Starting phenix.real_space_refine on Wed Apr 17 01:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr4_40719/04_2024/8sr4_40719.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr4_40719/04_2024/8sr4_40719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr4_40719/04_2024/8sr4_40719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr4_40719/04_2024/8sr4_40719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr4_40719/04_2024/8sr4_40719.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sr4_40719/04_2024/8sr4_40719.pdb" } resolution = 3.12 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= 0.003 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 20898 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 9 5.60 5 S 93 5.16 5 C 13818 2.51 5 N 3381 2.21 5 O 3606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 135": "OD1" <-> "OD2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 135": "OD1" <-> "OD2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 276": "OE1" <-> "OE2" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 343": "OE1" <-> "OE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 53": "OD1" <-> "OD2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "G PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "G PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K ASP 156": "OD1" <-> "OD2" Residue "K PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 228": "OE1" <-> "OE2" Residue "K PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20907 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.81, per 1000 atoms: 0.52 Number of scatterers: 20907 At special positions: 0 Unit cell: (107.407, 107.936, 117.989, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 9 28.99 S 93 16.00 O 3606 8.00 N 3381 7.00 C 13818 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: 8.35 Conformation dependent library (CDL) restraints added in 3.7 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 24 sheets defined 51.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.962A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 45 removed outlier: 3.696A pdb=" N ALA B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.961A pdb=" N TRP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 69 through 84 removed outlier: 4.196A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 140 through 155 removed outlier: 4.377A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.883A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.602A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 114 removed outlier: 5.244A pdb=" N ASN C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE C 92 " --> pdb=" O TYR C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 179 through 199 Processing helix chain 'C' and resid 208 through 224 Proline residue: C 217 - end of helix removed outlier: 4.203A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.727A pdb=" N TRP C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.529A pdb=" N ALA C 255 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 208 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 376 through 382 removed outlier: 3.962A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 208 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 376 through 382 removed outlier: 3.961A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 45 removed outlier: 3.695A pdb=" N ALA F 14 " --> pdb=" O SER F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.961A pdb=" N TRP F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 69 through 84 removed outlier: 4.197A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 140 through 155 removed outlier: 4.377A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.883A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 45 removed outlier: 3.696A pdb=" N ALA J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.961A pdb=" N TRP J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 Proline residue: J 65 - end of helix Processing helix chain 'J' and