Starting phenix.real_space_refine on Fri Sep 27 22:36:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/09_2024/7ub2_26434.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/09_2024/7ub2_26434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/09_2024/7ub2_26434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/09_2024/7ub2_26434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/09_2024/7ub2_26434.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ub2_26434/09_2024/7ub2_26434.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 6.37, per 1000 atoms: 0.36 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: 4.48 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 5.51 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: 4.85 Time building geometry restraints manager: 5.14 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 37.810 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.830 ------------------------------------------------------------------------------- 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= 0.162 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (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 TRP 0.003 0.000 TRP J 96 HIS 0.002 0.001 HIS L 185 PHE 0.013 0.001 PHE E 165 TYR 0.019 0.001 TYR E 60 ARG 0.001 0.000 ARG M 132 *********************** 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 fitting. rotamer outliers: 10 poor density : 384 time to evaluate : 1.865 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: 0.3136 time to fit residues: 181.3972 Evaluate side-chains 344 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 340 time to evaluate : 3.689 ------------------------------------------------------------------------------- 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 167 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 155 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 0.0370 chunk 115 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18152 Z= 0.150 Angle : 0.521 6.055 24901 Z= 0.294 Chirality : 0.039 0.151 2722 Planarity : 0.003 0.020 2758 Dihedral : 19.885 89.480 3258 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.22 % Allowed : 27.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 1890 helix: 2.92 (0.17), residues: 850 sheet: -0.29 (0.26), residues: 350 loop : -1.94 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 96 HIS 0.003 0.001 HIS H 185 PHE 0.015 0.001 PHE K 165 TYR 0.012 0.001 TYR N 200 ARG 0.001 0.000 ARG F 210 *********************** 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 372 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 335 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7602 (tmtt) REVERT: F 72 MET cc_start: 0.6387 (mmp) cc_final: 0.6012 (mmp) REVERT: F 124 LYS cc_start: 0.7847 (tttm) cc_final: 0.7515 (tttp) REVERT: F 159 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7770 (m) REVERT: F 187 GLN cc_start: 0.7009 (tp40) cc_final: 0.6553 (mm-40) REVERT: F 188 LYS cc_start: 0.7994 (tptm) cc_final: 0.7510 (ttmt) REVERT: G 166 GLN cc_start: 0.8794 (tt0) cc_final: 0.8551 (tt0) REVERT: G 188 LYS cc_start: 0.8471 (tttt) cc_final: 0.8200 (ttpt) REVERT: H 72 MET cc_start: 0.6668 (tpp) cc_final: 0.6405 (tpp) REVERT: H 105 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: H 197 LYS cc_start: 0.8346 (ttmm) cc_final: 0.7775 (tptp) REVERT: I 222 ASP cc_start: 0.8287 (m-30) cc_final: 0.8027 (m-30) REVERT: J 72 MET cc_start: 0.7730 (tpp) cc_final: 0.7386 (tpp) REVERT: K 40 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7493 (mttt) REVERT: K 68 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7856 (mmmt) REVERT: K 142 LEU cc_start: 0.9359 (tp) cc_final: 0.9116 (tp) REVERT: K 187 GLN cc_start: 0.8568 (tp40) cc_final: 0.8334 (mm110) REVERT: L 40 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7651 (mttp) REVERT: L 68 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8070 (mmtm) REVERT: L 197 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7959 (mttt) REVERT: M 124 LYS cc_start: 0.8024 (tttm) cc_final: 0.7779 (ttmm) REVERT: M 136 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7358 (pt) REVERT: M 152 ASN cc_start: 0.6786 (t0) cc_final: 0.6367 (p0) REVERT: M 187 GLN cc_start: 0.8130 (tp40) cc_final: 0.7620 (mm-40) REVERT: M 197 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7348 (mttt) REVERT: M 198 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7778 (mtmt) REVERT: N 94 TYR cc_start: 0.8814 (m-10) cc_final: 0.8610 (m-10) REVERT: N 124 LYS cc_start: 0.7568 (tttm) cc_final: 0.7307 (ttmt) REVERT: N 187 GLN cc_start: 0.7402 (tp40) cc_final: 0.7174 (mm110) outliers start: 37 outliers final: 20 residues processed: 357 average time/residue: 0.3024 time to fit residues: 159.7992 Evaluate side-chains 344 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 321 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 