Starting phenix.real_space_refine on Sat Aug 10 22:54:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rku_19283/08_2024/8rku_19283.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rku_19283/08_2024/8rku_19283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rku_19283/08_2024/8rku_19283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rku_19283/08_2024/8rku_19283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rku_19283/08_2024/8rku_19283.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rku_19283/08_2024/8rku_19283.cif" } resolution = 2.3 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.080 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: 6 Type Number sf(0) Gaussians P 82 5.49 5 Mg 14 5.21 5 S 112 5.16 5 C 18818 2.51 5 N 5491 2.21 5 O 6209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 145": "OE1" <-> "OE2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30726 Number of models: 1 Model: "" Number of chains: 46 Chain: "2" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "3" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "N" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "O" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "P" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "Q" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 17.27, per 1000 atoms: 0.56 Number of scatterers: 30726 At special positions: 0 Unit cell: (130.312, 147.056, 157.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 112 16.00 P 82 15.00 Mg 14 11.99 O 6209 8.00 N 5491 7.00 C 18818 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 - 3.50 Amino acid : False - 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: 13.71 Conformation dependent library (CDL) restraints added in 5.3 seconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 14 sheets defined 62.6% alpha, 6.9% beta 13 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 10.50 Creating SS restraints... Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.811A pdb=" N ALA D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 52 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 151 No H-bonds generated for 'chain 'D' and resid 150 through 151' Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.677A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.777A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.710A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.572A pdb=" N ARG E 74 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.860A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'F' and resid 20 through 30 removed outlier: 3.839A pdb=" N GLY F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.513A pdb=" N ARG F 74 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 134 Processing helix chain 'F' and resid 146 through 149 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 173 through 182 removed outlier: 3.814A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'F' and resid 200 through 215 Processing helix chain 'F' and resid 226 through 238 Processing helix chain 'F' and resid 240 through 258 Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 121 through 134 Processing helix chain 'G' and resid 146 through 149 Processing helix chain 'G' and resid 152 through 164 removed outlier: 4.172A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.944A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.634A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 146 through 149 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 173 through 182 removed outlier: 3.903A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 Processing helix chain 'H' and resid 240 through 258 Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'I' and resid 20 through 30 removed outlier: 3.785A pdb=" N GLY I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 101 through 113 Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 3.676A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'I' and resid 200 through 215 Processing helix chain 'I' and resid 226 through 238 Processing helix chain 'I' and resid 240 through 258 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'J' and resid 20 through 30 removed outlier: 3.847A pdb=" N GLY J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 101 through 113 Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 151 No H-bonds generated for 'chain 'J' and resid 150 through 151' Processing helix chain 'J' and resid 152 through 164 removed outlier: 4.300A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 182 removed outlier: 3.715A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS J 181 " --> pdb=" O ASP J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.594A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'J' and resid 240 through 258 Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 36 through 53 Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 101 through 113 Processing helix chain 'K' and resid 121 through 134 Processing helix chain 'K' and resid 146 through 149 Processing helix chain 'K' and resid 152 through 164 removed outlier: 4.089A pdb=" N ASP K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 182 removed outlier: 3.878A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'K' and resid 200 through 215 Processing helix chain 'K' and resid 226 through 238 Processing helix chain 'K' and resid 240 through 258 Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'L' and resid 20 through 29 Processing helix chain 'L' and resid 36 through 53 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 101 through 113 Processing helix chain 'L' and resid 121 through 134 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 153 through 164 Processing helix chain 'L' and resid 173 through 181 removed outlier: 3.780A pdb=" N ASP L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 3.543A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 215 Processing helix chain 'L' and resid 226 through 238 removed outlier: 3.894A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 258 Processing helix chain 'L' and resid 264 through 273 Processing helix chain 'M' and resid 20 through 29 Processing helix chain 'M' and resid 36 through 53 Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 101 through 113 Processing helix chain 'M' and resid 121 through 134 Processing helix chain 'M' and resid 146 through 149 Processing helix chain 'M' and resid 150 through 151 No H-bonds generated for 'chain 'M' and resid 150 through 151' Processing helix chain 'M' and resid 152 through 164 removed outlier: 4.265A pdb=" N ASP M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.993A pdb=" N ASP M 177 " --> pdb=" O THR M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 190 Processing helix chain 'M' and resid 200 through 215 Processing helix chain 'M' and resid 226 through 238 removed outlier: 4.002A pdb=" N ILE M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 258 Processing helix chain 'M' and resid 264 through 274 removed outlier: 3.876A pdb=" N GLU M 274 " --> pdb=" O GLU M 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 36 through 53 Processing helix chain 'N' and resid 65 through 77 Processing helix chain 'N' and resid 101 through 113 Processing helix chain 'N' and resid 121 through 134 Processing helix chain 'N' and resid 146 through 149 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 153 through 164 Processing helix chain 'N' and resid 173 through 181 removed outlier: 3.832A