resid 69 through 84 removed outlier: 4.196A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 124 through 137 Processing helix chain 'J' and resid 140 through 155 removed outlier: 4.377A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.884A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.601A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 114 removed outlier: 5.244A pdb=" N ASN G 91 " --> pdb=" O THR G 87 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE G 92 " --> pdb=" O TYR G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 150 Processing helix chain 'G' and resid 150 through 161 Processing helix chain 'G' and resid 170 through 176 Processing helix chain 'G' and resid 179 through 199 Processing helix chain 'G' and resid 208 through 224 Proline residue: G 217 - end of helix removed outlier: 4.203A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.726A pdb=" N TRP G 229 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY G 230 " --> pdb=" O LEU G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 removed outlier: 3.529A pdb=" N ALA G 255 " --> pdb=" O GLY G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 49 through 73 removed outlier: 3.602A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 5.244A pdb=" N ASN K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE K 92 " --> pdb=" O TYR K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 150 Processing helix chain 'K' and resid 150 through 161 Processing helix chain 'K' and resid 170 through 176 Processing helix chain 'K' and resid 179 through 199 Processing helix chain 'K' and resid 208 through 224 Proline residue: K 217 - end of helix removed outlier: 4.203A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix Processing helix chain 'K' and resid 225 through 233 removed outlier: 3.727A pdb=" N TRP K 229 " --> pdb=" O GLY K 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 256 removed outlier: 3.529A pdb=" N ALA K 255 " --> pdb=" O GLY K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.253A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 348 removed outlier: 5.669A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 removed outlier: 5.070A pdb=" N LEU A 314 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE A 394 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA8, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.253A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB4, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.669A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 341 through 342 removed outlier: 5.070A pdb=" N LEU E 314 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE E 394 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.254A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AB8, first strand: chain 'I' and resid 87 through 90 Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.669A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 341 through 342 removed outlier: 5.070A pdb=" N LEU I 314 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE I 394 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC4, first strand: chain 'F' and resid 243 through 244 Processing sheet with id=AC5, first strand: chain 'J' and resid 170 through 173 Processing sheet with id=AC6, first strand: chain 'J' and resid 243 through 244 1098 hydrogen bonds defined for protein. 3204 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: 6.98 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3170 1.31 - 1.43: 6679 1.43 - 1.56: 11580 1.56 - 1.68: 0 1.68 - 1.81: 180 Bond restraints: 21609 Sorted by residual: bond pdb=" CE1 HIS A 48 " pdb=" NE2 HIS A 48 " ideal model delta sigma weight residual 1.321 1.378 -0.057 1.00e-02 1.00e+04 3.21e+01 bond pdb=" CE1 HIS E 48 " pdb=" NE2 HIS E 48 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.19e+01 bond pdb=" CE1 HIS I 48 " pdb=" NE2 HIS I 48 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.16e+01 bond pdb=" CG HIS E 48 " pdb=" ND1 HIS E 48 " ideal model delta sigma weight residual 