ASP 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 199 ASP Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 199 ASP 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 99 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 107 GLN H 107 GLN I 61 ASN I 107 GLN I 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 18152 Z= 0.438 Angle : 0.702 7.639 24901 Z= 0.388 Chirality : 0.047 0.180 2722 Planarity : 0.004 0.033 2758 Dihedral : 20.006 88.882 3258 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.61 % Allowed : 23.71 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1890 helix: 2.35 (0.17), residues: 860 sheet: -0.47 (0.25), residues: 350 loop : -2.24 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 177 HIS 0.007 0.004 HIS I 185 PHE 0.034 0.003 PHE K 165 TYR 0.019 0.002 TYR J 60 ARG 0.003 0.001 ARG M 210 *********************** 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 385 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 308 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7679 (tmtt) REVERT: E 206 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5220 (pttp) REVERT: F 72 MET cc_start: 0.6263 (mmp) cc_final: 0.5906 (mmp) REVERT: F 79 MET cc_start: 0.7726 (tpt) cc_final: 0.6983 (ttm) REVERT: F 124 LYS cc_start: 0.8292 (tttm) cc_final: 0.7707 (ttpp) REVERT: F 187 GLN cc_start: 0.6870 (tp40) cc_final: 0.6471 (mm-40) REVERT: F 188 LYS cc_start: 0.7814 (tptm) cc_final: 0.7233 (ttmt) REVERT: G 133 GLU cc_start: 0.7272 (tp30) cc_final: 0.6886 (tp30) REVERT: G 188 LYS cc_start: 0.8404 (tttt) cc_final: 0.8091 (ttpt) REVERT: G 199 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7894 (p0) REVERT: H 197 LYS cc_start: 0.8479 (ttmm) cc_final: 0.7954 (tptp) REVERT: I 47 LYS cc_start: 0.8640 (tppt) cc_final: 0.8310 (ttmm) REVERT: I 133 GLU cc_start: 0.8687 (tp30) cc_final: 0.8151 (tp30) REVERT: I 222 ASP cc_start: 0.8468 (m-30) cc_final: 0.8193 (m-30) REVERT: J 72 MET cc_start: 0.7898 (tpp) cc_final: 0.7616 (tpp) REVERT: J 124 LYS cc_start: 0.8656 (tttm) cc_final: 0.8169 (ttpp) REVERT: J 133 GLU cc_start: 0.8746 (tp30) cc_final: 0.8489 (tp30) REVERT: K 64 ASP cc_start: 0.7920 (p0) cc_final: 0.7603 (p0) REVERT: K 68 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8096 (mmmt) REVERT: K 124 LYS cc_start: 0.8302 (tttp) cc_final: 0.8021 (ttpt) REVERT: L 40 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7907 (mttp) REVERT: L 68 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8265 (mmtm) REVERT: L 180 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7838 (ttpp) REVERT: L 187 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8244 (mm110) REVERT: L 197 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8164 (mttt) REVERT: L 206 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8421 (tttp) REVERT: M 136 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7905 (pt) REVERT: M 152 ASN cc_start: 0.7285 (t0) cc_final: 0.6662 (p0) REVERT: M 187 GLN cc_start: 0.7972 (tp40) cc_final: 0.7420 (mm-40) REVERT: M 197 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7366 (mttt) REVERT: M 198 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7797 (mtmt) REVERT: N 124 LYS cc_start: 0.7597 (tttm) cc_final: 0.7292 (ttmt) REVERT: N 187 GLN cc_start: 0.7332 (tp40) cc_final: 0.7051 (mm-40) REVERT: N 198 LYS cc_start: 0.7023 (mmtt) cc_final: 0.6790 (mmtt) REVERT: N 206 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7875 (pttp) outliers start: 77 outliers final: 45 residues processed: 349 average time/residue: 0.3143 time to fit residues: 158.8556 Evaluate side-chains 351 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 301 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 136 LEU 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 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 143 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 174 THR 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 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.0870 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 I 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18152 Z= 0.152 Angle : 0.533 9.366 24901 Z= 0.302 Chirality : 0.041 0.240 2722 Planarity : 0.003 0.026 2758 Dihedral : 20.045 88.772 3258 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.65 % Allowed : 24.85 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1890 helix: 2.52 (0.17), residues: 870 sheet: -0.42 (0.26), residues: 350 loop : -2.22 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 96 HIS 0.003 0.002 HIS H 185 PHE 0.017 0.001 PHE I 165 TYR 0.013 0.001 TYR J 60 ARG 0.001 0.000 ARG M 210 *********************** 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 fitting. rotamer outliers: 61 poor density : 313 time to evaluate : 2.