Starting phenix.real_space_refine on Sun Mar 17 22:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/03_2024/7rsl_24674.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/03_2024/7rsl_24674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/03_2024/7rsl_24674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/03_2024/7rsl_24674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/03_2024/7rsl_24674.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/03_2024/7rsl_24674.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 12460 2.51 5 N 3120 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 199": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "G GLU 199": "OE1" <-> "OE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 185": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E GLU 199": "OE1" <-> "OE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "I GLU 199": "OE1" <-> "OE2" Residue "I TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J GLU 185": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19150 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "E" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "J" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "D" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 9.80, per 1000 atoms: 0.51 Number of scatterers: 19150 At special positions: 0 Unit cell: (155.925, 154.275, 85.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3480 8.00 N 3120 7.00 C 12460 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: 6.56 Conformation dependent library (CDL) restraints added in 3.2 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 40 sheets defined 34.7% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 18 through 45 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 45 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 45 Proline residue: G 31 - end of helix Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 174 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'G' and resid 234 through 243 Processing helix chain 'G' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE G 252 " --> pdb=" O TYR G 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 45 Proline residue: H 31 - end of helix Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU H 187 " --> pdb=" O ASP H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU H 246 " --> pdb=" O ARG H 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 45 Proline residue: E 31 - end of helix Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 45 Proline residue: F 31 - end of helix Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 45 Proline residue: I 31 - end of helix Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE I 252 " --> pdb=" O TYR I 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 45 Proline residue: J 31 - end of helix Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 174 Processing helix chain 'J' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU J 187 " --> pdb=" O ASP J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU J 246 " --> pdb=" O ARG J 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 45 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 45 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.729A pdb=" N LEU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 264 removed outlier: 3.611A pdb=" N LEU D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE A 196 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU A 107 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP A 194 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 109 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A 192 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 111 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 190 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS A 113 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN A 188 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE A 71 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 205 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 204 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 132 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 131 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS A 149 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET A 97 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR B 103 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE B 196 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 105 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 194 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER B 206 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 131 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS B 149 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 54 removed outlier: 4.665A pdb=" N ILE G 196 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU G 107 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP G 194 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU G 109 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE G 192 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU G 111 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 190 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS G 113 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN G 188 " --> pdb=" O CYS G 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE G 71 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 205 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR G 204 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY G 132 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG G 131 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS G 149 " --> pdb=" O ARG G 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET G 97 " --> pdb=" O LYS G 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR H 103 " --> pdb=" O ILE H 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 196 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU H 105 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP H 194 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 50 through 54 Processing sheet with id=AB6, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER H 206 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 131 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS H 149 " --> pdb=" O ARG H 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE E 196 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU E 107 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP E 194 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 109 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE E 192 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU E 111 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE E 190 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS E 113 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN E 188 " --> pdb=" O CYS E 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.618A pdb=" N PHE E 71 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 205 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR E 204 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 132 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG E 131 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS E 149 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET E 97 " --> pdb=" O LYS E 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR F 103 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE F 196 " --> pdb=" O TYR F 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU F 105 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP F 194 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 50 through 54 Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER F 206 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG F 131 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS F 149 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC7, first strand: chain 'I' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE I 196 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N LEU I 107 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP I 194 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU I 109 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE I 192 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU I 111 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE I 190 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS I 113 " --> pdb=" O ASN I 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN I 188 " --> pdb=" O CYS I 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'I' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE I 71 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE I 205 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR I 204 " --> pdb=" O GLY I 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY I 132 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 131 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS I 149 " --> pdb=" O ARG I 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 74 through 77 removed outlier: 3.877A pdb=" N MET I 97 " --> pdb=" O LYS I 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR J 103 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE J 196 " --> pdb=" O TYR J 103 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU J 105 " --> pdb=" O ASP J 194 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP J 194 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 50 through 54 Processing sheet with id=AD4, first strand: chain 'J' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER J 206 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG J 131 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS J 149 " --> pdb=" O ARG J 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE C 196 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU C 107 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C 194 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU C 109 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 192 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU C 111 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE C 190 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS C 113 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN C 188 " --> pdb=" O CYS C 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD8, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE C 71 