pdb=" N ASP N 177 " --> pdb=" O THR N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 190 Processing helix chain 'N' and resid 200 through 215 removed outlier: 3.853A pdb=" N GLU N 212 " --> pdb=" O VAL N 208 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN N 213 " --> pdb=" O GLU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 238 removed outlier: 4.087A pdb=" N ILE N 232 " --> pdb=" O GLU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 258 Processing helix chain 'N' and resid 264 through 273 Processing helix chain 'O' and resid 20 through 30 Processing helix chain 'O' and resid 36 through 53 Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'O' and resid 121 through 134 Processing helix chain 'O' and resid 146 through 149 Processing helix chain 'O' and resid 152 through 164 removed outlier: 4.125A pdb=" N ASP O 156 " --> pdb=" O GLU O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 182 removed outlier: 3.839A pdb=" N ASP O 177 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 190 Processing helix chain 'O' and resid 201 through 215 Processing helix chain 'O' and resid 226 through 238 Processing helix chain 'O' and resid 240 through 258 removed outlier: 3.694A pdb=" N GLU O 246 " --> pdb=" O GLY O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 273 removed outlier: 3.992A pdb=" N GLU O 270 " --> pdb=" O ALA O 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 29 Processing helix chain 'P' and resid 36 through 53 Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 101 through 113 Processing helix chain 'P' and resid 121 through 134 Processing helix chain 'P' and resid 145 through 149 Processing helix chain 'P' and resid 153 through 164 Processing helix chain 'P' and resid 173 through 182 removed outlier: 3.833A pdb=" N ASP P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 190 Processing helix chain 'P' and resid 200 through 214 Processing helix chain 'P' and resid 228 through 238 removed outlier: 3.955A pdb=" N ILE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 259 removed outlier: 4.483A pdb=" N GLU P 246 " --> pdb=" O GLY P 242 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 273 removed outlier: 3.645A pdb=" N GLU P 270 " --> pdb=" O ALA P 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 30 removed outlier: 4.026A pdb=" N ARG Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 53 Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 101 through 113 Processing helix chain 'Q' and resid 121 through 134 Processing helix chain 'Q' and resid 146 through 149 Processing helix chain 'Q' and resid 152 through 164 removed outlier: 3.889A pdb=" N ASP Q 156 " --> pdb=" O GLU Q 152 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 182 removed outlier: 3.873A pdb=" N ASP Q 177 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG Q 182 " --> pdb=" O ALA Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 190 Processing helix chain 'Q' and resid 200 through 215 removed outlier: 3.954A pdb=" N GLU Q 212 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN Q 213 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 238 removed outlier: 3.648A pdb=" N ALA Q 236 " --> pdb=" O ILE Q 232 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU Q 238 " --> pdb=" O THR Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 257 removed outlier: 4.305A pdb=" N GLU Q 246 " --> pdb=" O GLY Q 242 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 273 Processing sheet with id=AA1, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.542A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP F 144 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE F 94 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.551A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP G 144 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE G 94 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.550A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASP H 144 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE H 94 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.500A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP I 144 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE I 94 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.530A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.504A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP K 144 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE K 94 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL K 59 " --> pdb=" O PHE K 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 91 through 94 removed outlier: 6.614A pdb=" N VAL L 92 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU L 141 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL L 171 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE L 143 " --> pdb=" O VAL L 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 91 through 94 removed outlier: 6.521A pdb=" N VAL M 92 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP M 144 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE M 94 " --> pdb=" O ASP M 144 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU M 141 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL M 171 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE M 143 " --> pdb=" O VAL M 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL N 92 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP N 144 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE N 94 " --> pdb=" O ASP N 144 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU N 141 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL N 171 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE N 143 " --> pdb=" O VAL N 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 91 through 94 removed outlier: 6.512A pdb=" N VAL O 92 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP O 144 " --> pdb=" O VAL O 92 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE O 94 " --> pdb=" O ASP O 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 91 through 94 removed outlier: 6.549A pdb=" N VAL P 92 " --> pdb=" O ILE P 142 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG P 57 " --> pdb=" O LEU P 194 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE P 196 " --> pdb=" O ARG P 57 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL P 59 " --> pdb=" O PHE P 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 91 through 94 1590 hydrogen bonds defined for protein. 