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7827 (tmtt) REVERT: F 72 MET cc_start: 0.6106 (mmp) cc_final: 0.5770 (mmp) REVERT: F 79 MET cc_start: 0.7778 (tpt) cc_final: 0.7116 (ttm) REVERT: F 124 LYS cc_start: 0.8024 (tttm) cc_final: 0.7445 (ttpp) REVERT: F 187 GLN cc_start: 0.7013 (tp40) cc_final: 0.6541 (mm-40) REVERT: F 188 LYS cc_start: 0.7835 (tptm) cc_final: 0.7258 (ttmt) REVERT: F 198 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.6140 (mtmt) REVERT: G 133 GLU cc_start: 0.7083 (tp30) cc_final: 0.6758 (tp30) REVERT: G 166 GLN cc_start: 0.8880 (tt0) cc_final: 0.8542 (tt0) REVERT: G 188 LYS cc_start: 0.8461 (tttt) cc_final: 0.8197 (ttpt) REVERT: H 72 MET cc_start: 0.6571 (tpp) cc_final: 0.6320 (tpp) REVERT: H 197 LYS cc_start: 0.8408 (ttmm) cc_final: 0.7925 (tptp) REVERT: I 222 ASP cc_start: 0.8405 (m-30) cc_final: 0.8122 (m-30) REVERT: J 68 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8359 (mmmm) REVERT: J 72 MET cc_start: 0.7625 (tpp) cc_final: 0.7290 (tpp) REVERT: J 124 LYS cc_start: 0.8412 (tttm) cc_final: 0.7924 (ttpp) REVERT: J 133 GLU cc_start: 0.8563 (tp30) cc_final: 0.8355 (tp30) REVERT: K 68 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8014 (mmmt) REVERT: K 79 MET cc_start: 0.9033 (ttt) cc_final: 0.8672 (ttm) REVERT: K 124 LYS cc_start: 0.8048 (tttp) cc_final: 0.7760 (ttpt) REVERT: L 40 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7751 (mttp) REVERT: L 68 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8225 (mmtm) REVERT: L 197 LYS cc_start: 0.8520 (ttmm) cc_final: 0.8059 (mttt) REVERT: M 43 LYS cc_start: 0.7522 (ttmm) cc_final: 0.7313 (mtpp) REVERT: M 152 ASN cc_start: 0.6978 (t0) cc_final: 0.6365 (p0) REVERT: M 187 GLN cc_start: 0.8046 (tp40) cc_final: 0.7516 (mm-40) REVERT: M 197 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7353 (mttt) REVERT: M 198 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7706 (mtmt) REVERT: N 124 LYS cc_start: 0.7486 (tttm) cc_final: 0.7195 (ttmt) REVERT: N 187 GLN cc_start: 0.7325 (tp40) cc_final: 0.7018 (mm-40) REVERT: N 199 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7329 (p0) outliers start: 61 outliers final: 38 residues processed: 348 average time/residue: 0.3148 time to fit residues: 162.2612 Evaluate side-chains 343 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 197 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 128 VAL 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 199 ASP Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 199 ASP 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 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 132 optimal weight: 0.0030 chunk 0 optimal weight: 50.0000 chunk 97 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN G 187 GLN H 187 GLN I 61 ASN L 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1942 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= 0.164 Angle : 0.524 7.995 24901 Z= 0.297 Chirality : 0.040 0.207 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.952 89.889 3258 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.71 % Allowed : 25.33 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1890 helix: 2.66 (0.17), residues: 860 sheet: -0.37 (0.26), residues: 350 loop : -2.23 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 177 HIS 0.003 0.002 HIS H 185 PHE 0.020 0.002 PHE I 165 TYR 0.022 0.001 TYR J 60 ARG 0.001 0.000 ARG M 210 *********************** 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 378 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 316 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6648 (mtm) cc_final: 0.6343 (tpp) REVERT: E 90 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7773 (tmtt) REVERT: E 206 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5161 (pttp) REVERT: E 209 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6130 (tt) REVERT: F 72 MET cc_start: 0.6163 (mmp) cc_final: 0.5939 (tpp) REVERT: F 79 MET cc_start: 0.7793 (tpt) cc_final: 0.7178 (ttm) REVERT: F 124 LYS cc_start: 0.8056 (tttm) cc_final: 0.7387 (ttpp) REVERT: F 187 GLN cc_start: 0.7034 (tp40) cc_final: 0.6557 (mm-40) REVERT: F 188 LYS cc_start: 0.7833 (tptm) cc_final: 0.7246 (ttmt) REVERT: F 198 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6140 (mtmt) REVERT: G 68 LYS cc_start: 0.8362 (mmmt) cc_final: 0.7989 (mmtm) REVERT: G 133 GLU cc_start: 0.7080 (tp30) cc_final: 0.6689 (tp30) REVERT: G 166 GLN cc_start: 0.8861 (tt0) cc_final: 0.8589 (tt0) REVERT: G 188 LYS cc_start: 0.8415 (tttt) cc_final: 0.8145 (ttpt) REVERT: H 72 MET cc_start: 0.6708 (tpp) cc_final: 0.6437 (tpp) REVERT: H 197 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7920 (tptp) REVERT: I 222 ASP cc_start: 0.8421 (m-30) cc_final: 0.8138 (m-30) REVERT: J 64 ASP cc_start: 0.8229 (p0) cc_final: 0.7959 (p0) REVERT: J 68 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8301 (mmmm) REVERT: J 72 MET cc_start: 0.7665 (tpp) cc_final: 0.7361 (tpp) REVERT: J 124 LYS cc_start: 