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 205 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR C 204 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 132 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG C 131 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS C 149 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET C 97 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 50 through 54 removed outlier: 7.215A pdb=" N TYR D 103 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 196 " --> pdb=" O TYR D 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 105 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP D 194 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 50 through 54 Processing sheet with id=AE3, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER D 206 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG D 131 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS D 149 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 74 through 76 1070 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 7.22 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: 4854 1.33 - 1.45: 3393 1.45 - 1.57: 11153 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 19540 Sorted by residual: bond pdb=" N ILE B 150 " pdb=" CA ILE B 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE J 150 " pdb=" CA ILE J 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE H 150 " pdb=" CA ILE H 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.25e+01 bond pdb=" N ILE F 150 " pdb=" CA ILE F 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.24e+01 ... (remaining 19535 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.82: 441 105.82 - 112.84: 10625 112.84 - 119.87: 6340 119.87 - 126.89: 8910 126.89 - 133.92: 174 Bond angle restraints: 26490 Sorted by residual: angle pdb=" N HIS J 119 " pdb=" CA HIS J 119 " pdb=" C HIS J 119 " ideal model delta sigma weight residual 110.50 100.67 9.83 1.41e+00 5.03e-01 4.86e+01 angle pdb=" N HIS H 119 " pdb=" CA HIS H 119 " pdb=" C HIS H 119 " ideal model delta sigma weight residual 110.50 100.70 9.80 1.41e+00 5.03e-01 4.83e+01 angle pdb=" N HIS B 119 " pdb=" CA HIS B 119 " pdb=" C HIS B 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS D 119 " pdb=" CA HIS D 119 " pdb=" C HIS D 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS F 119 " pdb=" CA HIS F 119 " pdb=" C HIS F 119 " ideal model delta sigma weight residual 110.50 100.76 9.74 1.41e+00 5.03e-01 4.77e+01 ... (remaining 26485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10796 17.74 - 35.48: 872 35.48 - 53.22: 119 53.22 - 70.96: 47 70.96 - 88.70: 16 Dihedral angle restraints: 11850 sinusoidal: 4910 harmonic: 6940 Sorted by residual: dihedral pdb=" CA MET J 101 " pdb=" C MET J 101 " pdb=" N GLU J 102 " pdb=" CA GLU J 102 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N GLU D 102 " pdb=" CA GLU D 102 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET B 101 " pdb=" C MET B 101 " pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta harmonic sigma weight residual 180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2091 0.041 - 0.082: 623 0.082 - 0.122: 315 0.122 - 0.163: 60 0.163 - 0.204: 21 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CA LEU J 91 " pdb=" N LEU J 91 " pdb=" C LEU J 91 " pdb=" CB LEU J 91 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA ILE D 205 " pdb=" N ILE D 205 " pdb=" C ILE D 205 " pdb=" CB ILE D 205 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 3107 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 118 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASP H 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP H 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP H 118 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 118 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" CG ASP J 118 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP J 118 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP J 118 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 118 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" CG ASP D 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP D 118 " 0.015 2.00e-02 2.50e+03 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1643 2.74 - 3.28: 19652 3.28 - 3.82: 30021 3.82 - 4.36: 37019 4.36 - 4.90: 64414 Nonbonded interactions: 152749 Sorted by model distance: nonbonded pdb=" OD1 ASP I 194 " pdb=" NH2 ARG I 229 " model vdw 2.200 2.520 nonbonded pdb=" OD1 ASP C 194 " pdb=" NH2 ARG C 229 " model vdw 2.200 2.520 nonbonded pdb=" OD1 ASP A 194 " pdb=" NH2 ARG A 229 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP E 194 " pdb=" NH2 ARG E 229 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASP G 194 " pdb=" NH2 ARG G 229 " model vdw 2.202 2.520 ... (remaining 152744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.330 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 47.880 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.120 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.007 0.041 19540 Z= 0.454 Angle : 0.818 9.828 26490 Z= 0.528 Chirality : 0.051 0.204 3110 Planarity : 0.005 0.043 3340 Dihedral : 13.619 88.702 7330 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.23 % Allowed : 1.71 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.76 (0.17), residues: 2310 helix: 0.67 (0.19), residues: 725 sheet: -2.21 (0.18), residues: 735 loop : -1.63 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP F 186 HIS 0.005 0.001 HIS F 152 PHE 0.017 0.002 PHE E 40 TYR 0.019 0.002 TYR G 103 ARG 0.013 0.001 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 515 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8706 (mmtt) REVERT: A 173 GLN cc_start: 0.8963 (mt0) cc_final: 0.8647 (mt0) REVERT: B 104 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8960 (tptp) REVERT: B 184 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 212 GLU cc_start: 0.8465 (tt0) cc_final: 0.8262 (tt0) REVERT: B 227 LYS cc_start: 0.9394 (mtpt) cc_final: 0.9175 (ttmm) REVERT: G 173 GLN cc_start: 0.8534 (mt0) cc_final: 0.8048 (mt0) REVERT: H 104 LYS cc_start: 0.9281 (ttmm) cc_final: 0.8962 (tptp) REVERT: H 184 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 173 GLN cc_start: 0.7977 (mt0) cc_final: 0.7383 (mt0) REVERT: E 202 TYR cc_start: 0.8810 (m-80) cc_final: 0.8502 (m-80) REVERT: F 103 TYR cc_start: 0.8091 (m-80) cc_final: 0.7859 (m-80) REVERT: F 183 ASP cc_start: 0.8909 (t70) cc_final: 0.8693 (t0) REVERT: F 184 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 195 LYS cc_start: 0.9268 (mmtp) cc_final: 0.8968 (mmmm) REVERT: F 212 GLU cc_start: 0.8506 (tt0) cc_final: 0.8292 (tt0) REVERT: F 227 LYS cc_start: 0.9395 (mtpt) cc_final: 0.9178 (tppp) REVERT: F 234 GLN cc_start: 0.9588 (mm-40) cc_final: 0.9354 (tp40) REVERT: I 97 MET cc_start: 0.7895 (ptm) cc_final: 0.7639 (ptm) REVERT: I 202 TYR cc_start: 0.8316 (m-80) cc_final: 0.8083 (m-80) REVERT: J 104 LYS cc_start: 0.9230 (ttmm) cc_final: 0.9000 (tptp) REVERT: J 184 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8284 (mm-30) REVERT: C 173 GLN cc_start: 0.8167 (mt0) cc_final: 0.7705 (mt0) REVERT: D 104 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8925 (tptp) REVERT: D 184 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8409 (mm-30) REVERT: D 195 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8978 (mmmm) REVERT: D 212 GLU cc_start: 0.8554 (tt0) cc_final: 0.8173 (tt0) REVERT: D 227 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9203 (ttmm) outliers start: 5 outliers final: 0 residues processed: 515 average time/residue: 0.3065 time to fit residues: 236.6529 Evaluate side-chains 308 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS I 121 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19540 Z= 0.418 Angle : 0.696 11.511 26490 Z= 0.349 Chirality : 0.044 0.147 3110 Planarity : 0.005 0.048 3340 Dihedral : 5.002 23.180 2530 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.80 % Allowed : 11.98 % Favored : 86.22 % 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: -1.29 (0.18), residues: 2310 helix: 0.91 (0.19), residues: 740 sheet: -1.75 (0.17), residues: 865 loop : -1.28 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 186 HIS 0.003 0.001 HIS B 119 PHE 0.012 0.001 PHE E 70 TYR 0.022 0.002 TYR G 37 ARG 0.009 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 290 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8144 (ptm) cc_final: 0.7618 (ptm) REVERT: B 166 MET cc_start: 0.8390 (mtm) cc_final: 0.8112 (mtm) REVERT: B 172 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7550 (mt-10) REVERT: B 227 LYS cc_start: 0.9465 (mtpt) cc_final: 0.9217 (ttmm) REVERT: G 101 MET cc_start: 0.8499 (tpt) cc_final: 0.7371 (tpp) REVERT: G 173 GLN cc_start: 0.8786 (mt0) cc_final: 0.8420 (mt0) REVERT: H 103 TYR cc_start: 0.8375 (m-80) cc_final: 0.8175 (m-80) REVERT: H 184 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8236 (mm-30) REVERT: F 17 TYR cc_start: 0.6071 (p90) cc_final: 0.5589 (p90) REVERT: F 169 GLN cc_start: 0.8624 (tp-100) cc_final: 0.8327 (tp-100) REVERT: F 172 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7958 (mt-10) REVERT: F 227 LYS cc_start: 0.9469 (mtpt) cc_final: 0.9245 (tppp) REVERT: I 230 MET cc_start: 0.8828 (tmm) cc_final: 0.8530 (tmm) REVERT: J 172 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 88 ASP cc_start: 0.8499 (p0) cc_final: 0.8274 (p0) REVERT: C 173 GLN cc_start: 0.8676 (mt0) cc_final: 0.8227 (mt0) REVERT: C 230 MET cc_start: 0.8911 (tmm) cc_final: 0.8409 (tmm) REVERT: D 103 TYR cc_start: 0.8440 (m-80) cc_final: 0.8173 (m-80) REVERT: D 195 LYS cc_start: 0.9051 (mmtp) cc_final: 0.8808 (mmmm) REVERT: D 212 GLU cc_start: 0.8526 (tt0) cc_final: 0.8168 (tt0) outliers start: 40 outliers final: 27 residues processed: 306 average time/residue: 0.3064 time to fit residues: 141.8904 Evaluate side-chains 276 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 163 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 226 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 207 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 167 optimal weight: 0.0270 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS G 121 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19540 Z= 0.289 Angle : 0.603 11.752 26490 Z= 0.301 Chirality : 0.042 0.148 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.682 22.179 2530 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.25 % Allowed : 13.96 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.82 (0.18), residues: 2310 helix: 1.10 (0.19), residues: 740 sheet: -1.38 (0.17), residues: 855 loop : -0.94 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 186 HIS 0.007 0.001 HIS D 38 PHE 0.012 0.001 PHE D 228 TYR 0.019 0.002 TYR A 182 ARG 0.005 0.001 ARG I 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 270 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 227 LYS cc_start: 0.9469 (mtpt) cc_final: 0.9228 (ttmm) REVERT: H 172 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8075 (tt0) REVERT: F 17 TYR cc_start: 0.6114 (p90) cc_final: 0.5602 (p90) REVERT: F 103 TYR cc_start: 0.8348 (m-80) cc_final: 0.7818 (m-10) REVERT: F 184 GLU cc_start: 0.8815 (tp30) cc_final: 0.8522 (mm-30) REVERT: I 202 TYR cc_start: 0.8431 (m-80) cc_final: 0.8166 (m-80) REVERT: I 230 MET cc_start: 0.8823 (tmm) cc_final: 0.8486 (tmm) REVERT: J 97 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8679 (ttp) REVERT: J 172 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 88 ASP cc_start: 0.8548 (p0) cc_final: 0.8329 (p0) REVERT: C 173 GLN cc_start: 0.8649 (mt0) cc_final: 0.8200 (mt0) REVERT: C 230 MET cc_start: 0.9031 (tmm) cc_final: 0.8469 (tmm) REVERT: D 103 TYR cc_start: 0.8395 (m-80) cc_final: 0.8144 (m-80) REVERT: D 195 LYS cc_start: 0.9116 (mmtp) cc_final: 0.8853 (mmmm) REVERT: D 212 GLU cc_start: 0.8497 (tt0) cc_final: 0.8131 (tt0) outliers start: 50 outliers final: 34 residues processed: 292 average time/residue: 0.3038 time to fit residues: 134.7908 Evaluate side-chains 286 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 222 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS G 121 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS E 121 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19540 Z= 0.321 Angle : 0.598 9.654 26490 Z= 0.297 Chirality : 0.042 0.137 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.568 21.956 2530 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.02 % Allowed : 14.95 % Favored : 82.03 % 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: -0.58 (0.17), residues: 2310 helix: 1.23 (0.19), residues: 740 sheet: -1.10 (0.18), residues: 835 loop : -0.97 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 186 HIS 0.007 0.001 HIS H 38 PHE 0.010 0.001 PHE D 228 TYR 0.024 0.002 TYR H 103 ARG 0.004 0.000 ARG I 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 264 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 LYS cc_start: 0.8883 (mppt) cc_final: 0.8545 (mttp) REVERT: B 172 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7769 (mt-10) REVERT: B 227 LYS cc_start: 0.9468 (mtpt) cc_final: 0.9220 (ttmm) REVERT: G 100 ASN cc_start: 0.8426 (m-40) cc_final: 0.8092 (m110) REVERT: H 130 TYR cc_start: 0.9119 (m-10) cc_final: 0.8777 (m-80) REVERT: H 195 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8502 (mmmm) REVERT: H 221 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8710 (t-90) REVERT: E 101 MET cc_start: 0.8986 (tpp) cc_final: 0.8770 (tpp) REVERT: F 103 TYR cc_start: 0.8516 (m-80) cc_final: 0.8138 (m-10) REVERT: F 169 GLN cc_start: 0.8461 (tp-100) cc_final: 0.8188 (tp-100) REVERT: F 184 GLU cc_start: 0.8847 (tp30) cc_final: 0.8598 (mm-30) REVERT: I 202 TYR cc_start: 0.8483 (m-80) cc_final: 0.8223 (m-80) REVERT: I 230 MET cc_start: 0.8794 (tmm) cc_final: 0.8424 (tmm) REVERT: J 172 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7718 (mt-10) REVERT: J 212 GLU cc_start: 0.8533 (tt0) cc_final: 0.8308 (tt0) REVERT: J 221 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8709 (t-90) REVERT: C 88 ASP cc_start: 0.8647 (p0) cc_final: 0.8342 (p0) REVERT: C 100 ASN cc_start: 0.8365 (m-40) cc_final: 0.8105 (m110) REVERT: C 230 MET cc_start: 0.9109 (tmm) cc_final: 0.8353 (tmm) REVERT: D 103 TYR cc_start: 0.8503 (m-80) cc_final: 0.8170 (m-80) REVERT: D 195 LYS cc_start: 0.9206 (mmtp) cc_final: 0.8922 (mmmm) REVERT: D 212 GLU cc_start: 0.8510 (tt0) cc_final: 0.8126 (tt0) REVERT: D 227 LYS cc_start: 0.9401 (ttmm) cc_final: 0.8982 (ttmm) outliers start: 67 outliers final: 45 residues processed: 297 average time/residue: 0.3073 time to fit residues: 138.4938 Evaluate side-chains 299 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 252 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 221 HIS Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 30.0000 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 165 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 113 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN E 173 GLN F 72 GLN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN I 100 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 19540 Z= 0.245 Angle : 0.586 11.781 26490 Z= 0.285 Chirality : 0.042 0.142 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.385 19.989 2530 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.97 % Allowed : 17.16 % Favored : 79.86 % 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: -0.32 (0.18), residues: 2310 helix: 1.46 (0.19), residues: 740 sheet: -0.95 (0.17), residues: 845 loop : -0.81 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 186 HIS 0.007 0.001 HIS G 119 PHE 0.010 0.001 PHE F 228 TYR 0.015 0.001 TYR D 103 ARG 0.003 0.000 ARG I 