4671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 11.01 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8846 1.33 - 1.45: 4052 1.45 - 1.57: 17538 1.57 - 1.69: 129 1.69 - 1.81: 168 Bond restraints: 30733 Sorted by residual: bond pdb=" N ASP L 144 " pdb=" CA ASP L 144 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.31e-02 5.83e+03 6.05e+00 bond pdb=" N ASP I 144 " pdb=" CA ASP I 144 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.30e-02 5.92e+03 5.26e+00 bond pdb=" N ASP H 144 " pdb=" CA ASP H 144 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.30e-02 5.92e+03 4.92e+00 bond pdb=" N ASP J 144 " pdb=" CA ASP J 144 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.31e-02 5.83e+03 4.86e+00 bond pdb=" CA ALA L 146 " pdb=" CB ALA L 146 " ideal model delta sigma weight residual 1.529 1.495 0.033 1.64e-02 3.72e+03 4.11e+00 ... (remaining 30728 not shown) Histogram of bond angle deviations from ideal: 99.00 - 107.22: 1198 107.22 - 115.43: 19161 115.43 - 123.64: 19928 123.64 - 131.85: 1182 131.85 - 140.06: 100 Bond angle restraints: 41569 Sorted by residual: angle pdb=" C2' DT 2 35 " pdb=" C1' DT 2 35 " pdb=" N1 DT 2 35 " ideal model delta sigma weight residual 113.50 119.79 -6.29 1.50e+00 4.44e-01 1.76e+01 angle pdb=" O3' DT 2 35 " pdb=" C3' DT 2 35 " pdb=" C2' DT 2 35 " ideal model delta sigma weight residual 111.50 117.16 -5.66 1.50e+00 4.44e-01 1.42e+01 angle pdb=" C GLU I 145 " pdb=" CA GLU I 145 " pdb=" CB GLU I 145 " ideal model delta sigma weight residual 111.73 117.08 -5.35 1.42e+00 4.96e-01 1.42e+01 angle pdb=" C4' DA 3 98 " pdb=" C3' DA 3 98 " pdb=" O3' DA 3 98 " ideal model delta sigma weight residual 110.00 115.50 -5.50 1.50e+00 4.44e-01 1.35e+01 angle pdb=" O3' DA 2 38 " pdb=" C3' DA 2 38 " pdb=" C2' DA 2 38 " ideal model delta sigma weight residual 111.50 106.03 5.47 1.50e+00 4.44e-01 1.33e+01 ... (remaining 41564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 18445 35.41 - 70.81: 756 70.81 - 106.22: 57 106.22 - 141.63: 0 141.63 - 177.04: 2 Dihedral angle restraints: 19260 sinusoidal: 8830 harmonic: 10430 Sorted by residual: dihedral pdb=" CA GLY M 135 " pdb=" C GLY M 135 " pdb=" N CYS M 136 " pdb=" CA CYS M 136 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR F 118 " pdb=" C THR F 118 " pdb=" N LYS F 119 " pdb=" CA LYS F 119 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR N 112 " pdb=" C TYR N 112 " pdb=" N LEU N 113 " pdb=" CA LEU N 113 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 19257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3871 0.074 - 0.147: 761 0.147 - 0.221: 33 0.221 - 0.295: 1 0.295 - 0.368: 2 Chirality restraints: 4668 Sorted by residual: chirality pdb=" C1' DT 2 35 " pdb=" O4' DT 2 35 " pdb=" C2' DT 2 35 " pdb=" N1 DT 2 35 " both_signs ideal model delta sigma weight residual False 2.47 2.10 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C3' DA 3 98 " pdb=" C4' DA 3 98 " pdb=" O3' DA 3 98 " pdb=" C2' DA 3 98 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C3' ATP M 300 " pdb=" C2' ATP M 300 " pdb=" C4' ATP M 300 " pdb=" O3' ATP M 300 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 4665 not shown) Planarity restraints: 5066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP P 300 " -0.036 2.00e-02 2.50e+03 2.82e-02 2.18e+01 pdb=" C2 ATP P 300 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ATP P 300 " -0.012 2.00e-02 2.50e+03 pdb=" C5 ATP P 300 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ATP P 300 " -0.002 2.00e-02 2.50e+03 pdb=" C8 ATP P 300 " -0.028 2.00e-02 2.50e+03 pdb=" N1 ATP P 300 " -0.002 2.00e-02 2.50e+03 pdb=" N3 ATP P 300 " 0.003 2.00e-02 2.50e+03 pdb=" N6 ATP P 300 " -0.002 2.00e-02 2.50e+03 pdb=" N7 ATP P 300 " 0.002 2.00e-02 2.50e+03 pdb=" N9 ATP P 300 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 2 35 " 0.044 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" N1 DT 2 35 " -0.046 2.00e-02 2.50e+03 pdb=" C2 DT 2 35 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT 2 35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT 2 35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT 2 35 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT 2 35 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT 2 35 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT 2 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT 2 35 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP O 300 " -0.025 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" C2 ATP O 300 " 0.001 2.00e-02 2.50e+03 pdb=" C4 ATP O 300 " -0.014 2.00e-02 2.50e+03 pdb=" C5 ATP O 300 " -0.001 2.00e-02 2.50e+03 pdb=" C6 ATP O 300 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ATP O 300 " -0.015 2.00e-02 2.50e+03 pdb=" N1 ATP O 300 " -0.001 2.00e-02 2.50e+03 pdb=" N3 ATP O 300 " 0.002 2.00e-02 2.50e+03 pdb=" N6 ATP O 300 " -0.001 2.00e-02 2.50e+03 pdb=" N7 ATP O 300 " 0.001 2.00e-02 2.50e+03 pdb=" N9 ATP O 300 " 0.055 2.00e-02 2.50e+03 ... (remaining 5063 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 128 2.37 - 3.00: 16362 3.00 - 3.64: 47813 3.64 - 4.27: 77297 4.27 - 4.90: 124031 Nonbonded interactions: 265631 Sorted by model distance: nonbonded pdb=" O2B ATP O 300 " pdb="MG MG O 301 " model vdw 1.738 2.170 nonbonded pdb="MG MG D 301 " pdb=" O2B ATP D 302 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR E 67 " pdb="MG MG E 301 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR D 67 " pdb="MG MG D 301 " model vdw 1.999 2.170 nonbonded pdb=" OG1 THR F 67 " pdb="MG MG F 301 " model vdw 2.011 2.170 ... (remaining 265626 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 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) selection = (chain 'I' and resid 19 through 275) selection = (chain 'J' and resid 19 through 275) selection = (chain 'K' and resid 19 through 275) selection = (chain 'L' and resid 19 through 275) selection = (chain 'M' and resid 19 through 275) selection = (chain 'N' and resid 19 through 275) selection = (chain 'O' and resid 19 through 275) selection = (chain 'P' and resid 19 through 275) selection = (chain 'Q' and resid 19 through 275) } 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: 0.010 Normalize map: mean=0, sd=1: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.430 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 89.080 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.006 0.062 30733 Z= 0.369 Angle : 0.812 8.432 41569 Z= 0.486 Chirality : 0.055 0.368 4668 Planarity : 0.012 0.111 5066 Dihedral : 17.117 177.037 12512 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.38 % Allowed : 5.01 % Favored : 94.61 % 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: -1.04 (0.12), residues: 3570 helix: -0.90 (0.10), residues: 2142 sheet: 0.49 (0.31), residues: 210 loop : -0.12 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP M 45 HIS 0.011 0.002 HIS I 77 PHE 0.019 0.002 PHE J 190 TYR 0.028 0.005 TYR P 240 ARG 0.029 0.004 ARG M 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 566 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 184 GLU cc_start: 0.6516 (tp30) cc_final: 0.5931 (tt0) REVERT: D 185 GLN cc_start: 0.6446 (tp40) cc_final: 0.6036 (mm-40) REVERT: D 189 ARG cc_start: 0.7051 (ptp-110) cc_final: 0.6707 (ptp90) REVERT: D 214 MET cc_start: 0.7847 (mtm) cc_final: 0.7599 (mtm) REVERT: D 229 MET cc_start: 0.7004 (mmt) cc_final: 0.6589 (mmt) REVERT: E 127 ASP cc_start: 0.6740 (m-30) cc_final: 0.6489 (m-30) REVERT: E 140 MET cc_start: 0.9210 (ttm) cc_final: 0.8805 (ttm) REVERT: E 227 LYS cc_start: 0.7292 (ttpp) cc_final: 0.7013 (ttmm) REVERT: E 231 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7034 (tpp-160) REVERT: F 128 ARG cc_start: 0.8308 (mmm160) cc_final: 0.8087 (tpt170) REVERT: F 131 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7469 (mm-30) REVERT: F 202 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7490 (mm-30) REVERT: F 205 LYS cc_start: 0.8291 (tttm) cc_final: 0.8083 (tttm) REVERT: F 209 GLU cc_start: 0.7945 (tt0) cc_final: 0.7738 (tp30) REVERT: F 210 MET cc_start: 0.8151 (mtp) cc_final: 0.7717 (mtp) REVERT: G 152 GLU cc_start: 0.8700 (pt0) cc_final: 0.8494 (pm20) REVERT: G 223 ASN cc_start: 0.6982 (m-40) cc_final: 0.6425 (m-40) REVERT: G 269 GLN cc_start: 0.7257 (mm110) cc_final: 0.6764 (mt0) REVERT: G 270 GLU cc_start: 0.7677 (tt0) cc_final: 0.7463 (tt0) REVERT: H 202 GLU cc_start: 0.7244 (tp30) cc_final: 0.7040 (tp30) REVERT: H 209 GLU cc_start: 0.6827 (tt0) cc_final: 0.6619 (tm-30) REVERT: H 261 LYS cc_start: 0.7656 (mptt) cc_final: 