0.8408 (tttm) cc_final: 0.7915 (ttpp) REVERT: J 133 GLU cc_start: 0.8565 (tp30) cc_final: 0.8353 (tp30) REVERT: K 40 LYS cc_start: 0.7725 (mtpt) cc_final: 0.7396 (mttp) REVERT: K 64 ASP cc_start: 0.7951 (p0) cc_final: 0.7665 (p0) REVERT: K 68 LYS cc_start: 0.8426 (mmmm) cc_final: 0.8044 (mmmt) REVERT: K 79 MET cc_start: 0.9063 (ttt) cc_final: 0.8684 (ttm) REVERT: K 124 LYS cc_start: 0.8014 (tttp) cc_final: 0.7734 (ttpt) REVERT: L 40 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7759 (mttp) REVERT: L 68 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8277 (mmtm) REVERT: L 197 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8094 (mttt) REVERT: M 152 ASN cc_start: 0.7162 (t0) cc_final: 0.6672 (p0) REVERT: M 187 GLN cc_start: 0.8058 (tp40) cc_final: 0.7514 (mm-40) REVERT: M 197 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7377 (mttt) REVERT: M 198 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7658 (mtmt) REVERT: N 72 MET cc_start: 0.4490 (ttm) cc_final: 0.4233 (tpp) REVERT: N 124 LYS cc_start: 0.7472 (tttm) cc_final: 0.7180 (ttmt) REVERT: N 159 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.6905 (m) REVERT: N 187 GLN cc_start: 0.7383 (tp40) cc_final: 0.7065 (mm-40) REVERT: N 199 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7427 (p0) REVERT: N 206 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7837 (pttp) outliers start: 62 outliers final: 46 residues processed: 353 average time/residue: 0.3188 time to fit residues: 165.3762 Evaluate side-chains 362 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 310 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 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 136 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 206 LYS 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 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 ASP 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 64 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.0670 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN H 187 GLN I 107 GLN L 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18152 Z= 0.167 Angle : 0.520 8.802 24901 Z= 0.295 Chirality : 0.040 0.221 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.876 89.831 3258 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.01 % Allowed : 25.03 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1890 helix: 2.65 (0.17), residues: 860 sheet: -0.35 (0.26), residues: 350 loop : -2.26 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 177 HIS 0.003 0.002 HIS H 185 PHE 0.020 0.002 PHE I 165 TYR 0.022 0.001 TYR J 60 ARG 0.001 0.000 ARG M 210 *********************** 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 fitting. rotamer outliers: 67 poor density : 311 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8169 (ttmt) cc_final: 0.7778 (tmtt) REVERT: E 206 LYS cc_start: 0.5985 (OUTLIER) cc_final: 0.5162 (pttp) REVERT: F 72 MET cc_start: 0.6156 (mmp) cc_final: 0.5954 (tpp) REVERT: F 79 MET cc_start: 0.7794 (tpt) cc_final: 0.7213 (ttm) REVERT: F 124 LYS cc_start: 0.8077 (tttm) cc_final: 0.7413 (ttpp) REVERT: F 132 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5990 (mtp180) REVERT: F 187 GLN cc_start: 0.7032 (tp40) cc_final: 0.6557 (mm-40) REVERT: F 188 LYS cc_start: 0.7850 (tptm) cc_final: 0.7258 (ttmt) REVERT: F 198 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6264 (mtmt) REVERT: G 133 GLU cc_start: 0.7044 (tp30) cc_final: 0.6693 (tp30) REVERT: G 166 GLN cc_start: 0.8869 (tt0) cc_final: 0.8598 (tt0) REVERT: G 188 LYS cc_start: 0.8411 (tttt) cc_final: 0.8141 (ttpt) REVERT: H 72 MET cc_start: 0.6783 (tpp) cc_final: 0.6569 (tpp) REVERT: H 140 ASN cc_start: 0.7971 (p0) cc_final: 0.7595 (p0) REVERT: H 197 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7926 (tptp) REVERT: I 133 GLU cc_start: 0.8444 (tp30) cc_final: 0.7897 (tp30) REVERT: I 222 ASP cc_start: 0.8424 (m-30) cc_final: 0.8137 (m-30) REVERT: J 64 ASP cc_start: 0.8217 (p0) cc_final: 0.8012 (p0) REVERT: J 68 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8311 (mmmm) REVERT: J 72 MET cc_start: 0.7657 (tpp) cc_final: 0.7342 (tpp) REVERT: J 124 LYS cc_start: 0.8396 (tttm) cc_final: 0.7894 (ttpp) REVERT: J 133 GLU cc_start: 0.8565 (tp30) cc_final: 0.8363 (tp30) REVERT: K 40 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7366 (mttp) REVERT: K 64 ASP cc_start: 0.7999 (p0) cc_final: 0.7684 (p0) REVERT: K 68 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8043 (mmmt) REVERT: K 72 MET cc_start: 0.8061 (mmm) cc_final: 0.7477 (tpp) REVERT: K 79 MET cc_start: 0.9049 (ttt) cc_final: 0.8674 (ttm) REVERT: K 124 LYS cc_start: 0.8001 (tttp) cc_final: 0.7708 (ttpt) REVERT: L 40 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7763 (mttp) REVERT: L 68 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8260 (mmtm) REVERT: L 197 