1.378 1.431 -0.053 1.10e-02 8.26e+03 2.33e+01 bond pdb=" CG HIS I 48 " pdb=" ND1 HIS I 48 " ideal model delta sigma weight residual 1.378 1.431 -0.053 1.10e-02 8.26e+03 2.31e+01 ... (remaining 21604 not shown) Histogram of bond angle deviations from ideal: 98.95 - 106.01: 583 106.01 - 113.08: 11367 113.08 - 120.14: 8077 120.14 - 127.21: 9076 127.21 - 134.27: 402 Bond angle restraints: 29505 Sorted by residual: angle pdb=" N PHE C 248 " pdb=" CA PHE C 248 " pdb=" C PHE C 248 " ideal model delta sigma weight residual 113.97 107.23 6.74 1.28e+00 6.10e-01 2.77e+01 angle pdb=" N PHE G 248 " pdb=" CA PHE G 248 " pdb=" C PHE G 248 " ideal model delta sigma weight residual 113.97 107.24 6.73 1.28e+00 6.10e-01 2.76e+01 angle pdb=" N PHE K 248 " pdb=" CA PHE K 248 " pdb=" C PHE K 248 " ideal model delta sigma weight residual 113.97 107.26 6.71 1.28e+00 6.10e-01 2.75e+01 angle pdb=" C LEU B 124 " pdb=" N VAL B 125 " pdb=" CA VAL B 125 " ideal model delta sigma weight residual 120.24 123.41 -3.17 6.30e-01 2.52e+00 2.53e+01 angle pdb=" C LEU J 124 " pdb=" N VAL J 125 " pdb=" CA VAL J 125 " ideal model delta sigma weight residual 120.24 123.40 -3.16 6.30e-01 2.52e+00 2.52e+01 ... (remaining 29500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 11005 17.46 - 34.93: 1004 34.93 - 52.39: 144 52.39 - 69.85: 48 69.85 - 87.32: 18 Dihedral angle restraints: 12219 sinusoidal: 4767 harmonic: 7452 Sorted by residual: dihedral pdb=" CA ILE E 211 " pdb=" C ILE E 211 " pdb=" N PHE E 212 " pdb=" CA PHE E 212 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE A 211 " pdb=" C ILE A 211 " pdb=" N PHE A 212 " pdb=" CA PHE A 212 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ILE I 211 " pdb=" C ILE I 211 " pdb=" N PHE I 212 " pdb=" CA PHE I 212 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 12216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2424 0.056 - 0.112: 624 0.112 - 0.168: 84 0.168 - 0.224: 33 0.224 - 0.280: 6 Chirality restraints: 3171 Sorted by residual: chirality pdb=" CA HIS C 231 " pdb=" N HIS C 231 " pdb=" C HIS C 231 " pdb=" CB HIS C 231 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA HIS G 231 " pdb=" N HIS G 231 " pdb=" C HIS G 231 " pdb=" CB HIS G 231 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA HIS K 231 " pdb=" N HIS K 231 " pdb=" C HIS K 231 " pdb=" CB HIS K 231 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3168 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 72 " -0.030 2.00e-02 2.50e+03 2.75e-02 1.13e+01 pdb=" CG HIS I 72 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS I 72 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS I 72 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS I 72 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 HIS I 72 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 72 " -0.030 2.00e-02 2.50e+03 2.73e-02 1.12e+01 pdb=" CG HIS A 72 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS A 72 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS A 72 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 72 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 HIS A 72 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 72 " -0.030 2.00e-02 2.50e+03 2.72e-02 1.11e+01 pdb=" CG HIS E 72 " 0.023 2.00e-02 2.50e+03 pdb=" ND1 HIS E 72 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS E 72 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS E 72 " -0.040 2.00e-02 2.50e+03 pdb=" NE2 HIS E 72 " 0.000 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 30 2.11 - 2.81: 5939 2.81 - 3.51: 31466 3.51 - 4.20: 54059 4.20 - 4.90: 94743 Nonbonded interactions: 186237 Sorted by model distance: nonbonded pdb=" O GLU C 237 " pdb=" NH1 ARG F 206 " model vdw 1.413 2.520 nonbonded pdb=" NH1 ARG J 206 " pdb=" O GLU G 237 " model vdw 1.530 2.520 nonbonded pdb=" NH1 ARG B 206 " pdb=" O GLU K 237 " model vdw 1.648 2.520 nonbonded pdb=" NE2 GLN E 404 " pdb="CU CU E 502 " model vdw 1.650 2.320 nonbonded pdb=" NE2 GLN A 404 " pdb="CU CU A 502 " model vdw 1.651 2.320 ... (remaining 186232 