0.7020 (mmtm) REVERT: I 37 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7728 (tp40) REVERT: I 99 LYS cc_start: 0.8649 (mttm) cc_final: 0.8408 (mttm) REVERT: I 107 LYS cc_start: 0.8746 (mtpm) cc_final: 0.8458 (mtpt) REVERT: I 231 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.7175 (ttp80) REVERT: J 196 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: J 206 ASN cc_start: 0.8199 (m110) cc_final: 0.7534 (m110) REVERT: J 227 LYS cc_start: 0.7121 (tmmt) cc_final: 0.6858 (tmmt) REVERT: J 228 GLU cc_start: 0.7204 (mp0) cc_final: 0.6962 (mp0) REVERT: J 231 ARG cc_start: 0.7330 (tpm170) cc_final: 0.7082 (tpp-160) REVERT: J 269 GLN cc_start: 0.7305 (mt0) cc_final: 0.7071 (mt0) REVERT: K 22 GLN cc_start: 0.7348 (mp10) cc_final: 0.7068 (mp10) REVERT: K 175 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7898 (ttp80) REVERT: K 231 ARG cc_start: 0.7212 (tmm160) cc_final: 0.6794 (tmm160) REVERT: L 37 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7843 (tp40) REVERT: L 103 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8397 (ttpp) REVERT: L 175 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7649 (ttm170) REVERT: L 188 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7416 (tp30) REVERT: M 37 GLN cc_start: 0.7427 (tp40) cc_final: 0.6978 (tp40) REVERT: M 82 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6363 (tt0) REVERT: M 184 GLU cc_start: 0.7824 (tt0) cc_final: 0.7086 (pt0) REVERT: M 194 LEU cc_start: 0.8949 (tp) cc_final: 0.8722 (tt) REVERT: M 205 LYS cc_start: 0.7328 (mtpp) cc_final: 0.6746 (mttt) REVERT: N 40 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7825 (tptt) REVERT: N 116 ARG cc_start: 0.8322 (mmp-170) cc_final: 0.8122 (mmp-170) REVERT: N 131 GLU cc_start: 0.8275 (tt0) cc_final: 0.7882 (tm-30) REVERT: N 246 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6086 (tp30) REVERT: O 37 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7111 (tm130) REVERT: O 78 LYS cc_start: 0.6763 (pttt) cc_final: 0.6346 (mttm) REVERT: O 238 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: O 265 LYS cc_start: 0.5749 (ttmt) cc_final: 0.5507 (tmtt) REVERT: O 269 GLN cc_start: 0.6806 (tp40) cc_final: 0.6484 (tp-100) REVERT: O 274 GLU cc_start: 0.7637 (tt0) cc_final: 0.7339 (tt0) REVERT: P 47 ASP cc_start: 0.7470 (m-30) cc_final: 0.7196 (m-30) REVERT: Q 143 ILE cc_start: 0.7323 (mt) cc_final: 0.6865 (mt) REVERT: Q 229 MET cc_start: 0.2661 (mpt) cc_final: 0.1529 (tpp) outliers start: 12 outliers final: 2 residues processed: 574 average time/residue: 1.9925 time to fit residues: 1286.4398 Evaluate side-chains 427 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 421 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 255 SER Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain O residue 238 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 320 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 ASN D 269 GLN F 213 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 38 GLN G 206 ASN H 38 GLN H 213 GLN J 38 GLN K 206 ASN N 81 GLN N 213 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30733 Z= 0.287 Angle : 0.635 8.376 41569 Z= 0.345 Chirality : 0.046 0.167 4668 Planarity : 0.005 0.048 5066 Dihedral : 16.049 178.724 4966 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.69 % Allowed : 9.28 % Favored : 89.03 % 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: 0.78 (0.13), residues: 3570 helix: 0.71 (0.11), residues: 2198 sheet: 0.17 (0.29), residues: 210 loop : 0.52 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP M 45 HIS 0.009 0.002 HIS I 77 PHE 0.013 0.002 PHE J 190 TYR 0.018 0.002 TYR O 75 ARG 0.007 0.001 ARG M 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 441 time to evaluate : 3.779 Fit side-chains revert: symmetry clash REVERT: D 184 GLU cc_start: 0.6782 (tp30) cc_final: 0.6060 (tt0) REVERT: D 189 ARG cc_start: 0.7031 (ptp-110) cc_final: 0.6717 (ptp90) REVERT: E 38 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8171 (tp-100) REVERT: E 140 MET cc_start: 0.9164 (ttm) cc_final: 0.8847 (ttm) REVERT: E 227 LYS cc_start: 0.6937 (ttpp) cc_final: 0.6393 (tptp) REVERT: F 131 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7382 (mm-30) REVERT: F 202 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7443 (mm-30) REVERT: G 217 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7103 (mtmp) REVERT: G 223 ASN cc_start: 0.6995 (m-40) cc_final: 0.6444 (m-40) REVERT: G 269 GLN cc_start: 0.7290 (mm110) cc_final: 0.6735 (mt0) REVERT: G 270 GLU cc_start: 0.7639 (tt0) cc_final: 0.7394 (tt0) REVERT: H 202 GLU cc_start: 0.7358 (tp30) cc_final: 0.7055 (tp30) REVERT: H 209 GLU cc_start: 0.6824 (tt0) cc_final: 0.6617 (tm-30) REVERT: H 261 LYS cc_start: 0.7635 (mptt) cc_final: 0.7002 (mmtm) REVERT: I 37 GLN cc_start: 0.7883 (tp-100) cc_final: 0.7642 (tp40) REVERT: I 99 LYS cc_start: 0.8672 (mttm) cc_final: 0.8419 (mttm) REVERT: I 231 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7259 (ttp80) REVERT: J 76 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6501 (ptm-80) REVERT: J 196 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: J 206 ASN cc_start: 0.8100 (m110) cc_final: 0.7587 (m110) REVERT: J 269 GLN cc_start: 0.7124 (mt0) cc_final: 0.6909 (mt0) REVERT: K 22 GLN cc_start: 0.7266 (mp10) cc_final: 0.6898 (mm-40) REVERT: K 54 LYS cc_start: 0.8464 (tptm) cc_final: 0.8189 (tppt) REVERT: K 225 LYS cc_start: 0.7069 (ttpm) cc_final: 0.6428 (tttm) REVERT: L 37 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7644 (tp40) REVERT: L 103 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8583 (ttpp) REVERT: L 175 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7519 (ttm170) REVERT: L 210 MET cc_start: 0.6878 (ttp) cc_final: 0.6467 (ttp) REVERT: M 37 GLN cc_start: 0.7319 (tp40) cc_final: 0.6872 (tp40) REVERT: M 184 GLU cc_start: 0.7751 (tt0) cc_final: 0.7304 (pt0) REVERT: M 205 LYS cc_start: 0.7406 (mtpp) cc_final: 0.7175 (mtpp) REVERT: N 40 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7825 (tptt) REVERT: N 74 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7919 (ttt-90) REVERT: N 116 ARG cc_start: 0.8277 (mmp-170) cc_final: 0.7982 (mmp-170) REVERT: N 131 GLU cc_start: 0.8243 (tt0) cc_final: 0.7804 (tm-30) REVERT: N 181 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7318 (mtmt) REVERT: N 182 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6942 (mtp180) REVERT: N 229 MET cc_start: 0.3673 (OUTLIER) cc_final: 0.2966 (mmt) REVERT: O 37 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7138 (tm130) REVERT: O 38 GLN cc_start: 0.7530 (tp40) cc_final: 0.7240 (tt0) REVERT: O 78 LYS cc_start: 0.6791 (pttt) cc_final: 0.6314 (mttm) REVERT: O 116 ARG cc_start: 0.8262 (mmm160) cc_final: 0.8011 (mmm160) REVERT: O 191 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.8006 (mtp85) REVERT: O 210 MET cc_start: 0.6383 (mtp) cc_final: 0.6029 (mtp) REVERT: O 269 GLN cc_start: 0.6558 (tp40) cc_final: 0.6340 (tp40) REVERT: O 274 GLU cc_start: 0.7705 (tt0) cc_final: 0.7297 (tt0) REVERT: P 182 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6470 (mtp180) REVERT: Q 94 ILE cc_start: 0.7428 (pt) cc_final: 0.7218 (pt) REVERT: Q 143 ILE cc_start: 0.7253 (mt) cc_final: 0.6794 (mt) REVERT: Q 229 MET cc_start: 0.2719 (mpt) cc_final: 0.1533 (tpp) outliers start: 53 outliers final: 14 residues processed: 469 average time/residue: 1.9736 time to fit residues: 1043.8528 Evaluate side-chains 408 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 385 