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8095 (mttt) REVERT: M 152 ASN cc_start: 0.7130 (t0) cc_final: 0.6641 (p0) REVERT: M 187 GLN cc_start: 0.8058 (tp40) cc_final: 0.7528 (mm-40) REVERT: M 197 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7365 (mttt) REVERT: M 198 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7650 (mtmt) REVERT: N 72 MET cc_start: 0.4461 (ttm) cc_final: 0.4208 (tpp) REVERT: N 124 LYS cc_start: 0.7474 (tttm) cc_final: 0.7181 (ttmt) REVERT: N 159 VAL cc_start: 0.7446 (OUTLIER) cc_final: 0.6889 (m) REVERT: N 187 GLN cc_start: 0.7406 (tp40) cc_final: 0.7030 (mm-40) REVERT: N 206 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7878 (pttp) outliers start: 67 outliers final: 50 residues processed: 351 average time/residue: 0.3187 time to fit residues: 163.8316 Evaluate side-chains 363 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 308 time to evaluate : 1.947 ------------------------------------------------------------------------------- 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 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 198 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 206 LYS 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 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 206 LYS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 0.0670 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 0.0030 overall best weight: 0.7530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN H 187 GLN I 61 ASN L 61 ASN L 187 GLN N 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18152 Z= 0.141 Angle : 0.496 8.851 24901 Z= 0.282 Chirality : 0.039 0.208 2722 Planarity : 0.003 0.023 2758 Dihedral : 19.780 89.531 3258 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.47 % Allowed : 25.57 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 1890 helix: 2.63 (0.17), residues: 870 sheet: -0.34 (0.26), residues: 350 loop : -2.24 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 96 HIS 0.003 0.001 HIS H 185 PHE 0.017 0.001 PHE I 165 TYR 0.017 0.001 TYR J 60 ARG 0.002 0.000 ARG J 132 *********************** 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 370 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 312 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6573 (mtm) cc_final: 0.6358 (tpp) REVERT: E 90 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7763 (tmtt) REVERT: E 209 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6068 (tt) REVERT: F 72 MET cc_start: 0.6126 (mmp) cc_final: 0.5923 (tpp) REVERT: F 79 MET cc_start: 0.7785 (tpt) cc_final: 0.7231 (ttm) REVERT: F 124 LYS cc_start: 0.8020 (tttm) cc_final: 0.7361 (ttpp) REVERT: F 132 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6012 (mtp180) REVERT: F 187 GLN cc_start: 0.7076 (tp40) cc_final: 0.6599 (mm-40) REVERT: F 188 LYS cc_start: 0.7858 (tptm) cc_final: 0.7253 (ttmt) REVERT: F 198 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6153 (mtmt) REVERT: G 68 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8065 (mmtt) REVERT: G 166 GLN cc_start: 0.8851 (tt0) cc_final: 0.8627 (tt0) REVERT: G 188 LYS cc_start: 0.8402 (tttt) cc_final: 0.8127 (ttpt) REVERT: H 197 LYS cc_start: 0.8452 (ttmm) cc_final: 0.7974 (tptp) REVERT: I 133 GLU cc_start: 0.8390 (tp30) cc_final: 0.7808 (tp30) REVERT: I 222 ASP cc_start: 0.8391 (m-30) cc_final: 0.8098 (m-30) REVERT: J 68 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8235 (mmmm) REVERT: J 72 MET cc_start: 0.7641 (tpp) cc_final: 0.7324 (tpp) REVERT: J 133 GLU cc_start: 0.8531 (tp30) cc_final: 0.8330 (tp30) REVERT: K 40 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7353 (mttp) REVERT: K 64 ASP cc_start: 0.8037 (p0) cc_final: 0.7800 (p0) REVERT: K 68 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8028 (mmmt) REVERT: K 72 MET cc_start: 0.8024 (mmm) cc_final: 0.7455 (tpp) REVERT: K 79 MET cc_start: 0.9030 (ttt) cc_final: 0.8693 (ttm) REVERT: K 124 LYS cc_start: 0.7949 (tttp) cc_final: 0.7661 (ttpt) REVERT: L 40 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7737 (mttp) REVERT: L 68 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8266 (mmtm) REVERT: L 197 LYS cc_start: 0.8538 (ttmm) cc_final: 0.8087 (mttt) REVERT: M 152 ASN cc_start: 0.6946 (t0) cc_final: 0.6312 (p0) REVERT: M 187 GLN cc_start: 0.8098 (tp40) cc_final: 0.7555 (mm-40) REVERT: M 197 LYS cc_start: 0.7857 (ttmm) cc_final: 0.7431 (mttt) REVERT: M 198 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7630 (mtmt) REVERT: N 72 MET cc_start: 0.4444 (ttm) cc_final: 0.4203 (tpp) REVERT: N 124 LYS cc_start: 0.7435 (tttm) cc_final: 0.7143 (ttmt) REVERT: N 159 VAL cc_start: 0.7479 (OUTLIER) cc_final: 0.6916 (m) REVERT: N 187 GLN cc_start: 0.7429 (tp40) cc_final: 0.7037 (mm-40) REVERT: N 199 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7523 (p0) REVERT: N 206 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7821 (pttp) outliers start: 58 outliers final: 44 residues processed: 343 average time/residue: 0.3209 time to fit residues: 161.9358 Evaluate side-chains 356 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 306 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 209 LEU 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 198 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 172 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 206 LYS Chi-restraints excluded: chain J residue 37 MET Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 206 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 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 199 ASP Chi-restraints excluded: chain N residue 206 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN H 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18152 Z= 0.204 Angle : 0.550 9.636 24901 Z= 0.309 Chirality : 0.040 0.216 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.770 89.666 3258 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.89 % Allowed : 25.15 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1890 helix: 2.61 (0.17), residues: 870 sheet: -0.36 (0.26), residues: 350 loop : -2.28 (0.19), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 177 HIS 0.004 0.002 HIS H 185 PHE 0.022 0.002 PHE K 165 TYR 0.010 0.001 TYR G 110 ARG 0.002 0.000 ARG M 210 *********************** 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 368 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 303 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7756 (tmtt) REVERT: E 206 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5253 (pttp) REVERT: E 209 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6161 (tt) REVERT: F 79 MET cc_start: 0.7826 (tpt) cc_final: 0.7276 (ttm) REVERT: F 124 LYS cc_start: 0.8111 (tttm) cc_final: 0.7524 (ttpp) REVERT: F 132 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6033 (mtp180) REVERT: F 187 GLN cc_start: 0.7059 (tp40) cc_final: 0.6574 (mm-40) REVERT: F 188 LYS cc_start: 0.7841 (tptm) cc_final: 0.7246 (ttmt) REVERT: F 198 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6479 (mtmt) REVERT: G 133 GLU cc_start: 0.7012 (tp30) cc_final: 0.6711 (tp30) REVERT: G 188 LYS cc_start: 0.8408 (tttt) cc_final: 0.8144 (ttpt) REVERT: H 72 MET cc_start: 0.6723 (tpp) cc_final: 0.6453 (tpp) REVERT: H 140 ASN cc_start: 0.8046 (p0) cc_final: 0.7678 (p0) REVERT: H 197 LYS cc_start: 0.8431 (ttmm) cc_final: 0.7942 (tptp) REVERT: I 83 THR cc_start: 0.8653 (m) cc_final: 0.8421 (m) REVERT: I 133 GLU cc_start: 0.8520 (tp30) cc_final: 0.7950 (tp30) REVERT: I 222 ASP cc_start: 0.8405 (m-30) cc_final: 0.8107 (m-30) REVERT: J 68 LYS cc_start: 0.8674 (mmmm) cc_final: 0.8290 (mmmm) REVERT: J 72 MET cc_start: 0.7695 (tpp) cc_final: 0.7380 (tpp) REVERT: J 124 LYS cc_start: 0.8468 (tttm) cc_final: 0.7978 (ttpp) REVERT: J 133 GLU cc_start: 0.8586 (tp30) cc_final: 0.8371 (tp30) REVERT: K 40 LYS cc_start: 0.7692 (mtpt) cc_final: 0.7375 (mttp) REVERT: K 64 ASP cc_start: 0.8045 (p0) cc_final: 0.7831 (p0) REVERT: K 68 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8055 (mmmt) REVERT: K 72 MET cc_start: 0.8135 (mmm) cc_final: 0.7559 (tpp) REVERT: K 79 MET cc_start: 0.9038 (ttt) cc_final: 0.8690 (ttm) REVERT: K 124 LYS cc_start: 0.8058 (tttp) cc_final: 0.7771 (ttpt) REVERT: L 40 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7722 (mttp) REVERT: L 68 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8283 (mmtm) REVERT: L 197 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8119 (mttt) REVERT: M 152 ASN cc_start: 0.7190 (t0) cc_final: 0.6401 (m-40) REVERT: M 187 GLN cc_start: 0.8055 (tp40) cc_final: 0.7504 (mm-40) REVERT: M 197 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7369 (mttt) REVERT: M 198 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7634 (mtmt) REVERT: N 72 MET cc_start: 0.4482 (ttm) cc_final: 0.4231 (tpp) REVERT: N 124 LYS cc_start: 0.7502 (tttm) cc_final: 0.7210 (ttmt) REVERT: N 187 GLN cc_start: 0.7429 (tp40) cc_final: 0.6968 (mm-40) REVERT: N 206 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7882 (pttp) outliers start: 65 outliers final: 48 residues processed: 338 average time/residue: 0.3081 time to fit residues: 152.6037 Evaluate side-chains 354 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 301 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 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 198 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 206 LYS 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 128 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 168 ILE Chi-restraints excluded: chain K residue 199 ASP Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain 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 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain N residue 37 