVERT: E 209 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6742 (tt) REVERT: F 72 MET cc_start: 0.6451 (mmp) cc_final: 0.6109 (mmp) REVERT: F 124 LYS cc_start: 0.8367 (tttm) cc_final: 0.7938 (ttpp) REVERT: F 187 GLN cc_start: 0.7486 (tp40) cc_final: 0.7073 (mm-40) REVERT: F 188 LYS cc_start: 0.8262 (tptm) cc_final: 0.7756 (ttmt) REVERT: G 133 GLU cc_start: 0.7344 (tp30) cc_final: 0.7002 (tp30) REVERT: G 188 LYS cc_start: 0.8839 (tttt) cc_final: 0.8613 (ttpt) REVERT: G 206 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8759 (pttp) REVERT: H 72 MET cc_start: 0.6834 (tpp) cc_final: 0.6612 (tpp) REVERT: H 197 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8400 (tptt) REVERT: H 210 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8984 (ttt180) REVERT: J 64 ASP cc_start: 0.8312 (p0) cc_final: 0.7998 (p0) REVERT: J 68 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8480 (mmmm) REVERT: J 124 LYS cc_start: 0.8598 (tttm) cc_final: 0.8308 (ttpp) REVERT: K 64 ASP cc_start: 0.8119 (p0) cc_final: 0.7866 (p0) REVERT: K 68 LYS cc_start: 0.8594 (mmmm) cc_final: 0.8244 (mmmt) REVERT: L 40 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7878 (mttp) REVERT: L 68 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8380 (mmtm) REVERT: L 197 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8415 (mttt) REVERT: L 206 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8585 (tttp) REVERT: M 136 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8175 (pt) REVERT: M 152 ASN cc_start: 0.7380 (t0) cc_final: 0.6972 (p0) REVERT: M 187 GLN cc_start: 0.8338 (tp40) cc_final: 0.7881 (mm-40) REVERT: M 197 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7658 (mttt) REVERT: M 198 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8016 (mtmt) REVERT: N 72 MET cc_start: 0.5164 (mmt) cc_final: 0.4943 (ttm) REVERT: N 206 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8436 (pttp) outliers start: 68 outliers final: 47 residues processed: 345 average time/residue: 0.1511 time to fit residues: 76.8182 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 : 0.651 ------------------------------------------------------------------------------- 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 37 MET 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 206 LYS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain 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 182 ILE 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 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 222 ASP Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU 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 Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 61 ASN G 187 GLN K 107 GLN L 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.145787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.102538 restraints weight = 21974.523| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.36 r_work: 0.2729 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18152 Z= 0.200 Angle : 0.598 6.766 24901 Z= 0.338 Chirality : 0.042 0.163 2722 Planarity : 0.003 0.032 2758 Dihedral : 19.998 89.568 3258 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.67 % Allowed : 24.67 % 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 aren not related in a simple way. whole: 0.42 (0.19), residues: 1890 helix: 2.45 (0.17), residues: 860 sheet: -0.41 (0.26), residues: 350 loop : -2.34 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 210 TYR 0.012 0.001 TYR K 200 PHE 0.026 0.002 PHE K 165 TRP 0.010 0.002 TRP F 196 HIS 0.005 0.003 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00466 (18152) covalent geometry : angle 0.59752 (24901) hydrogen bonds : bond 0.05928 ( 869) hydrogen bonds : angle 4.47814 ( 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 372 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 294 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 206 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6219 (pttp) REVERT: E 209 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7020 (tt) REVERT: F 124 LYS cc_start: 0.8584 (tttm) cc_final: 0.8167 (ttpp) REVERT: F 132 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6557 (mtp180) REVERT: F 187 GLN cc_start: 0.7592 (tp40) cc_final: 0.7185 (mm-40) REVERT: F 188 LYS cc_start: 0.8356 (tptm) cc_final: 0.7829 (ttmt) REVERT: G 133 GLU cc_start: 0.7455 (tp30) cc_final: 0.7172 (tp30) REVERT: G 188 LYS cc_start: 0.8916 (tttt) cc_final: 0.8651 (ttpt) REVERT: H 152 ASN cc_start: 0.8237 (t0) cc_final: 0.7735 (m-40) REVERT: H 197 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8519 (tptt) REVERT: H 210 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.9027 (ttt180) REVERT: I 133 GLU cc_start: 0.8845 (tp30) cc_final: 