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 227 LYS Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain N residue 182 ARG Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 318 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 213 GLN F 269 GLN G 22 GLN G 38 GLN G 206 ASN J 38 GLN K 206 ASN N 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30733 Z= 0.204 Angle : 0.540 7.977 41569 Z= 0.294 Chirality : 0.043 0.143 4668 Planarity : 0.004 0.044 5066 Dihedral : 15.869 176.841 4959 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.88 % Allowed : 10.65 % Favored : 87.47 % 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: 1.34 (0.14), residues: 3570 helix: 1.22 (0.11), residues: 2198 sheet: 0.17 (0.29), residues: 210 loop : 0.63 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 45 HIS 0.007 0.001 HIS L 77 PHE 0.012 0.001 PHE M 204 TYR 0.015 0.001 TYR E 115 ARG 0.008 0.000 ARG O 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 415 time to evaluate : 3.416 Fit side-chains revert: symmetry clash REVERT: D 184 GLU cc_start: 0.6902 (tp30) cc_final: 0.6106 (tt0) REVERT: D 189 ARG cc_start: 0.7007 (ptp-110) cc_final: 0.6665 (ptp90) REVERT: E 140 MET cc_start: 0.9147 (ttm) cc_final: 0.8900 (ttm) REVERT: E 225 LYS cc_start: 0.6738 (ttpp) cc_final: 0.6426 (tptt) REVERT: E 227 LYS cc_start: 0.7079 (ttpp) cc_final: 0.6601 (tptp) REVERT: E 229 MET cc_start: 0.7635 (mmm) cc_final: 0.7331 (mmm) REVERT: E 270 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7092 (mt-10) REVERT: F 131 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7362 (mm-30) REVERT: F 202 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7429 (tp30) REVERT: F 209 GLU cc_start: 0.8038 (tp30) cc_final: 0.7834 (tm-30) REVERT: G 181 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7963 (mttm) REVERT: G 223 ASN cc_start: 0.6965 (m-40) cc_final: 0.6413 (m-40) REVERT: G 269 GLN cc_start: 0.7298 (mm110) cc_final: 0.6702 (mt0) REVERT: G 270 GLU cc_start: 0.7695 (tt0) cc_final: 0.7481 (tt0) REVERT: H 202 GLU cc_start: 0.7329 (tp30) cc_final: 0.7025 (tp30) REVERT: H 261 LYS cc_start: 0.7715 (mptt) cc_final: 0.6977 (mptm) REVERT: I 37 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7647 (tp40) REVERT: I 99 LYS cc_start: 0.8683 (mttm) cc_final: 0.8434 (mttm) REVERT: I 231 ARG cc_start: 0.7536 (ttp-170) cc_final: 0.7287 (ttp80) REVERT: J 196 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: J 206 ASN cc_start: 0.8130 (m110) cc_final: 0.7694 (m110) REVERT: J 269 GLN cc_start: 0.7189 (mt0) cc_final: 0.6973 (mt0) REVERT: K 22 GLN cc_start: 0.7314 (mp10) cc_final: 0.6897 (mm-40) REVERT: K 54 LYS cc_start: 0.8413 (tptm) cc_final: 0.8112 (tppt) REVERT: K 196 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8839 (t80) REVERT: K 221 SER cc_start: 0.7450 (m) cc_final: 0.7127 (p) REVERT: K 225 LYS cc_start: 0.7008 (ttpm) cc_final: 0.6722 (ttmt) REVERT: L 37 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7565 (tp40) REVERT: L 103 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8572 (ttpp) REVERT: L 149 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8323 (mp) REVERT: L 175 ARG cc_start: 0.7953 (ttp80) cc_final: 0.7523 (ttm170) REVERT: L 210 MET cc_start: 0.6914 (ttp) cc_final: 0.6561 (ttp) REVERT: M 37 GLN cc_start: 0.7267 (tp40) cc_final: 0.6855 (tp40) REVERT: M 184 GLU cc_start: 0.7802 (tt0) cc_final: 0.7274 (pt0) REVERT: M 205 LYS cc_start: 0.7384 (mtpp) cc_final: 0.7142 (mtpp) REVERT: M 211 TRP cc_start: 0.7198 (t-100) cc_final: 0.6938 (t-100) REVERT: N 27 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.5273 (ptm-80) REVERT: N 40 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7826 (tptt) REVERT: N 74 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7918 (ttt-90) REVERT: N 116 ARG cc_start: 0.8221 (mmp-170) cc_final: 0.7905 (mmp-170) REVERT: N 131 GLU cc_start: 0.8157 (tt0) cc_final: 0.7740 (tm-30) REVERT: N 181 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7231 (mtmt) REVERT: N 229 MET cc_start: 0.3684 (OUTLIER) cc_final: 0.3023 (mmt) REVERT: O 37 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7152 (tm130) REVERT: O 71 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7677 (t70) REVERT: O 78 LYS cc_start: 0.6752 (pttt) cc_final: 0.6257 (mttm) REVERT: O 116 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7991 (mmm160) REVERT: O 152 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: O 191 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7991 (ttt180) REVERT: O 210 MET cc_start: 0.6389 (mtp) cc_final: 0.6148 (mtp) REVERT: O 273 LYS cc_start: 0.7589 (tttp) cc_final: 0.7296 (ttpt) REVERT: O 274 GLU cc_start: 0.7766 (tt0) cc_final: 0.7320 (tt0) REVERT: P 182 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6475 (mtp180) REVERT: Q 94 ILE cc_start: 0.7379 (pt) cc_final: 0.7162 (pt) REVERT: Q 143 ILE cc_start: 0.7239 (mt) cc_final: 0.6784 (mt) REVERT: Q 187 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7751 (tp) REVERT: Q 214 MET cc_start: 0.3292 (mpt) cc_final: 0.3069 (mpp) REVERT: Q 229 MET cc_start: 0.2625 (mpt) cc_final: 0.1407 (tpp) outliers start: 59 outliers final: 19 residues processed: 453 average time/residue: 1.9842 time to fit residues: 1014.5868 Evaluate side-chains 411 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 380 time to evaluate : 3.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 153 optimal weight: 0.0050 chunk 215 optimal weight: 8.9990 chunk 322 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 213 GLN F 269 GLN G 22 GLN G 38 GLN G 206 ASN J 38 GLN K 206 ASN N 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30733 Z= 0.258 Angle : 0.565 7.880 41569 Z= 0.306 Chirality : 0.044 0.150 4668 Planarity : 0.005 0.049 5066 Dihedral : 15.903 175.828 4958 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.26 % Allowed : 12.09 % Favored : 85.65 % 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: 1.35 (0.14), residues: 3570 helix: 1.27 (0.11), residues: 2198 sheet: 0.14 (0.29), residues: 210 loop : 0.56 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 45 HIS 0.009 0.001 HIS L 77 PHE 0.012 0.001 PHE J 125 TYR 0.013 0.002 TYR E 115 ARG 0.007 0.000 ARG N 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 398 time to evaluate : 3.564 Fit side-chains revert: symmetry clash REVERT: D 116 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.5984 (mpp-170) REVERT: D 184 GLU cc_start: 0.6887 (tp30) cc_final: 0.6059 (tt0) REVERT: D 189 ARG cc_start: 0.7021 (ptp-110) cc_final: 0.6749 (ptp90) REVERT: E 38 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8179 (tp-100) REVERT: E 140 MET cc_start: 0.9161 (ttm) cc_final: 0.8829 (ttm) REVERT: E 225 LYS cc_start: 0.6648 (ttpp) cc_final: 0.6326 (tptt) REVERT: E 227 LYS cc_start: 0.7211 (ttpp) cc_final: 0.6744 (tptp) REVERT: E 270 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7103 (mt-10) REVERT: F 131 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7392 (mm-30) REVERT: F 202 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7445 (tp30) REVERT: F 209 GLU cc_start: 0.8087 (tp30) cc_final: 0.7877 (tm-30) REVERT: F 210 MET cc_start: 0.8132 (mtp) cc_final: 0.7884 (mtp) REVERT: G 181 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8005 (mttm) REVERT: G 223 ASN cc_start: 0.6959 (m-40) cc_final: 0.6404 (m-40) REVERT: G 227 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7320 (tmmm) REVERT: G 270 GLU cc_start: 0.7691 (tt0) cc_final: 0.7428 (tt0) REVERT: H 202 GLU cc_start: 0.7345 (tp30) cc_final: 