MET Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 167 LEU 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 173 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN H 187 GLN I 61 ASN L 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2191 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= 0.177 Angle : 0.531 9.374 24901 Z= 0.300 Chirality : 0.040 0.201 2722 Planarity : 0.003 0.024 2758 Dihedral : 19.765 89.245 3258 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.47 % Allowed : 25.39 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1890 helix: 2.67 (0.17), residues: 860 sheet: -0.35 (0.26), residues: 350 loop : -2.27 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 177 HIS 0.003 0.002 HIS H 185 PHE 0.020 0.002 PHE I 165 TYR 0.011 0.001 TYR J 60 ARG 0.001 0.000 ARG M 210 *********************** 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 356 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 298 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.7028 (tpp) cc_final: 0.5907 (mtm) REVERT: E 90 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7745 (tmtt) REVERT: E 206 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5188 (pttp) REVERT: F 79 MET cc_start: 0.7823 (tpt) cc_final: 0.7293 (ttm) REVERT: F 124 LYS cc_start: 0.8065 (tttm) cc_final: 0.7471 (ttpp) REVERT: F 132 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6029 (mtp180) REVERT: F 187 GLN cc_start: 0.7053 (tp40) cc_final: 0.6697 (mm-40) REVERT: F 188 LYS cc_start: 0.7832 (tptm) cc_final: 0.7236 (ttmt) REVERT: F 198 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6495 (mtmt) REVERT: G 133 GLU cc_start: 0.6933 (tp30) cc_final: 0.6659 (tp30) REVERT: G 188 LYS cc_start: 0.8404 (tttt) cc_final: 0.8141 (ttpt) REVERT: H 72 MET cc_start: 0.6732 (tpp) cc_final: 0.6420 (tpp) REVERT: H 140 ASN cc_start: 0.8013 (p0) cc_final: 0.7638 (p0) REVERT: H 197 LYS cc_start: 0.8432 (ttmm) cc_final: 0.7954 (tptp) REVERT: I 133 GLU cc_start: 0.8484 (tp30) cc_final: 0.7902 (tp30) REVERT: I 222 ASP cc_start: 0.8414 (m-30) cc_final: 0.8117 (m-30) REVERT: J 68 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8267 (mmmm) REVERT: J 72 MET cc_start: 0.7674 (tpp) cc_final: 0.7364 (tpp) REVERT: J 124 LYS cc_start: 0.8426 (tttm) cc_final: 0.7931 (ttpp) REVERT: J 133 GLU cc_start: 0.8590 (tp30) cc_final: 0.8374 (tp30) REVERT: K 40 LYS cc_start: 0.7635 (mtpt) cc_final: 0.7320 (mttp) REVERT: K 68 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8060 (mmmt) REVERT: K 72 MET cc_start: 0.8115 (mmm) cc_final: 0.7526 (tpp) REVERT: K 79 MET cc_start: 0.9041 (ttt) cc_final: 0.8708 (ttm) REVERT: K 124 LYS cc_start: 0.7999 (tttp) cc_final: 0.7733 (ttpt) REVERT: L 68 LYS cc_start: 0.8499 (mmmm) cc_final: 0.8283 (mmtm) REVERT: L 197 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8095 (mttt) REVERT: M 152 ASN cc_start: 0.7098 (t0) cc_final: 0.6254 (m-40) REVERT: M 187 GLN cc_start: 0.8092 (tp40) cc_final: 0.7532 (mm-40) REVERT: M 198 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7702 (mtmt) REVERT: M 210 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8359 (ttm170) REVERT: N 72 MET cc_start: 0.4505 (ttm) cc_final: 0.4242 (tpp) REVERT: N 124 LYS cc_start: 0.7481 (tttm) cc_final: 0.7191 (ttmt) REVERT: N 159 VAL cc_start: 0.7665 (OUTLIER) cc_final: 0.7117 (m) REVERT: N 187 GLN cc_start: 0.7436 (tp40) cc_final: 0.6892 (mm-40) REVERT: N 206 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7878 (pttp) outliers start: 58 outliers final: 43 residues processed: 331 average time/residue: 0.3161 time to fit residues: 153.0299 Evaluate side-chains 347 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 298 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 206 LYS Chi-restraints excluded: chain E residue 209 LEU 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 198 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 206 LYS 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 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 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 172 GLU Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 199 ASP Chi-restraints excluded: chain M residue 210 ARG Chi-restraints excluded: chain N residue 37 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 181 optimal weight: 0.0980 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN H 187 GLN L 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18152 Z= 0.195 Angle : 0.545 7.642 24901 Z= 0.308 Chirality : 0.040 0.175 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.765 89.396 3258 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.05 % Allowed : 25.93 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1890 helix: 2.66 (0.17), residues: 860 sheet: -0.36 (0.26), residues: 350 loop : -2.28 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 177 HIS 0.004 0.002 HIS H 185 PHE 0.022 0.002 PHE K 165 TYR 