0.8354 (tp30) REVERT: J 68 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8527 (mmmm) REVERT: J 124 LYS cc_start: 0.8784 (tttm) cc_final: 0.8490 (ttpp) REVERT: J 206 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8557 (tttp) REVERT: K 64 ASP cc_start: 0.8205 (p0) cc_final: 0.7955 (p0) REVERT: K 68 LYS cc_start: 0.8681 (mmmm) cc_final: 0.8307 (mmmt) REVERT: K 72 MET cc_start: 0.8261 (mmm) cc_final: 0.7846 (tpp) REVERT: K 152 ASN cc_start: 0.8225 (t0) cc_final: 0.7553 (m110) REVERT: K 197 LYS cc_start: 0.8955 (tppt) cc_final: 0.8720 (tppt) REVERT: L 40 LYS cc_start: 0.8250 (mtpt) cc_final: 0.8006 (mttp) REVERT: L 68 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8409 (mmtm) REVERT: L 197 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8503 (mttt) REVERT: L 206 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8764 (tttp) REVERT: M 136 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8334 (pt) REVERT: M 152 ASN cc_start: 0.7530 (t0) cc_final: 0.6936 (p0) REVERT: M 187 GLN cc_start: 0.8454 (tp40) cc_final: 0.7974 (mm-40) REVERT: M 197 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7748 (mttt) REVERT: M 198 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8054 (mtmt) REVERT: N 72 MET cc_start: 0.5267 (mmt) cc_final: 0.5016 (ttm) REVERT: N 157 LYS cc_start: 0.6314 (tptp) cc_final: 0.6051 (tptp) REVERT: N 206 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8567 (pttp) outliers start: 78 outliers final: 53 residues processed: 339 average time/residue: 0.1448 time to fit residues: 72.0750 Evaluate side-chains 353 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 292 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 132 ARG 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 182 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL 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 I residue 222 ASP Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 128 VAL 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 182 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 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 61 ASN L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.145689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.102358 restraints weight = 21960.879| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.27 r_work: 0.2738 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18152 Z= 0.199 Angle : 0.593 7.688 24901 Z= 0.336 Chirality : 0.042 0.160 2722 Planarity : 0.003 0.033 2758 Dihedral : 20.003 89.720 3258 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.85 % Allowed : 24.37 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.19), residues: 1890 helix: 2.38 (0.17), residues: 860 sheet: -0.45 (0.26), residues: 350 loop : -2.39 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 210 TYR 0.013 0.001 TYR L 65 PHE 0.026 0.002 PHE K 165 TRP 0.009 0.001 TRP F 196 HIS 0.005 0.003 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00463 (18152) covalent geometry : angle 0.59269 (24901) hydrogen bonds : bond 0.05770 ( 869) hydrogen bonds : angle 4.49934 ( 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 378 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 297 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6932 (mtm) cc_final: 0.6565 (tpp) REVERT: E 203 MET cc_start: 0.6225 (mmm) cc_final: 0.5791 (mmt) REVERT: E 206 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6034 (pttp) REVERT: F 72 MET cc_start: 0.6479 (tpp) cc_final: 0.6069 (tpp) REVERT: F 124 LYS cc_start: 0.8501 (tttm) cc_final: 0.8100 (ttpp) REVERT: F 132 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6533 (mtp180) REVERT: F 135 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8246 (mt-10) REVERT: F 187 GLN cc_start: 0.7518 (tp40) cc_final: 0.7155 (mm-40) REVERT: F 188 LYS cc_start: 0.8328 (tptm) cc_final: 0.7828 (ttmt) REVERT: F 210 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8756 (ttt180) REVERT: G 133 GLU cc_start: 0.7351 (tp30) cc_final: 0.7067 (tp30) REVERT: G 188 LYS cc_start: 0.8880 (tttt) cc_final: 0.8596 (ttpt) REVERT: H 72 MET cc_start: 0.6963 (tpp) cc_final: 0.6719 (tpp) REVERT: H 152 ASN cc_start: 0.8222 (t0) cc_final: 0.7848 (m-40) REVERT: H 197 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8275 (tptp) REVERT: H 210 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8975 (ttt180) REVERT: I 133 GLU cc_start: 0.8840 (tp30) cc_final: 0.8371 (tp30) REVERT: J 68 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8578 (mmmm) REVERT: J 124 LYS cc_start: 0.8681 (tttm) cc_final: 0.8425 (ttpp) REVERT: J 206 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8442 (tttp) REVERT: K 68 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8340 (mmmt) REVERT: K 72 MET cc_start: 0.8078 (mmm) cc_final: 