0.7037 (tp30) REVERT: H 241 ILE cc_start: 0.8653 (tp) cc_final: 0.8448 (tp) REVERT: H 261 LYS cc_start: 0.7746 (mptt) cc_final: 0.7033 (mptm) REVERT: I 33 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8476 (mm) REVERT: I 37 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7735 (tp40) REVERT: I 99 LYS cc_start: 0.8710 (mttm) cc_final: 0.8441 (mttm) REVERT: J 76 ARG cc_start: 0.7190 (ttp-170) cc_final: 0.6684 (ptm-80) REVERT: J 196 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: J 206 ASN cc_start: 0.8105 (m110) cc_final: 0.7688 (m110) REVERT: J 269 GLN cc_start: 0.7126 (mt0) cc_final: 0.6908 (mt0) REVERT: K 54 LYS cc_start: 0.8501 (tptm) cc_final: 0.8211 (tppt) REVERT: K 61 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7470 (mp0) REVERT: K 149 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7976 (mp) REVERT: K 196 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8757 (t80) REVERT: K 221 SER cc_start: 0.7483 (m) cc_final: 0.7138 (p) REVERT: L 37 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7580 (tp40) REVERT: L 103 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8571 (ttpp) REVERT: L 149 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8337 (mp) REVERT: L 175 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7503 (ttm170) REVERT: L 213 GLN cc_start: 0.6722 (mm110) cc_final: 0.6085 (mt0) REVERT: M 37 GLN cc_start: 0.7313 (tp40) cc_final: 0.6907 (tp40) REVERT: M 184 GLU cc_start: 0.7776 (tt0) cc_final: 0.7169 (pt0) REVERT: M 205 LYS cc_start: 0.7378 (mtpp) cc_final: 0.7153 (mtpp) REVERT: M 211 TRP cc_start: 0.7215 (t-100) cc_final: 0.6947 (t-100) REVERT: M 270 GLU cc_start: 0.7147 (pt0) cc_final: 0.6866 (pt0) REVERT: N 27 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.5264 (ptm-80) REVERT: N 40 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7859 (tptt) REVERT: N 74 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7923 (ttt-90) REVERT: N 131 GLU cc_start: 0.8131 (tt0) cc_final: 0.7726 (tm-30) REVERT: O 37 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7168 (tm130) REVERT: O 38 GLN cc_start: 0.7486 (tp40) cc_final: 0.7165 (tt0) REVERT: O 71 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7669 (t70) REVERT: O 78 LYS cc_start: 0.6740 (pttt) cc_final: 0.6219 (mttm) REVERT: O 116 ARG cc_start: 0.8269 (mmm160) cc_final: 0.8001 (mmm160) REVERT: O 152 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: O 210 MET cc_start: 0.6439 (mtp) cc_final: 0.6182 (mtp) REVERT: O 273 LYS cc_start: 0.7510 (tttp) cc_final: 0.7299 (ttpt) REVERT: O 274 GLU cc_start: 0.7714 (tt0) cc_final: 0.7284 (tt0) REVERT: P 175 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6632 (ttt-90) REVERT: P 182 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6494 (mtp180) REVERT: Q 22 GLN cc_start: 0.2586 (OUTLIER) cc_final: 0.2021 (pt0) REVERT: Q 94 ILE cc_start: 0.7476 (pt) cc_final: 0.7246 (pt) REVERT: Q 143 ILE cc_start: 0.7254 (mt) cc_final: 0.6792 (mt) REVERT: Q 187 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7785 (tp) REVERT: Q 214 MET cc_start: 0.3289 (mpt) cc_final: 0.0972 (tpt) REVERT: Q 229 MET cc_start: 0.2666 (mpt) cc_final: 0.1408 (tpp) outliers start: 71 outliers final: 25 residues processed: 444 average time/residue: 2.0204 time to fit residues: 1009.8469 Evaluate side-chains 421 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 379 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 187 LEU Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 0.1980 chunk 193 optimal weight: 5.9990 chunk 4 optimal weight: 0.0770 chunk 254 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 213 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 38 GLN G 206 ASN I 22 GLN J 38 GLN K 206 ASN N 81 GLN N 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30733 Z= 0.128 Angle : 0.466 7.203 41569 Z= 0.255 Chirality : 0.040 0.140 4668 Planarity : 0.004 0.047 5066 Dihedral : 15.364 177.222 4958 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.59 % Allowed : 13.39 % Favored : 85.01 % 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: 1.84 (0.14), residues: 3570 helix: 1.67 (0.11), residues: 2198 sheet: 0.39 (0.31), residues: 210 loop : 0.71 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 45 HIS 0.004 0.001 HIS O 77 PHE 0.015 0.001 PHE M 204 TYR 0.014 0.001 TYR E 115 ARG 0.008 0.000 ARG O 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 434 time to evaluate : 3.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 95 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7552 (ttm170) REVERT: D 184 GLU cc_start: 0.6770 (tp30) cc_final: 0.6046 (tt0) REVERT: D 189 ARG cc_start: 0.6894 (ptp-110) cc_final: 0.6621 (ptp90) REVERT: E 38 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8155 (tp-100) REVERT: E 227 LYS cc_start: 0.7276 (ttpp) cc_final: 0.6934 (ttmm) REVERT: E 229 MET cc_start: 0.8014 (mmm) cc_final: 0.7788 (mtm) REVERT: F 131 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7408 (mm-30) REVERT: F 202 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7371 (tp30) REVERT: G 181 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7987 (mttm) REVERT: G 223 ASN cc_start: 0.6902 (m-40) cc_final: 0.6367 (m110) REVERT: G 227 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7241 (tmmm) REVERT: G 270 GLU cc_start: 0.7661 (tt0) cc_final: 0.7457 (tt0) REVERT: H 202 GLU cc_start: 0.7231 (tp30) cc_final: 0.6948 (tp30) REVERT: H 261 LYS cc_start: 0.7705 (mptt) cc_final: 0.7032 (mptm) REVERT: I 37 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7521 (tp40) REVERT: I 99 LYS cc_start: 0.8707 (mttm) cc_final: 0.8406 (mttm) REVERT: J 2------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 213 GLN F 269 GLN G 22 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN N 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30733 Z= 0.289 Angle : 0.575 7.734 41569 Z= 0.310 Chirality : 0.045 0.146 4668 Planarity : 0.005 0.051 5066 Dihedral : 15.786 175.851 4958 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.10 % Allowed : 13.93 % Favored : 83.96 % 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: 1.54 (0.14), residues: 3570 helix: 1.45 (0.11), residues: 2198 sheet: 0.22 (0.30), residues: 210 loop : 0.55 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 45 HIS 0.009 0.001 HIS L 77 PHE 0.013 0.002 PHE J 125 TYR 0.014 0.002 TYR H 275 ARG 0.009 0.001 ARG O 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 398 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.5849 (mpp-170) REVERT: D 175 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7766 (ttp80) REVERT: D 184 GLU cc_start: 0.6805 (tp30) cc_final: 0.6038 (tt0) REVERT: D 189 ARG cc_start: 0.6979 (ptp-110) cc_final: 0.6702 (ptp90) REVERT: E 38 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8178 (tp-100) REVERT: E 227 LYS cc_start: 0.7302 (ttpp) cc_final: 0.6966 (ttmm) REVERT: E 229 MET cc_start: 0.8053 (mmm) cc_final: 0.7801 (mtm) REVERT: F 74 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7454 (ppt-90) REVERT: F 131 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7412 (mm-30) REVERT: F 202 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7445 (tp30) REVERT: F 209 GLU cc_start: 0.7918 (tp30) cc_final: 0.7431 (tm-30) REVERT: F 213 GLN cc_start: 0.7160 (mt0) cc_final: 0.6680 (mt0) REVERT: G 181 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8060 (mttm) REVERT: G 217 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7106 (mtEvaluate side-chains 436 