0.011 0.001 TYR J 60 ARG 0.002 0.000 ARG M 210 ********************** 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 348 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 297 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 79 MET cc_start: 0.6950 (tpp) cc_final: 0.5791 (mtm) REVERT: E 90 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7748 (tmtt) REVERT: E 206 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5099 (pttp) REVERT: E 218 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7651 (tt) REVERT: F 79 MET cc_start: 0.7826 (tpt) cc_final: 0.7297 (ttm) REVERT: F 124 LYS cc_start: 0.8080 (tttm) cc_final: 0.7481 (ttpp) REVERT: F 132 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6026 (mtp180) REVERT: F 187 GLN cc_start: 0.7061 (tp40) cc_final: 0.6691 (mm-40) REVERT: F 188 LYS cc_start: 0.7826 (tptm) cc_final: 0.7236 (ttmt) REVERT: F 198 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6500 (mtmt) REVERT: G 64 ASP cc_start: 0.8116 (p0) cc_final: 0.7821 (p0) REVERT: G 133 GLU cc_start: 0.6987 (tp30) cc_final: 0.6707 (tp30) REVERT: G 188 LYS cc_start: 0.8407 (tttt) cc_final: 0.8145 (ttpt) REVERT: H 72 MET cc_start: 0.6794 (tpp) cc_final: 0.6483 (tpp) REVERT: H 140 ASN cc_start: 0.8039 (p0) cc_final: 0.7668 (p0) REVERT: H 197 LYS cc_start: 0.8461 (ttmm) cc_final: 0.7980 (tptp) REVERT: I 133 GLU cc_start: 0.8490 (tp30) cc_final: 0.7938 (tp30) REVERT: I 222 ASP cc_start: 0.8405 (m-30) cc_final: 0.8097 (m-30) REVERT: J 68 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8280 (mmmm) REVERT: J 72 MET cc_start: 0.7703 (tpp) cc_final: 0.7438 (tpp) REVERT: J 105 GLN cc_start: 0.8529 (mm-40) cc_final: 0.7950 (mt0) REVERT: J 124 LYS cc_start: 0.8458 (tttm) cc_final: 0.7967 (ttpp) REVERT: J 133 GLU cc_start: 0.8618 (tp30) cc_final: 0.8397 (tp30) REVERT: K 40 LYS cc_start: 0.7648 (mtpt) cc_final: 0.7324 (mttp) REVERT: K 68 LYS cc_start: 0.8467 (mmmm) cc_final: 0.8092 (mmmt) REVERT: K 72 MET cc_start: 0.8114 (mmm) cc_final: 0.7561 (tpp) REVERT: K 79 MET cc_start: 0.9040 (ttt) cc_final: 0.8702 (ttm) REVERT: K 124 LYS cc_start: 0.8046 (tttp) cc_final: 0.7762 (ttpt) REVERT: K 152 ASN cc_start: 0.7997 (t0) cc_final: 0.7288 (m-40) REVERT: L 40 LYS cc_start: 0.8264 (mttp) cc_final: 0.7993 (mttm) REVERT: L 68 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8323 (mmtm) REVERT: L 197 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8092 (mttt) REVERT: M 152 ASN cc_start: 0.7123 (t0) cc_final: 0.6309 (m-40) REVERT: M 187 GLN cc_start: 0.8039 (tp40) cc_final: 0.7480 (mm-40) REVERT: M 198 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7781 (mtmt) REVERT: M 210 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8368 (ttm170) REVERT: N 72 MET cc_start: 0.4491 (ttm) cc_final: 0.4237 (tpp) REVERT: N 124 LYS cc_start: 0.7499 (tttm) cc_final: 0.7206 (ttmt) REVERT: N 159 VAL cc_start: 0.7619 (OUTLIER) cc_final: 0.7049 (m) REVERT: N 187 GLN cc_start: 0.7433 (tp40) cc_final: 0.6938 (mm-40) REVERT: N 206 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7856 (pttp) outliers start: 51 outliers final: 42 residues processed: 326 average time/residue: 0.3381 time to fit residues: 161.9355 Evaluate side-chains 347 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 298 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 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 198 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 199 ASP Chi-restraints excluded: chain I residue 37 MET Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 159 VAL Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 206 LYS 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 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 222 ASP Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain 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 37 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 122 GLN H 187 GLN I 61 ASN J 105 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 = 0.3591 r_free = 0.3591 target = 0.149747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109069 restraints weight = 22069.039| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.21 r_work: 0.2796 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18152 Z= 0.188 Angle : 0.534 7.374 24901 Z= 0.303 Chirality : 0.040 0.172 2722 Planarity : 0.003 0.025 2758 Dihedral : 19.771 89.296 3258 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.59 % Allowed : 25.27 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1890 helix: 2.66 (0.17), residues: 860 sheet: -0.37 (0.26), residues: 350 loop : -2.28 (0.18), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 177 HIS 0.004 0.002 HIS H 185 PHE 0.021 0.002 PHE K 165 TYR 0.010 0.001 TYR G 110 ARG 0.001 0.000 ARG M 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3809.99 seconds wall clock time: 68 minutes 28.28 seconds (4108.28 seconds total)