0.7692 (tpp) REVERT: K 152 ASN cc_start: 0.8268 (t0) cc_final: 0.7696 (m-40) REVERT: K 197 LYS cc_start: 0.8935 (tppt) cc_final: 0.8663 (tppt) REVERT: L 40 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7928 (mttp) REVERT: L 68 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8451 (mmtm) REVERT: L 197 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8454 (mttt) REVERT: L 206 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8652 (tttp) REVERT: L 210 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8937 (ttt180) REVERT: M 43 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7484 (mtpp) REVERT: M 136 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8387 (pt) REVERT: M 152 ASN cc_start: 0.7558 (t0) cc_final: 0.6861 (m-40) REVERT: M 187 GLN cc_start: 0.8316 (tp40) cc_final: 0.7831 (mm-40) REVERT: M 197 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7637 (mttt) REVERT: M 198 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8049 (mtmt) REVERT: N 72 MET cc_start: 0.5269 (mmt) cc_final: 0.5002 (ttm) REVERT: N 157 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6124 (tptp) REVERT: N 206 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8493 (pttp) outliers start: 81 outliers final: 57 residues processed: 342 average time/residue: 0.1339 time to fit residues: 66.9956 Evaluate side-chains 362 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 294 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 142 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 210 ARG 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 182 ILE Chi-restraints excluded: chain H residue 83 THR 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 I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 128 VAL 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 182 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 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 157 LYS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain N residue 223 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN J 61 ASN L 187 GLN N 107 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.144248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.102560 restraints weight = 22129.088| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.27 r_work: 0.2713 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 18152 Z= 0.239 Angle : 0.640 11.403 24901 Z= 0.360 Chirality : 0.044 0.243 2722 Planarity : 0.004 0.038 2758 Dihedral : 19.964 89.709 3258 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.79 % Allowed : 24.61 % 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 aren not related in a simple way. whole: 0.18 (0.18), residues: 1890 helix: 2.25 (0.17), residues: 860 sheet: -0.52 (0.26), residues: 350 loop : -2.46 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 210 TYR 0.012 0.002 TYR K 200 PHE 0.029 0.003 PHE K 165 TRP 0.011 0.002 TRP E 177 HIS 0.006 0.003 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00563 (18152) covalent geometry : angle 0.63964 (24901) hydrogen bonds : bond 0.06608 ( 869) hydrogen bonds : angle 4.55240 ( 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 375 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.6307 (mmm) cc_final: 0.5846 (mmt) REVERT: E 206 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6219 (pttp) REVERT: E 218 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8034 (tt) REVERT: F 72 MET cc_start: 0.6544 (tpp) cc_final: 0.6290 (tpp) REVERT: F 124 LYS cc_start: 0.8559 (tttm) cc_final: 0.8181 (ttpp) REVERT: F 132 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6555 (mtp180) REVERT: F 135 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8212 (mt-10) REVERT: F 164 TYR cc_start: 0.8502 (t80) cc_final: 0.8256 (t80) REVERT: F 187 GLN cc_start: 0.7593 (tp40) cc_final: 0.7210 (mm-40) REVERT: F 188 LYS cc_start: 0.8312 (tptm) cc_final: 0.7816 (ttmt) REVERT: F 210 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8768 (ttt180) REVERT: G 64 ASP cc_start: 0.8247 (p0) cc_final: 0.7901 (p0) REVERT: G 133 GLU cc_start: 0.7409 (tp30) cc_final: 0.7151 (tp30) REVERT: G 188 LYS cc_start: 0.8889 (tttt) cc_final: 0.8619 (ttpt) REVERT: H 68 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8177 (mtpt) REVERT: H 152 ASN cc_start: 0.8265 (t0) cc_final: 0.7874 (m110) REVERT: H 197 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8347 (tptp) REVERT: H 210 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8990 (ttt180) REVERT: I 133 GLU cc_start: 0.8900 (tp30) cc_final: 0.8455 (tp30) REVERT: J 68 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8602 (mmmm) REVERT: J 124 LYS cc_start: 0.8733 (tttm) cc_final: 0.8485 (ttpp) REVERT: K 68 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8379 (mmmt) REVERT: K 72 MET cc_start: 0.8104 (mmm) cc_final: 0.7743 (tpp) REVERT: K 152 ASN cc_start: 0.8335 (t0) cc_final: 0.7824 (m-40) REVERT: K 197 LYS cc_start: 0.8946 (tppt) cc_final: 0.8665 (tppt) REVERT: K 210 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8978 (ttt180) REVERT: L 68 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8424 (mmtm) REVERT: L 197 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8440 (mttm) REVERT: L 199 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.7958 (p0) REVERT: L 206 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8751 (tttp) REVERT: L 210 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8978 (ttt180) REVERT: M 40 LYS cc_start: 0.7315 (mtpt) cc_final: 0.6864 (mptt) REVERT: M 43 LYS cc_start: 0.7701 (ttmm) cc_final: 0.7460 (mtpp) REVERT: M 136 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8512 (pt) REVERT: M 152 ASN cc_start: 0.7635 (t0) cc_final: 0.6867 (m-40) REVERT: M 187 GLN cc_start: 0.8331 (tp40) cc_final: 0.7832 (mm-40) REVERT: M 197 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7669 (mttt) REVERT: M 198 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8056 (mtmt) REVERT: N 72 MET cc_start: 0.5304 (mmt) cc_final: 0.5020 (ttm) REVERT: N 157 LYS cc_start: 0.6459 (OUTLIER) cc_final: 0.6110 (tptp) REVERT: N 206 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8479 (pttp) outliers start: 80 outliers final: 58 residues processed: 341 average time/residue: 0.1215 time to fit residues: 60.3924 Evaluate side-chains 366 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 295 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 E residue 222 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 142 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 210 ARG 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 83 THR 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 I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 182 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 218 ILE Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 139 TRP 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 120 THR 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 182 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 210 ARG Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 210 ARG Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain N residue 206 LYS Chi-restraints excluded: chain N residue 223 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 98 optimal weight: 0.0010 chunk 23 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 61 ASN 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 = 0.3610 r_free = 0.3610 target = 0.151241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.109499 restraints weight = 21887.789| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.31 r_work: 0.2820 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18152 Z= 0.122 Angle : 0.528 9.847 24901 Z= 0.301 Chirality : 0.040 0.237 2722 Planarity : 0.003 0.027 2758 Dihedral : 19.943 89.993 3258 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.89 % Allowed : 25.33 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 1890 helix: 2.50 (0.17), residues: 860 sheet: -0.40 (0.26), residues: 350 loop : -2.37 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 210 TYR 0.012 0.001 TYR L 110 PHE 0.019 0.001 PHE K 165 TRP 0.006 0.001 TRP H 96 HIS 0.003 0.002 HIS K 185 Details of bonding type rmsd covalent geometry : bond 0.00256 (18152) covalent geometry : angle 0.52757 (24901) hydrogen bonds : bond 0.04015 ( 869) hydrogen bonds : angle 4.44487 ( 2499) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3780 Ramachandran restraints generated. 1890 Oldfield, 0 Emsley, 1890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 314 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 203 MET cc_start: 0.6364 (mmm) cc_final: 0.5875 (mmt) REVERT: E 206 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6206 (pptt) REVERT: E 218 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8036 (tt) REVERT: F 72 MET cc_start: 0.6557 (tpp) cc_final: 0.6339 (tpp) REVERT: F 124 LYS cc_start: 0.8440 (tttm) cc_final: 0.8024 (ttpp) REVERT: F 135 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8185 (mt-10) REVERT: F 187 GLN cc_start: 0.7669 (tp40) cc_final: 0.7320 (mm-40) REVERT: F 188 LYS cc_start: 0.8386 (tptm) cc_final: 0.7820 (ttmt) REVERT: F 198 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6803 (mtmt) REVERT: G 64 ASP cc_start: 0.8336 (p0) cc_final: 0.8006 (p0) REVERT: G 105 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8028 (mt0) REVERT: G 188 LYS cc_start: 0.8918 (tttt) cc_final: 0.8624 (ttpt) REVERT: H 68 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8075 (mtpt) REVERT: H 140 ASN cc_start: 