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 387 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 213 GLN F 269 GLN G 206 ASN I 22 GLN J 38 GLN J 269 GLN K 206 ASN ** L 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30733 Z= 0.149 Angle : 0.485 7.213 41569 Z= 0.264 Chirality : 0.041 0.151 4668 Planarity : 0.004 0.051 5066 Dihedral : 15.424 177.142 4958 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.72 % Allowed : 14.92 % Favored : 83.35 % 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: 1.80 (0.14), residues: 3570 helix: 1.67 (0.11), residues: 2198 sheet: 0.37 (0.31), residues: 210 loop : 0.61 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 45 HIS 0.004 0.001 HIS I 77 PHE 0.011 0.001 PHE M 204 TYR 0.014 0.001 TYR E 115 ARG 0.009 0.000 ARG O 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 407 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6125 (ttm170) REVERT: D 95 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: D 184 GLU cc_start: 0.6802 (tp30) cc_final: 0.6012 (tt0) REVERT: E 38 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8167 (tp-100) REVERT: E 227 LYS cc_start: 0.7378 (ttpp) cc_final: 0.7099 (ttmm) REVERT: E 229 MET cc_start: 0.8012 (mmm) cc_final: 0.7796 (mtm) REVERT: F 131 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7431 (mm-30) REVERT: F 202 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7428 (tp30) REVERT: G 181 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8016 (mttm) REVERT: G 223 ASN cc_start: 0.6921 (m-40) cc_final: 0.6384 (m-40) REVERT: G 270 GLU cc_start: 0.7712 (tt0) cc_final: 0.7470 (tt0) REVERT: H 202 GLU cc_start: 0.7245 (tp30) cc_final: 0.6956 (tp30) REVERT: H 241 ILE cc_start: 0.8723 (tp) cc_final: 0.8486 (tp) REVERT: H 261 LYS cc_start: 0.7725 (mptt) cc_final: 0.7049 (mptm) REVERT: I 33 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8366 (mm) REVERT: I 37 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7574 (tp40) REVERT: I 99 LYS cc_start: 0.8729 (mttm) cc_final: 0.8478 (mttm) REVERT: J 22 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6639 (mt0) REVERT: J 76 ARG cc_start: 0.7182 (ttp-170) cc_final: 0.6645 (ptm-80) REVERT: J 78 LYS cc_start: 0.7308 (mmmm) cc_final: 0.6930 (mmmt) REVERT: J 124 ASP cc_start: 0.7687 (m-30) cc_final: 0.7477 (m-30) REVERT: J 196 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: J 206 ASN cc_start: 0.8097 (m110) cc_final: 0.7644 (m110) REVERT: K 61 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7536 (mp0) REVERT: K 196 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8725 (t80) REVERT: L 37 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7530 (tp40) REVERT: L 103 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8330 (ttpp) REVERT: L 175 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7493 (ttm170) REVERT: L 213 GLN cc_start: 0.6685 (mm110) cc_final: 0.6100 (mt0) REVERT: L 238 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6508 (tm-30) REVERT: L 273 LYS cc_start: 0.7192 (pptt) cc_final: 0.6626 (tmmt) REVERT: M 37 GLN cc_start: 0.7285 (tp40) cc_final: 0.6917 (tp40) REVERT: M 184 GLU cc_start: 0.7737 (tt0) cc_final: 0.7152 (pt0) REVERT: M 205 LYS cc_start: 0.7369 (mtpp) cc_final: 0.7142 (mtpp) REVERT: M 211 TRP cc_start: 0.7208 (OUTLIER) cc_final: 0.6970 (t-100) REVERT: M 269 GLN cc_start: 0.5842 (mt0) cc_final: 0.5170 (mm-40) REVERT: N 40 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7831 (tptt) REVERT: N 131 GLU cc_start: 0.8024 (tt0) cc_final: 0.7607 (tm-30) REVERT: O 38 GLN cc_start: 0.7425 (tp40) cc_final: 0.7159 (tt0) REVERT: O 75 TYR cc_start: 0.7500 (m-10) cc_final: 0.7099 (m-80) REVERT: O 78 LYS cc_start: 0.6711 (pttt) cc_final: 0.6127 (mttm) REVERT: O 229 MET cc_start: 0.5427 (OUTLIER) cc_final: 0.4872 (mtp) REVERT: O 238 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6626 (tm-30) REVERT: O 269 GLN cc_start: 0.6664 (tp-100) cc_final: 0.6349 (tp40) REVERT: O 273 LYS cc_start: 0.7477 (tttp) cc_final: 0.6891 (mtmt) REVERT: O 274 GLU cc_start: 0.7734 (tt0) cc_final: 0.6997 (tp30) REVERT: P 182 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6372 (mtp180) REVERT: Q 94 ILE cc_start: 0.7437 (pt) cc_final: 0.7167 (pt) REVERT: Q 143 ILE cc_start: 0.7289 (mt) cc_final: 0.6811 (mt) REVERT: Q 214 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.3071 (mtm) REVERT: Q 229 MET cc_start: 0.2602 (mpt) cc_final: 0.1318 (tpp) outliers start: 54 outliers final: 26 residues processed: 436 average time/residue: 1.9134 time to fit residues: 942.1063 Evaluate side-chains 428 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 390 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 211 TRP Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 0.0970 chunk 325 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 213 GLN F 269 GLN G 22 GLN G 206 ASN I 22 GLN J 38 GLN J 269 GLN K 206 ASN ** L 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 30733 Z= 0.307 Angle : 0.591 7.785 41569 Z= 0.317 Chirality : 0.045 0.159 4668 Planarity : 0.005 0.052 5066 Dihedral : 15.820 175.544 4958 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.79 % Allowed : 14.99 % Favored : 83.23 % 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: 1.43 (0.14), residues: 3570 helix: 1.38 (0.11), residues: 2198 sheet: 0.20 (0.30), residues: 210 loop : 0.45 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 45 HIS 0.007 0.001 HIS L 77 PHE 0.012 0.002 PHE J 125 TYR 0.014 0.002 TYR H 275 ARG 0.008 0.001 ARG O 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 389 time to evaluate : 3.513 Fit side-chains revert: symmetry clash REVERT: D 74 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6245 (ttm170) REVERT: D 116 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5790 (mpp-170) REVERT: D 184 GLU cc_start: 0.6795 (tp30) cc_final: 0.5999 (tt0) REVERT: E 38 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8183 (tp-100) REVERT: E 227 LYS cc_start: 0.7340 (ttpp) cc_final: 0.7017 (ttmm) REVERT: E 229 MET cc_start: 0.8016 (mmm) cc_final: 0.7764 (mtt) REVERT: E 270 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6674 (mp0) REVERT: F 74 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7100 (ppt170) REVERT: F 131 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7409 (mm-30) REVERT: F 202 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7445 (tp30) REVERT: G 181 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8065 (mttm) REVERT: G 217 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7129 (mttp) REVERT: G 223 ASN cc_start: 0.6911 (m-40) cc_final: 0.6363 (m-40) REVERT: G 270 GLU cc_start: 0.7725 (tt0) cc_final: 0.7438 (tt0) REVERT: H 202 GLU cc_start: 0.7265 (tp30) cc_final: 0.6964 (tp30) REVERT: H 241 ILE cc_start: 0.8725 (tp) cc_final: 0.8500 (tp) REVERT: H 261 LYS cc_start: 0.7747 (mptt) cc_final: 0.7050 (mptm) REVERT: I 33 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8465 (mm) REVERT: I 37 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7775 (tp40) REVERT: I 99 LYS cc_start: 0.8729 (mttm) cc_final: 0.8459 (mttm) REVERT: J 76 ARG cc_start: 0.7187 (ttp-170) cc_final: 0.6678 (ptm-80) REVERT: J 78 LYS cc_start: 0.7359 (mmmm) cc_final: 0.6975 (mmmt) REVERT: J 196 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: J 206 ASN cc_start: 0.8103 (m110) cc_final: 0.7696 (m110) REVERT: K 196 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8864 (t80) REVERT: K 213 GLN cc_start: 0.7406 (mt0) cc_final: 0.6837 (tp40) REVERT: K 231 ARG cc_start: 0.7217 (tmm160) cc_final: 