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } 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: 16.740 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: 0.000 Extract box with map and model: 28.020 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 55.110 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.005 0.069 21609 Z= 0.335 Angle : 0.782 7.533 29505 Z= 0.489 Chirality : 0.053 0.280 3171 Planarity : 0.005 0.041 3660 Dihedral : 13.995 87.316 7461 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.23 % Favored : 92.07 % Rotamer: Outliers : 2.19 % Allowed : 2.42 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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 (0.17), residues: 2559 helix: 0.86 (0.16), residues: 1152 sheet: 0.04 (0.28), residues: 378 loop : -0.81 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 229 HIS 0.025 0.003 HIS I 72 PHE 0.015 0.001 PHE G 169 TYR 0.015 0.002 TYR J 37 ARG 0.004 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 347 time to evaluate : 2.257 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: A 117 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6765 (mp0) REVERT: A 141 MET cc_start: 0.8139 (ptp) cc_final: 0.7643 (ptp) REVERT: A 375 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7618 (mtp85) REVERT: B 11 HIS cc_start: 0.8367 (m-70) cc_final: 0.8102 (m90) REVERT: B 23 TRP cc_start: 0.6877 (m-10) cc_final: 0.6519 (m100) REVERT: B 44 THR cc_start: 0.7336 (p) cc_final: 0.7102 (p) REVERT: B 199 MET cc_start: 0.6734 (mtp) cc_final: 0.5758 (mtt) REVERT: C 113 LYS cc_start: 0.8269 (mptt) cc_final: 0.8057 (mptt) REVERT: C 126 GLU cc_start: 0.7703 (tm-30) cc_final: 0.6985 (tm-30) REVERT: E 117 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6795 (mp0) REVERT: E 375 ARG cc_start: 0.7852 (mtt-85) cc_final: 0.7603 (mtp85) REVERT: I 117 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6742 (mp0) REVERT: I 375 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7583 (mtp85) REVERT: F 11 HIS cc_start: 0.8371 (m-70) cc_final: 0.8091 (m90) REVERT: F 23 TRP cc_start: 0.6829 (m-10) cc_final: 0.6474 (m100) REVERT: F 199 MET cc_start: 0.6772 (mtp) cc_final: 0.5912 (mtm) REVERT: J 11 HIS cc_start: 0.8374 (m-70) cc_final: 0.8126 (m90) REVERT: J 23 TRP cc_start: 0.6847 (m-10) cc_final: 0.6497 (m100) REVERT: J 44 THR cc_start: 0.7396 (p) cc_final: 0.7172 (p) REVERT: J 199 MET cc_start: 0.6796 (mtp) cc_final: 0.5810 (mtt) REVERT: G 113 LYS cc_start: 0.8218 (mptt) cc_final: 0.7987 (mptt) REVERT: G 126 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7282 (tp30) REVERT: K 113 LYS cc_start: 0.8239 (mptt) cc_final: 0.7980 (mptt) REVERT: K 126 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7109 (tp30) outliers start: 48 outliers final: 24 residues processed: 380 average time/residue: 0.3723 time to fit residues: 209.2287 Evaluate side-chains 256 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 177 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 177 PHE Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 177 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 chunk 107 optimal weight: 0.0030 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 148 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 ASN E 108 GLN I 401 GLN F 160 ASN F 245 GLN J 160 ASN J 187 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21609 Z= 0.262 Angle : 0.602 7.826 29505 Z= 0.314 Chirality : 0.045 0.147 3171 Planarity : 0.005 0.047 3660 Dihedral : 6.715 58.385 2874 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.41 % Rotamer: Outliers : 1.87 % Allowed : 9.69 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.34 (0.17), residues: 2559 helix: 0.94 (0.15), residues: 1167 sheet: 0.37 (0.29), residues: 360 loop : -0.55 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 137 HIS 0.006 0.001 HIS E 72 PHE 0.018 0.002 PHE A 324 TYR 0.031 0.002 TYR K 184 ARG 0.006 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 242 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6990 (mp0) REVERT: A 141 MET cc_start: 0.8016 (ptp) cc_final: 0.7677 (ptp) REVERT: A 375 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7481 (mtp85) REVERT: B 11 HIS cc_start: 0.8270 (m-70) cc_final: 0.8002 (m-70) REVERT: B 23 TRP cc_start: 0.6940 (m-10) cc_final: 0.6626 (m100) REVERT: B 199 MET cc_start: 0.6927 (mtp) cc_final: 0.5887 (mtt) REVERT: C 154 GLU cc_start: 0.6376 (mm-30) cc_final: 0.6126 (mm-30) REVERT: E 117 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7002 (mp0) REVERT: E 375 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7507 (mtp85) REVERT: I 108 GLN cc_start: 0.7434 (tt0) cc_final: 0.7156 (tt0) REVERT: I 117 GLU cc_start: 0.7726 (mm-30) cc_final: 0.6957 (mp0) REVERT: I 141 MET cc_start: 0.8215 (ptp) cc_final: 0.7839 (ptp) REVERT: I 375 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7483 (mtp85) REVERT: F 11 HIS cc_start: 0.8225 (m-70) cc_final: 0.7887 (m-70) REVERT: F 23 TRP cc_start: 0.6893 (m-10) cc_final: 0.6523 (m100) REVERT: F 199 MET cc_start: 0.6945 (mtp) cc_final: 0.6042 (mtm) REVERT: F 230 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7042 (ptt) REVERT: J 11 HIS cc_start: 0.8231 (m-70) cc_final: 0.7940 (m-70) REVERT: J 23 TRP cc_start: 0.6927 (m-10) cc_final: 0.6614 (m100) REVERT: J 199 MET cc_start: 0.6942 (mtp) cc_final: 0.5895 (mtt) REVERT: J 230 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7002 (ptt) REVERT: J 241 GLU cc_start: 0.8295 (mp0) cc_final: 0.8093 (mp0) REVERT: G 113 LYS cc_start: 0.8199 (mptt) cc_final: 0.7965 (mptt) REVERT: K 113 LYS cc_start: 0.8175 (mptt) cc_final: 0.7933 (mptt) REVERT: K 226 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6521 (tp) outliers start: 41 outliers final: 23 residues processed: 265 average time/residue: 0.3728 time to fit residues: 148.7266 Evaluate side-chains 251 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 chunk 230 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN B 160 ASN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 401 GLN F 160 ASN J 160 ASN J 245 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21609 Z= 0.217 Angle : 0.545 5.878 29505 Z= 0.284 Chirality : 0.043 0.137 3171 Planarity : 0.004 0.047 3660 Dihedral : 5.975 59.830 2860 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 2.56 % Allowed : 10.65 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.66 (0.17), residues: 2559 helix: 1.07 (0.15), residues: 1203 sheet: 0.57 (0.28), residues: 390 loop : -0.32 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 137 HIS 0.003 0.001 HIS B 232 PHE 0.017 0.001 PHE K 177 TYR 0.028 0.001 TYR K 184 ARG 0.008 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 226 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7006 (mp0) REVERT: A 163 MET cc_start: 0.8360 (ttt) cc_final: 0.7958 (ttt) REVERT: A 375 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7537 (mtp85) REVERT: B 11 HIS cc_start: 0.8259 (m-70) cc_final: 0.7993 (m-70) REVERT: B 23 TRP cc_start: 0.7001 (m-10) cc_final: 0.6707 (m100) REVERT: B 160 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8037 (m110) REVERT: B 199 MET cc_start: 0.6956 (mtp) cc_final: 0.6217 (mtp) REVERT: C 241 VAL cc_start: 0.6537 (OUTLIER) cc_final: 0.6175 (t) REVERT: E 117 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7009 (mp0) REVERT: E 163 MET cc_start: 0.8386 (ttt) cc_final: 0.7992 (ttt) REVERT: E 375 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7498 (mtp85) REVERT: I 108 GLN cc_start: 0.7389 (tt0) cc_final: 0.7146 (tt0) REVERT: I 117 GLU cc_start: 0.7743 (mm-30) cc_final: 0.6968 (mp0) REVERT: I 163 MET cc_start: 0.8355 (ttt) cc_final: 0.7959 (ttt) REVERT: I 375 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7491 (mtp85) REVERT: F 11 HIS cc_start: 0.8217 (m-70) cc_final: 0.7903 (m-70) REVERT: F 23 TRP cc_start: 0.6940 (m-10) cc_final: 0.6620 (m100) REVERT: F 160 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.8047 (m110) REVERT: F 199 MET cc_start: 0.6971 (mtp) cc_final: 0.6097 (mtm) REVERT: F 230 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7023 (ptt) REVERT: J 11 HIS cc_start: 0.8257 (m-70) cc_final: 0.7992 (m-70) REVERT: J 23 TRP cc_start: 0.6982 (m-10) cc_final: 0.6692 (m100) REVERT: J 160 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8037 (m-40) REVERT: J 199 MET cc_start: 0.6965 (mtp) cc_final: 0.5946 (mtt) REVERT: J 230 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6992 (ptt) REVERT: G 113 LYS cc_start: 0.8167 (mptt) cc_final: 0.7939 (mptt) REVERT: K 90 MET cc_start: 0.5940 (mmt) cc_final: 0.5404 (mmt) REVERT: K 113 LYS cc_start: 0.8141 (mptt) cc_final: 0.7908 (mptt) outliers start: 56 outliers final: 30 residues processed: 256 average time/residue: 0.3351 time to fit residues: 132.4399 Evaluate side-chains 252 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 216 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 160 ASN Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 HIS Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 187 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN F 187 ASN J 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21609 Z= 0.395 Angle : 0.610 5.621 29505 Z= 0.321 Chirality : 0.047 0.174 3171 Planarity : 0.005 0.049 3660 Dihedral : 5.810 59.809 2848 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.31 % Favored : 94.45 % Rotamer: Outliers : 2.74 % Allowed : 12.89 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.48 (0.17), residues: 2559 helix: 1.05 (0.15), residues: 1182 sheet: 0.27 (0.29), residues: 372 loop : -0.44 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 137 HIS 0.004 0.001 HIS E 72 PHE 0.016 0.002 PHE K 251 TYR 0.026 0.002 TYR K 184 ARG 0.005 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 2.396 Fit side-chains REVERT: A 117 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7008 (mp0) REVERT: A 375 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7601 (mtp85) REVERT: B 9 ARG cc_start: 0.8476 (mmt-90) cc_final: 0.8051 (mpt180) REVERT: B 11 HIS cc_start: 0.8294 (m-70) cc_final: 0.7836 (m-70) REVERT: B 23 TRP cc_start: 0.7043 (m-10) cc_final: 0.6762 (m100) REVERT: B 178 MET cc_start: 0.8691 (mtp) cc_final: 0.8210 (mtp) REVERT: B 199 MET cc_start: 0.7143 (mtp) cc_final: 0.6426 (mtp) REVERT: B 205 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6173 (mm) REVERT: C 219 MET cc_start: 0.7314 (tpp) cc_final: 0.7082 (tpp) REVERT: C 241 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6763 (t) REVERT: E 117 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7023 (mp0) REVERT: E 163 MET cc_start: 0.8455 (ttt) cc_final: 0.8139 (ttt) REVERT: I 117 GLU cc_start: 0.7755 (mm-30) cc_final: 0.6981 (mp0) REVERT: I 141 MET cc_start: 0.8520 (ptp) cc_final: 0.8024 (ptm) REVERT: I 251 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7581 (ttt) REVERT: F 9 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8062 (mpt180) REVERT: F 11 HIS cc_start: 0.8280 (m-70) cc_final: 0.7961 (m-70) REVERT: F 23 TRP cc_start: 0.7067 (m-10) cc_final: 0.6774 (m100) REVERT: F 199 MET cc_start: 0.7050 (mtp) cc_final: 0.6190 (mtm) REVERT: F 230 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6986 (ptt) REVERT: J 9 ARG cc_start: 0.8486 (mmt-90) cc_final: 0.8053 (mpt180) REVERT: J 11 HIS cc_start: 0.8280 (m-70) cc_final: 0.7830 (m-70) REVERT: J 23 TRP cc_start: 0.7055 (m-10) cc_final: 0.6769 (m100) REVERT: J 178 MET cc_start: 0.8719 (mtp) cc_final: 0.8232 (mtp) REVERT: J 199 MET cc_start: 0.7037 (mtp) cc_final: 0.6048 (mtt) REVERT: J 205 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6046 (mm) REVERT: J 210 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7258 (tptt) REVERT: J 230 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6977 (ptt) REVERT: K 90 MET cc_start: 0.5992 (mmt) cc_final: 0.5432 (mmt) REVERT: K 113 LYS cc_start: 0.8115 (mptt) cc_final: 0.7867 (mptt) outliers start: 60 outliers final: 35 residues processed: 266 average time/residue: 0.3513 time to fit residues: 142.9921 Evaluate side-chains 263 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 245 HIS Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.0040 