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 276 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8545 (m-40) cc_final: 0.8295 (m110) REVERT: A 101 MET cc_start: 0.8761 (tpp) cc_final: 0.8431 (tpp) REVERT: A 116 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8595 (tptt) REVERT: B 116 LYS cc_start: 0.8898 (mppt) cc_final: 0.8566 (mttp) REVERT: B 227 LYS cc_start: 0.9449 (mtpt) cc_final: 0.9224 (ttmm) REVERT: G 100 ASN cc_start: 0.8495 (m-40) cc_final: 0.8181 (m110) REVERT: G 202 TYR cc_start: 0.8745 (m-80) cc_final: 0.8517 (m-80) REVERT: H 130 TYR cc_start: 0.9099 (m-10) cc_final: 0.8752 (m-80) REVERT: H 184 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8238 (mm-30) REVERT: F 103 TYR cc_start: 0.8679 (m-80) cc_final: 0.8105 (m-10) REVERT: F 173 GLN cc_start: 0.8741 (mt0) cc_final: 0.8355 (mt0) REVERT: F 184 GLU cc_start: 0.8822 (tp30) cc_final: 0.8588 (mm-30) REVERT: I 101 MET cc_start: 0.8708 (tpp) cc_final: 0.8372 (tpp) REVERT: I 202 TYR cc_start: 0.8483 (m-80) cc_final: 0.8232 (m-80) REVERT: J 221 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8457 (t-90) REVERT: J 223 GLU cc_start: 0.8639 (mp0) cc_final: 0.8361 (mp0) REVERT: C 42 LEU cc_start: 0.9010 (mm) cc_final: 0.8657 (pp) REVERT: C 88 ASP cc_start: 0.8678 (p0) cc_final: 0.8380 (p0) REVERT: C 100 ASN cc_start: 0.8413 (m-40) cc_final: 0.8101 (m110) REVERT: C 230 MET cc_start: 0.9058 (tmm) cc_final: 0.8513 (tmm) REVERT: D 103 TYR cc_start: 0.8297 (m-80) cc_final: 0.7722 (m-10) REVERT: D 195 LYS cc_start: 0.9217 (mmtp) cc_final: 0.8938 (mmmm) REVERT: D 212 GLU cc_start: 0.8481 (tt0) cc_final: 0.8083 (tt0) REVERT: D 221 HIS cc_start: 0.8962 (OUTLIER) cc_final: 0.8253 (t-90) REVERT: D 227 LYS cc_start: 0.9364 (ttmm) cc_final: 0.8924 (ttmm) outliers start: 66 outliers final: 43 residues processed: 316 average time/residue: 0.2691 time to fit residues: 130.1715 Evaluate side-chains 301 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 221 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 184 optimal weight: 50.0000 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 ASN E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19540 Z= 0.195 Angle : 0.572 11.371 26490 Z= 0.279 Chirality : 0.042 0.139 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.285 18.469 2530 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.52 % Allowed : 18.02 % Favored : 79.46 % 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: -0.11 (0.18), residues: 2310 helix: 1.51 (0.19), residues: 750 sheet: -0.73 (0.17), residues: 850 loop : -0.74 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 186 HIS 0.014 0.001 HIS I 119 PHE 0.010 0.001 PHE D 40 TYR 0.014 0.001 TYR G 130 ARG 0.003 0.000 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 285 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8583 (m-40) cc_final: 0.8325 (m110) REVERT: A 101 MET cc_start: 0.8756 (tpp) cc_final: 0.8523 (tpp) REVERT: A 116 LYS cc_start: 0.8745 (mmmt) cc_final: 0.8409 (tptt) REVERT: B 116 LYS cc_start: 0.8908 (mppt) cc_final: 0.8568 (mttp) REVERT: B 227 LYS cc_start: 0.9425 (mtpt) cc_final: 0.9200 (ttmm) REVERT: G 100 ASN cc_start: 0.8521 (m-40) cc_final: 0.8258 (m110) REVERT: G 202 TYR cc_start: 0.8686 (m-80) cc_final: 0.8275 (m-80) REVERT: H 130 TYR cc_start: 0.9089 (m-10) cc_final: 0.8725 (m-80) REVERT: H 184 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8220 (mm-30) REVERT: E 42 LEU cc_start: 0.9054 (mm) cc_final: 0.8723 (pp) REVERT: F 103 TYR cc_start: 0.8693 (m-80) cc_final: 0.8268 (m-10) REVERT: F 173 GLN cc_start: 0.8706 (mt0) cc_final: 0.8350 (mt0) REVERT: F 184 GLU cc_start: 0.8810 (tp30) cc_final: 0.8584 (mm-30) REVERT: I 202 TYR cc_start: 0.8462 (m-80) cc_final: 0.8202 (m-80) REVERT: J 184 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8216 (mm-30) REVERT: J 221 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8758 (t-90) REVERT: C 88 ASP cc_start: 0.8659 (p0) cc_final: 0.8372 (p0) REVERT: C 100 ASN cc_start: 0.8389 (m-40) cc_final: 0.8166 (m110) REVERT: C 230 MET cc_start: 0.9075 (tmm) cc_final: 0.8515 (tmm) REVERT: D 103 TYR cc_start: 0.8471 (m-80) cc_final: 0.7909 (m-10) REVERT: D 184 GLU cc_start: 0.8754 (tp30) cc_final: 0.8478 (mm-30) REVERT: D 195 LYS cc_start: 0.9168 (mmtp) cc_final: 0.8892 (mmmm) REVERT: D 212 GLU cc_start: 0.8460 (tt0) cc_final: 0.8066 (tt0) REVERT: D 227 LYS cc_start: 0.9321 (ttmm) cc_final: 0.8912 (ttmm) outliers start: 56 outliers final: 41 residues processed: 315 average time/residue: 0.3010 time to fit residues: 145.7371 Evaluate side-chains 300 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 258 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 221 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 138 optimal weight: 50.0000 chunk 135 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 HIS I 173 GLN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19540 Z= 0.215 Angle : 0.592 12.263 26490 Z= 0.286 Chirality : 0.042 0.140 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.258 19.501 2530 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.75 % Allowed : 18.29 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2310 helix: 1.53 (0.19), residues: 750 sheet: -0.50 (0.18), residues: 820 loop : -0.70 