0.7014 (tmm160) REVERT: L 37 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7571 (tp40) REVERT: L 103 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8573 (ttpp) REVERT: L 175 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7531 (ttm170) REVERT: L 213 GLN cc_start: 0.6699 (mm110) cc_final: 0.6092 (mt0) REVERT: M 37 GLN cc_start: 0.7379 (tp40) cc_final: 0.6975 (tp40) REVERT: M 184 GLU cc_start: 0.7852 (tt0) cc_final: 0.7225 (pt0) REVERT: M 205 LYS cc_start: 0.7435 (mtpp) cc_final: 0.7179 (mtpp) REVERT: M 211 TRP cc_start: 0.7258 (OUTLIER) cc_final: 0.7006 (t-100) REVERT: M 238 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6539 (mm-30) REVERT: M 270 GLU cc_start: 0.7126 (pt0) cc_final: 0.6842 (pt0) REVERT: N 40 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7867 (tptt) REVERT: N 131 GLU cc_start: 0.8155 (tt0) cc_final: 0.7746 (tm-30) REVERT: N 246 GLU cc_start: 0.6813 (tt0) cc_final: 0.6259 (tp30) REVERT: O 38 GLN cc_start: 0.7476 (tp40) cc_final: 0.7192 (tt0) REVERT: O 78 LYS cc_start: 0.6757 (pttt) cc_final: 0.6166 (mttm) REVERT: O 210 MET cc_start: 0.6306 (mtp) cc_final: 0.6011 (mtt) REVERT: O 229 MET cc_start: 0.5495 (OUTLIER) cc_final: 0.5017 (mtp) REVERT: O 238 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6650 (tm-30) REVERT: O 269 GLN cc_start: 0.6577 (tp-100) cc_final: 0.6211 (tp40) REVERT: O 273 LYS cc_start: 0.7420 (tttp) cc_final: 0.6849 (mtmt) REVERT: O 274 GLU cc_start: 0.7750 (tt0) cc_final: 0.7065 (tp30) REVERT: P 182 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6402 (mtp180) REVERT: Q 22 GLN cc_start: 0.2662 (OUTLIER) cc_final: 0.2001 (pt0) REVERT: Q 94 ILE cc_start: 0.7557 (pt) cc_final: 0.7307 (pt) REVERT: Q 143 ILE cc_start: 0.7269 (mt) cc_final: 0.6768 (mt) REVERT: Q 214 MET cc_start: 0.3619 (OUTLIER) cc_final: 0.3084 (mtm) REVERT: Q 229 MET cc_start: 0.2492 (mpt) cc_final: 0.1251 (tpp) outliers start: 56 outliers final: 28 residues processed: 421 average time/residue: 1.9229 time to fit residues: 914.4925 Evaluate side-chains 425 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 382 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 227 LYS Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain M residue 211 TRP Chi-restraints excluded: chain M residue 238 GLU Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 199 LEU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 0.9980 chunk 335 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 159 optimal weight: 0.0000 chunk 233 optimal weight: 1.9990 chunk 351 optimal weight: 20.0000 chunk 323 optimal weight: 0.6980 chunk 280 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 216 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 206 ASN F 213 GLN F 269 GLN G 22 GLN G 206 ASN I 22 GLN J 38 GLN K 206 ASN ** L 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30733 Z= 0.131 Angle : 0.476 8.779 41569 Z= 0.259 Chirality : 0.040 0.147 4668 Planarity : 0.004 0.054 5066 Dihedral : 15.275 177.894 4958 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.21 % Allowed : 15.69 % Favored : 83.10 % 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: 1.85 (0.14), residues: 3570 helix: 1.73 (0.11), residues: 2184 sheet: 0.40 (0.32), residues: 238 loop : 0.61 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 45 HIS 0.004 0.001 HIS O 77 PHE 0.016 0.001 PHE M 204 TYR 0.013 0.001 TYR E 75 ARG 0.010 0.000 ARG O 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 412 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6163 (ttm170) REVERT: D 184 GLU cc_start: 0.6824 (tp30) cc_final: 0.6032 (tt0) REVERT: E 227 LYS cc_start: 0.7394 (ttpp) cc_final: 0.7042 (tttm) REVERT: E 229 MET cc_start: 0.7993 (mmm) cc_final: 0.7772 (mtm) REVERT: E 270 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6490 (mp0) REVERT: F 128 ARG cc_start: 0.8359 (tpt-90) cc_final: 0.8090 (tpt90) REVERT: F 131 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7402 (mm-30) REVERT: G 181 LYS cc_start: 0.8363 (mtmt) cc_final: 0.8000 (mttm) REVERT: G 223 ASN cc_start: 0.6899 (m-40) cc_final: 0.6380 (m110) REVERT: G 270 GLU cc_start: 0.7660 (tt0) cc_final: 0.7441 (tt0) REVERT: H 202 GLU cc_start: 0.7215 (tp30) cc_final: 0.6941 (tp30) REVERT: H 261 LYS cc_start: 0.7729 (mptt) cc_final: 0.7049 (mptm) REVERT: I 37 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7515 (tp40) REVERT: J 78 LYS cc_start: 0.7288 (mmmm) cc_final: 0.6923 (mmmt) REVERT: J 196 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: J 202 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6456 (tm-30) REVERT: J 206 ASN cc_start: 0.8064 (m110) cc_final: 0.7434 (m110) REVERT: K 61 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7536 (mp0) REVERT: K 99 LYS cc_start: 0.8567 (mttp) cc_final: 0.7769 (mmpt) REVERT: K 191 ARG cc_start: 0.8273 (ptp-110) cc_final: 0.8016 (ptm160) REVERT: K 196 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8756 (t80) REVERT: K 213 GLN cc_start: 0.7369 (mt0) cc_final: 0.6828 (tp40) REVERT: L 37 GLN cc_start: 0.7711 (tp-100) cc_final: 0.7430 (tp40) REVERT: L 103 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8285 (ttpp) REVERT: L 175 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7483 (ttm170) REVERT: L 210 MET cc_start: 0.6913 (ttp) cc_final: 0.6505 (ttp) REVERT: L 213 GLN cc_start: 0.6701 (mm110) cc_final: 0.6045 (mt0) REVERT: L 238 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6478 (tm-30) REVERT: L 273 LYS cc_start: 0.7326 (pptt) cc_final: 0.6755 (tmmt) REVERT: M 37 GLN cc_start: 0.7221 (tp40) cc_final: 0.6836 (tp40) REVERT: M 184 GLU cc_start: 0.7736 (tt0) cc_final: 0.7244 (pt0) REVERT: M 205 LYS cc_start: 0.7430 (mtpp) cc_final: 0.7174 (mtpp) REVERT: M 269 GLN cc_start: 0.5921 (mt0) cc_final: 0.5259 (mm-40) REVERT: N 40 LYS cc_start: 0.8034 (ttpp) cc_final: 0.7793 (tptt) REVERT: N 131 GLU cc_start: 0.7922 (tt0) cc_final: 0.7540 (tm-30) REVERT: N 246 GLU cc_start: 0.6674 (tt0) cc_final: 0.6096 (tp30) REVERT: O 38 GLN cc_start: 0.7390 (tp40) cc_final: 0.7113 (tt0) REVERT: O 210 MET cc_start: 0.6403 (mtp) cc_final: 0.6113 (mtt) REVERT: O 214 MET cc_start: 0.5865 (pmt) cc_final: 0.5464 (pmm) REVERT: O 229 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.4906 (mtp) REVERT: O 273 LYS cc_start: 0.7472 (tttp) cc_final: 0.7260 (ttpt) REVERT: O 274 GLU cc_start: 0.7684 (tt0) cc_final------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 269 GLN F 213 GLN F 269 GLN G 22 GLN G 206 ASN I 22 GLN J 38 GLN K 206 ASN Q 77 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.200760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158924 restraints weight = 29815.774| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.47 r_work: 0.3770 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 30733 Z= 0.139 Angle : 0.478 9.739 41569 Z= 0.258 Chirality : 0.040 0.152 4668 Planarity : 0.004 0.053 5066 Dihedral : 15.263 177.673 4958 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.02 % Allowed : 16.45 % Favored : 82.53 % 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: 2.00 (0.14), residues: 3570 helix: 1.83 (0.11), residues: 2184 sheet: 0.50 (0.32), residues: 210 loop : 0.71 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 211 HIS 0.003 0.001 HIS I 77 PHE 0.015 0.001 PHE M 204 TYR 0.017 0.001 TYR O 75 ARG 0.009 0.000 ARG O 175 =============================================================================== Job complete usr+sys time: 14268.54 seconds wall clock time: 511 minutes 46.88 seconds (30706.88 seconds total)