0.8525 (p0) cc_final: 0.8226 (p0) REVERT: H 152 ASN cc_start: 0.8216 (t0) cc_final: 0.7744 (m110) REVERT: H 197 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8345 (tptp) REVERT: H 210 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.9018 (ttt180) REVERT: I 133 GLU cc_start: 0.8718 (tp30) cc_final: 0.8263 (tp30) REVERT: J 68 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8456 (mmmm) REVERT: J 124 LYS cc_start: 0.8654 (tttm) cc_final: 0.8346 (ttpp) REVERT: K 64 ASP cc_start: 0.8249 (p0) cc_final: 0.7970 (p0) REVERT: K 68 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8239 (mmmt) REVERT: K 72 MET cc_start: 0.8271 (mmm) cc_final: 0.7807 (tpp) REVERT: K 152 ASN cc_start: 0.8248 (t0) cc_final: 0.7593 (m-40) REVERT: K 197 LYS cc_start: 0.8874 (tppt) cc_final: 0.8597 (tppt) REVERT: K 210 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.9027 (ttt180) REVERT: L 40 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7792 (mttm) REVERT: L 68 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8342 (mmtm) REVERT: L 197 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8447 (mttm) REVERT: L 206 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8601 (tttp) REVERT: M 43 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7421 (mtpp) REVERT: M 152 ASN cc_start: 0.7432 (t0) cc_final: 0.6636 (m-40) REVERT: M 187 GLN cc_start: 0.8425 (tp40) cc_final: 0.7949 (mm-40) REVERT: M 197 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7632 (mttt) REVERT: M 198 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8058 (mtmt) REVERT: M 210 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.8561 (ttm170) REVERT: N 72 MET cc_start: 0.5192 (mmt) cc_final: 0.4927 (ttm) REVERT: N 132 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.6258 (ttm110) REVERT: N 206 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8495 (pttp) outliers start: 65 outliers final: 38 residues processed: 356 average time/residue: 0.1232 time to fit residues: 64.3159 Evaluate side-chains 355 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 307 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 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 H residue 130 GLU Chi-restraints excluded: chain H residue 174 THR 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 168 ILE 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 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 210 ARG Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 206 LYS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 128 VAL 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 M residue 210 ARG Chi-restraints excluded: chain N residue 132 ARG Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 56 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 chunk 142 optimal weight: 1.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 61 ASN ** I 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN J 61 ASN L 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.150674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.109694 restraints weight = 22042.684| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.22 r_work: 0.2823 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18152 Z= 0.129 Angle : 0.541 11.596 24901 Z= 0.306 Chirality : 0.040 0.223 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.876 89.605 3258 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.53 % Allowed : 26.11 % 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 aren not related in a simple way. whole: 0.54 (0.19), residues: 1890 helix: 2.60 (0.17), residues: 860 sheet: -0.37 (0.26), residues: 350 loop : -2.36 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 210 TYR 0.012 0.001 TYR L 110 PHE 0.019 0.002 PHE I 165 TRP 0.006 0.001 TRP H 96 HIS 0.003 0.002 HIS K 185 Details of bonding type rmsd covalent geometry : bond 0.00278 (18152) covalent geometry : angle 0.54069 (24901) hydrogen bonds : bond 0.04291 ( 869) hydrogen bonds : angle 4.31105 ( 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 371 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 312 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6853 (mtm) cc_final: 0.6570 (tpp) REVERT: E 203 MET cc_start: 0.5946 (mmm) cc_final: 0.5665 (mmt) REVERT: E 206 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.5888 (pttp) REVERT: E 218 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7922 (tt) REVERT: F 72 MET cc_start: 0.6497 (tpp) cc_final: 0.6252 (tpp) REVERT: F 124 LYS cc_start: 0.8348 (tttm) cc_final: 0.7938 (ttpp) REVERT: F 132 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6426 (mtp180) REVERT: F 135 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8123 (mt-10) REVERT: F 187 GLN cc_start: 0.7558 (tp40) cc_final: 0.7209 (mm-40) REVERT: F 188 LYS cc_start: 0.8331 (tptm) cc_final: 0.7800 (ttmt) REVERT: F 198 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6796 (mtmt) REVERT: G 64 ASP cc_start: 0.8209 (p0) cc_final: 0.7866 (p0) REVERT: G 133 GLU cc_start: 0.7060 (tp30) cc_final: 0.6852 (tp30) REVERT: G 188 LYS cc_start: 0.8856 (tttt) cc_final: 0.8580 (ttpt) REVERT: H 68 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8086 (mtpt) REVERT: H 140 ASN cc_start: 0.8470 (p0) cc_final: 0.8165 (p0) REVERT: H 152 ASN cc_start: 0.8185 (t0) cc_final: 0.7812 (m110) REVERT: H 197 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8335 (tptp) REVERT: H 210 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8996 (ttt180) REVERT: I 133 GLU cc_start: 0.8710 (tp30) cc_final: 0.8245 (tp30) REVERT: J 68 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8448 (mmmm) REVERT: J 105 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8075 (mt0) REVERT: J 124 LYS cc_start: 0.8545 (tttm) cc_final: 0.8280 (ttpp) REVERT: K 64 ASP cc_start: 0.8204 (p0) cc_final: 0.7931 (p0) REVERT: K 68 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8248 (mmmt) REVERT: K 72 MET cc_start: 0.8022 (mmm) cc_final: 0.7626 (tpp) REVERT: K 152 ASN cc_start: 0.8225 (t0) cc_final: 0.7648 (m-40) REVERT: K 197 LYS cc_start: 0.8916 (tppt) cc_final: 0.8638 (tppt) REVERT: K 210 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8962 (ttt180) REVERT: L 40 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7891 (mttp) REVERT: L 68 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8388 (mmtm) REVERT: L 197 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8393 (mttm) REVERT: L 206 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8562 (tttp) REVERT: L 210 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8925 (ttt180) REVERT: M 43 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7389 (mtpp) REVERT: M 152 ASN cc_start: 0.7496 (t0) cc_final: 0.6813 (m-40) REVERT: M 187 GLN cc_start: 0.8336 (tp40) cc_final: 0.7852 (mm-40) REVERT: M 197 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7673 (mttt) REVERT: M 198 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8048 (mtmt) REVERT: M 210 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8518 (ttm170) REVERT: N 72 MET cc_start: 0.5198 (mmt) cc_final: 0.4953 (ttm) REVERT: N 132 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6279 (ttm110) REVERT: N 206 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8420 (pttp) outliers start: 59 outliers final: 37 residues processed: 352 average time/residue: 0.1272 time to fit residues: 65.2195 Evaluate side-chains 356 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 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 H residue 210 ARG Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 128 VAL 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 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 210 ARG 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 130 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 M residue 210 ARG Chi-restraints excluded: chain N residue 132 ARG Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 162 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 133 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 61 ASN J 105 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 = 0.3587 r_free = 0.3587 target = 0.149293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.106367 restraints weight = 21935.265| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.27 r_work: 0.2794 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18152 Z= 0.139 Angle : 0.548 12.606 24901 Z= 0.310 Chirality : 0.040 0.211 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.853 89.159 3258 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.29 % Allowed : 26.35 % 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 aren not related in a simple way. whole: 0.53 (0.19), residues: 1890 helix: 2.60 (0.17), residues: 860 sheet: -0.38 (0.26), residues: 350 loop : -2.37 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 210 TYR 0.012 0.001 TYR L 110 PHE 0.020 0.002 PHE K 165 TRP 0.007 0.001 TRP F 177 HIS 0.003 0.002 HIS H 185 Details of bonding type rmsd covalent geometry : bond 0.00307 (18152) covalent geometry : angle 0.54842 (24901) hydrogen bonds : bond 0.04472 ( 869) hydrogen bonds : angle 4.31639 ( 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 359 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 304 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6860 (mtm) cc_final: 0.6577 (tpp) REVERT: E 203 MET cc_start: 0.5860 (mmm) cc_final: 0.5582 (mmt) REVERT: E 206 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.5944 (pttp) REVERT: E 218 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7847 (tt) REVERT: F 72 MET cc_start: 0.6534 (tpp) cc_final: 0.6277 (tpp) REVERT: F 124 LYS cc_start: 0.8351 (tttm) cc_final: 0.7943 (ttpp) REVERT: F 132 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6451 (mtp180) REVERT: F 135 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8111 (mt-10) REVERT: F 187 GLN cc_start: 0.7562 (tp40) cc_final: 0.7218 (mm-40) REVERT: F 188 LYS cc_start: 0.8357 (tptm) cc_final: 0.7818 (ttmt) REVERT: F 198 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6799 (mtmt) REVERT: G 64 ASP cc_start: 0.8225 (p0) cc_final: 0.7885 (p0) REVERT: G 133 GLU cc_start: 0.7108 (tp30) cc_final: 0.6883 (tp30) REVERT: G 188 LYS cc_start: 0.8848 (tttt) cc_final: 0.8574 (ttpt) REVERT: H 68 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8083 (mtpt) REVERT: H 140 ASN cc_start: 0.8498 (p0) cc_final: 0.8210 (p0) REVERT: H 152 ASN cc_start: 0.8179 (t0) cc_final: 0.7810 (m-40) REVERT: H 197 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8325 (tptp) REVERT: H 210 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8999 (ttt180) REVERT: I 133 GLU cc_start: 0.8734 (tp30) cc_final: 0.8241 (tp30) REVERT: J 68 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8507 (mmmm) REVERT: J 124 LYS cc_start: 0.8568 (tttm) cc_final: 0.8306 (ttpp) REVERT: K 40 LYS cc_start: 0.7847 (mtpt) cc_final: 0.7411 (mttp) REVERT: K 64 ASP cc_start: 0.8253 (p0) cc_final: 0.7969 (p0) REVERT: K 68 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8230 (mmmt) REVERT: K 72 MET cc_start: 0.8025 (mmm) cc_final: 0.7631 (tpp) REVERT: K 152 ASN cc_start: 0.8229 (t0) cc_final: 0.7652 (m-40) REVERT: K 197 LYS cc_start: 0.8928 (tppt) cc_final: 0.8651 (tppt) REVERT: K 210 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8940 (ttt180) REVERT: L 68 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8387 (mmtm) REVERT: L 197 LYS cc_start: 0.8907 (ttmm) cc_final: 0.8456 (mttt) REVERT: L 206 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8582 (tttp) REVERT: L 210 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8927 (ttt180) REVERT: M 43 LYS cc_start: 0.7632 (ttmm) cc_final: 0.7406 (mtpp) REVERT: M 152 ASN cc_start: 0.7457 (t0) cc_final: 0.6731 (m-40) REVERT: M 187 GLN cc_start: 0.8331 (tp40) cc_final: 0.7856 (mm-40) REVERT: M 198 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8103 (mtmt) REVERT: M 210 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8497 (ttm170) REVERT: N 72 MET cc_start: 0.5175 (mmt) cc_final: 0.4927 (ttm) REVERT: N 132 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.6083 (ttm110) REVERT: N 159 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7649 (m) REVERT: N 206 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8443 (pttp) outliers start: 55 outliers final: 39 residues processed: 339 average time/residue: 0.1282 time to fit residues: 63.2934 Evaluate side-chains 354 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 206 LYS Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 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 H residue 210 ARG Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 128 VAL 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 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 210 ARG 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 199 ASP Chi-restraints excluded: chain M residue 210 ARG Chi-restraints excluded: chain N residue 132 ARG Chi-restraints excluded: chain N residue 157 LYS Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 0.0170 chunk 173 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN I 61 ASN ** I 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.151204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.109957 restraints weight = 22121.915| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.19 r_work: 0.2802 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18152 Z= 0.123 Angle : 0.526 12.691 24901 Z= 0.297 Chirality : 0.039 0.214 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.785 89.702 3258 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.17 % Allowed : 26.35 % 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 aren not related in a simple way. whole: 0.58 (0.19), residues: 1890 helix: 2.64 (0.17), residues: 860 sheet: -0.36 (0.26), residues: 350 loop : -2.35 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 210 TYR 0.012 0.001 TYR L 110 PHE 0.019 0.002 PHE K 165 TRP 0.006 0.001 TRP G 96 HIS 0.003 0.002 HIS K 185 Details of bonding type rmsd covalent geometry : bond 0.00265 (18152) covalent geometry : angle 0.52565 (24901) hydrogen bonds : bond 0.03997 ( 869) hydrogen bonds : angle 4.29121 ( 2499) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3769.92 seconds wall clock time: 65 minutes 35.48 seconds (3935.48 seconds total)