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP J 186 HIS 0.016 0.001 HIS I 119 PHE 0.010 0.001 PHE J 40 TYR 0.014 0.001 TYR J 202 ARG 0.002 0.000 ARG I 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 273 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8586 (m-40) cc_final: 0.8350 (m110) REVERT: A 230 MET cc_start: 0.8984 (tpp) cc_final: 0.8666 (tpp) REVERT: A 248 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: B 17 TYR cc_start: 0.6622 (p90) cc_final: 0.6118 (p90) REVERT: B 116 LYS cc_start: 0.8910 (mppt) cc_final: 0.8566 (mttp) REVERT: B 227 LYS cc_start: 0.9429 (mtpt) cc_final: 0.9193 (ttmm) REVERT: G 100 ASN cc_start: 0.8580 (m-40) cc_final: 0.8290 (m-40) REVERT: G 202 TYR cc_start: 0.8661 (m-80) cc_final: 0.8250 (m-80) REVERT: H 184 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8232 (mm-30) REVERT: E 42 LEU cc_start: 0.9059 (mm) cc_final: 0.8731 (pp) REVERT: F 103 TYR cc_start: 0.8702 (m-80) cc_final: 0.8116 (m-10) REVERT: I 42 LEU cc_start: 0.8991 (mm) cc_final: 0.8668 (pp) REVERT: I 202 TYR cc_start: 0.8474 (m-80) cc_final: 0.8209 (m-80) REVERT: C 42 LEU cc_start: 0.8996 (mm) cc_final: 0.8603 (pp) REVERT: C 88 ASP cc_start: 0.8672 (p0) cc_final: 0.8376 (p0) REVERT: D 103 TYR cc_start: 0.8354 (m-80) cc_final: 0.7814 (m-80) REVERT: D 184 GLU cc_start: 0.8737 (tp30) cc_final: 0.8482 (mm-30) REVERT: D 195 LYS cc_start: 0.9165 (mmtp) cc_final: 0.8863 (mmmm) REVERT: D 212 GLU cc_start: 0.8466 (tt0) cc_final: 0.8064 (tt0) REVERT: D 227 LYS cc_start: 0.9319 (ttmm) cc_final: 0.8920 (ttmm) outliers start: 61 outliers final: 48 residues processed: 305 average time/residue: 0.3094 time to fit residues: 143.9965 Evaluate side-chains 314 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 265 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 221 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 30.0000 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 121 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 173 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19540 Z= 0.387 Angle : 0.667 14.820 26490 Z= 0.327 Chirality : 0.042 0.175 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.509 19.908 2530 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.88 % Allowed : 18.74 % Favored : 78.38 % 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: -0.07 (0.18), residues: 2310 helix: 1.40 (0.19), residues: 750 sheet: -0.46 (0.18), residues: 830 loop : -0.89 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I 186 HIS 0.018 0.002 HIS I 119 PHE 0.012 0.001 PHE H 228 TYR 0.015 0.002 TYR B 103 ARG 0.003 0.000 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 256 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASN cc_start: 0.8609 (m-40) cc_final: 0.8262 (m110) REVERT: A 238 ASN cc_start: 0.9577 (OUTLIER) cc_final: 0.9352 (m-40) REVERT: A 248 TYR cc_start: 0.8892 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: B 17 TYR cc_start: 0.6640 (p90) cc_final: 0.6148 (p90) REVERT: B 116 LYS cc_start: 0.8892 (mppt) cc_final: 0.8520 (mttp) REVERT: B 227 LYS cc_start: 0.9447 (mtpt) cc_final: 0.9152 (ttmm) REVERT: G 100 ASN cc_start: 0.8638 (m-40) cc_final: 0.8402 (m-40) REVERT: G 248 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: H 130 TYR cc_start: 0.9163 (m-10) cc_final: 0.8832 (m-10) REVERT: E 101 MET cc_start: 0.8704 (tpp) cc_final: 0.8296 (tpp) REVERT: F 169 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8250 (tp-100) REVERT: C 42 LEU cc_start: 0.9048 (mm) cc_final: 0.8667 (pp) REVERT: C 88 ASP cc_start: 0.8780 (p0) cc_final: 0.8439 (p0) REVERT: C 202 TYR cc_start: 0.8904 (m-80) cc_final: 0.8696 (m-80) REVERT: C 248 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: D 195 LYS cc_start: 0.9238 (mmtp) cc_final: 0.8929 (mmmm) REVERT: D 212 GLU cc_start: 0.8511 (tt0) cc_final: 0.8087 (tt0) REVERT: D 227 LYS cc_start: 0.9301 (ttmm) cc_final: 0.8923 (ttmm) outliers start: 64 outliers final: 46 residues processed: 294 average time/residue: 0.3064 time to fit residues: 137.2046 Evaluate side-chains 284 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 234 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 221 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19540 Z= 0.356 Angle : 0.680 16.700 26490 Z= 0.328 Chirality : 0.042 0.173 3110 Planarity : 0.004 0.036 3340 Dihedral : 4.526 19.769 2530 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.84 % Allowed : 19.10 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.18), residues: 2310 helix: 1.42 (0.19), residues: 750 sheet: -0.44 (0.18), residues: 830 loop : -0.88 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 186 HIS 0.021 0.002 HIS A 119 PHE 0.010 0.001 PHE F 228 TYR 0.013 0.002 TYR J 202 ARG 0.003 0.000 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 243 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: A 100 ASN cc_start: 0.8538 (m-40) cc_final: 0.8330 (m110) REVERT: A 248 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 17 TYR cc_start: 0.6655 (p90) cc_final: 0.6177 (p90) REVERT: B 116 LYS cc_start: 0.8883 (mppt) cc_final: 0.8499 (mttp) REVERT: B 227 LYS cc_start: 0.9441 (mtpt) cc_final: 0.9146 (ttmm) REVERT: G 100 ASN cc_start: 0.8636 (m-40) cc_final: 0.8422 (m-40) REVERT: G 202 TYR cc_start: 0.8647 (m-80) cc_final: 0.8366 (m-80) REVERT: G 248 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: H 97 MET cc_start: 0.8613 (mmm) cc_final: 0.8174 (tpt) REVERT: H 130 TYR cc_start: 0.9164 (m-10) cc_final: 0.8817 (m-80) REVERT: E 42 LEU cc_start: 0.9124 (mm) cc_final: 0.8787 (pp) REVERT: F 194 ASP cc_start: 0.8304 (t0) cc_final: 0.8046 (m-30) REVERT: I 42 LEU cc_start: 0.9011 (mm) cc_final: 0.8683 (pp) REVERT: I 248 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8285 (m-80) REVERT: C 42 LEU cc_start: 0.9057 (mm) cc_final: 0.8677 (pp) REVERT: C 88 ASP cc_start: 0.8768 (p0) cc_final: 0.8482 (p0) REVERT: C 248 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: D 184 GLU cc_start: 0.8787 (tp30) cc_final: 0.8516 (mm-30) REVERT: D 195 LYS cc_start: 0.9232 (mmtp) cc_final: 0.8920 (mmmm) REVERT: D 212 GLU cc_start: 0.8503 (tt0) cc_final: 0.8079 (tt0) REVERT: D 227 LYS cc_start: 0.9318 (ttmm) cc_final: 0.8941 (ttmm) outliers start: 63 outliers final: 49 residues processed: 280 average time/residue: 0.2997 time to fit residues: 128.3766 Evaluate side-chains 298 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 244 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 221 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 182 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 72 GLN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19540 Z= 0.308 Angle : 0.665 14.296 26490 Z= 0.322 Chirality : 0.042 0.194 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.544 22.187 2530 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.70 % Allowed : 19.37 % Favored : 77.93 % 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: -0.08 (0.18), residues: 2310 helix: 1.46 (0.19), residues: 750 sheet: -0.56 (0.17), residues: 870 loop : -0.87 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 186 HIS 0.018 0.002 HIS A 119 PHE 0.010 0.001 PHE D 40 TYR 0.019 0.001 TYR H 103 ARG 0.006 0.000 ARG G 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 251 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: A 100 ASN cc_start: 0.8544 (m-40) cc_final: 0.8114 (m-40) REVERT: A 116 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8496 (tptt) REVERT: A 248 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: B 17 TYR cc_start: 0.6672 (p90) cc_final: 0.6205 (p90) REVERT: B 116 LYS cc_start: 0.8900 (mppt) cc_final: 0.8513 (mttp) REVERT: B 227 LYS cc_start: 0.9429 (mtpt) cc_final: 0.9164 (ttmm) REVERT: G 100 ASN cc_start: 0.8627 (m-40) cc_final: 0.8351 (m-40) REVERT: G 116 LYS cc_start: 0.8459 (tptt) cc_final: 0.7968 (mptt) REVERT: G 202 TYR cc_start: 0.8517 (m-80) cc_final: 0.8234 (m-80) REVERT: G 248 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: H 130 TYR cc_start: 0.9164 (m-10) cc_final: 0.8815 (m-80) REVERT: H 195 LYS cc_start: 0.9305 (mmtm) cc_final: 0.9093 (mmmm) REVERT: H 230 MET cc_start: 0.8027 (tpt) cc_final: 0.7697 (tpp) REVERT: E 42 LEU cc_start: 0.9114 (mm) cc_final: 0.8793 (pp) REVERT: F 173 GLN cc_start: 0.8781 (mt0) cc_final: 0.8409 (mt0) REVERT: F 195 LYS cc_start: 0.9423 (mmtm) cc_final: 0.9216 (mmmm) REVERT: I 42 LEU cc_start: 0.9013 (mm) cc_final: 0.8691 (pp) REVERT: I 116 LYS cc_start: 0.8445 (tptt) cc_final: 0.8206 (mptt) REVERT: I 202 TYR cc_start: 0.8583 (m-80) cc_final: 0.8375 (m-80) REVERT: I 248 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: C 42 LEU cc_start: 0.9068 (mm) cc_final: 0.8685 (pp) REVERT: C 88 ASP cc_start: 0.8756 (p0) cc_final: 0.8474 (p0) REVERT: C 230 MET cc_start: 0.9007 (tpp) cc_final: 0.8607 (tpp) REVERT: C 238 ASN cc_start: 0.9599 (OUTLIER) cc_final: 0.9368 (m-40) REVERT: C 248 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: D 195 LYS cc_start: 0.9231 (mmtp) cc_final: 0.8911 (mmmm) REVERT: D 212 GLU cc_start: 0.8502 (tt0) cc_final: 0.8072 (tt0) REVERT: D 227 LYS cc_start: 0.9315 (ttmm) cc_final: 0.8942 (ttmm) outliers start: 60 outliers final: 49 residues processed: 281 average time/residue: 0.3161 time to fit residues: 134.7125 Evaluate side-chains 297 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 242 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 163 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 221 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 76 optimal weight: 0.0060 chunk 187 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.079243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.051978 restraints weight = 72468.814| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.69 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19540 Z= 0.258 Angle : 0.678 13.873 26490 Z= 0.327 Chirality : 0.042 0.191 3110 Planarity : 0.004 0.040 3340 Dihedral : 4.571 27.678 2530 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.52 % Allowed : 19.86 % Favored : 77.61 % 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: -0.02 (0.18), residues: 2310 helix: 1.50 (0.19), residues: 750 sheet: -0.55 (0.17), residues: 860 loop : -0.77 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 186 HIS 0.017 0.001 HIS I 119 PHE 0.010 0.001 PHE H 228 TYR 0.032 0.002 TYR H 103 ARG 0.004 0.000 ARG G 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3686.69 seconds wall clock time: 69 minutes 43.47 seconds (4183.47 seconds total)