chunk 139 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 210 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 221 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 245 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN J 160 ASN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21609 Z= 0.171 Angle : 0.519 5.679 29505 Z= 0.272 Chirality : 0.043 0.144 3171 Planarity : 0.004 0.048 3660 Dihedral : 5.505 59.780 2845 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 2.29 % Allowed : 14.36 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.66 (0.17), residues: 2559 helix: 1.27 (0.15), residues: 1185 sheet: 0.25 (0.28), residues: 387 loop : -0.40 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 202 HIS 0.003 0.001 HIS F 232 PHE 0.018 0.001 PHE K 251 TYR 0.024 0.001 TYR K 184 ARG 0.008 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7040 (mp0) REVERT: A 375 ARG cc_start: 0.8054 (mtt-85) cc_final: 0.7586 (mtp85) REVERT: B 9 ARG cc_start: 0.8459 (mmt-90) cc_final: 0.8025 (mpt180) REVERT: B 11 HIS cc_start: 0.8285 (m-70) cc_final: 0.8039 (m90) REVERT: B 23 TRP cc_start: 0.7004 (m-10) cc_final: 0.6766 (m100) REVERT: B 160 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8110 (m110) REVERT: B 178 MET cc_start: 0.8651 (mtp) cc_final: 0.8228 (mtp) REVERT: B 199 MET cc_start: 0.6890 (mtp) cc_final: 0.6162 (mtp) REVERT: B 205 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6107 (mm) REVERT: B 210 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7197 (tptt) REVERT: B 237 TRP cc_start: 0.7535 (t60) cc_final: 0.7289 (t60) REVERT: C 241 VAL cc_start: 0.7101 (m) cc_final: 0.6864 (t) REVERT: E 117 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7030 (mp0) REVERT: E 163 MET cc_start: 0.8358 (ttt) cc_final: 0.7979 (ttt) REVERT: I 108 GLN cc_start: 0.7252 (tt0) cc_final: 0.6978 (tt0) REVERT: I 117 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6983 (mp0) REVERT: I 163 MET cc_start: 0.8330 (ttt) cc_final: 0.7953 (ttt) REVERT: I 176 GLN cc_start: 0.8079 (mt0) cc_final: 0.7685 (mm-40) REVERT: F 9 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.8030 (mpt180) REVERT: F 11 HIS cc_start: 0.8228 (m-70) cc_final: 0.7936 (m90) REVERT: F 23 TRP cc_start: 0.7044 (m-10) cc_final: 0.6783 (m100) REVERT: F 160 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8075 (m110) REVERT: F 199 MET cc_start: 0.6893 (mtp) cc_final: 0.5827 (mtm) REVERT: F 210 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7219 (tptt) REVERT: F 230 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6961 (ptt) REVERT: J 9 ARG cc_start: 0.8501 (mmt-90) cc_final: 0.8022 (mpt180) REVERT: J 11 HIS cc_start: 0.8232 (m-70) cc_final: 0.7995 (m90) REVERT: J 23 TRP cc_start: 0.7020 (m-10) cc_final: 0.6782 (m100) REVERT: J 178 MET cc_start: 0.8672 (mtp) cc_final: 0.8254 (mtp) REVERT: J 199 MET cc_start: 0.6869 (mtp) cc_final: 0.5863 (mtt) REVERT: J 210 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7196 (tptt) REVERT: J 230 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6965 (ptt) REVERT: K 90 MET cc_start: 0.6008 (mmt) cc_final: 0.5401 (mmt) REVERT: K 113 LYS cc_start: 0.8099 (mptt) cc_final: 0.7869 (mptt) REVERT: K 154 GLU cc_start: 0.5849 (mm-30) cc_final: 0.5353 (mm-30) outliers start: 50 outliers final: 32 residues processed: 260 average time/residue: 0.3560 time to fit residues: 141.5150 Evaluate side-chains 259 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 0.3980 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21609 Z= 0.263 Angle : 0.545 6.025 29505 Z= 0.285 Chirality : 0.044 0.152 3171 Planarity : 0.004 0.047 3660 Dihedral : 5.344 58.818 2843 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.96 % Favored : 94.92 % Rotamer: Outliers : 2.15 % Allowed : 15.36 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.69 (0.17), residues: 2559 helix: 1.25 (0.15), residues: 1197 sheet: 0.28 (0.28), residues: 387 loop : -0.37 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 54 HIS 0.003 0.001 HIS E 72 PHE 0.017 0.001 PHE K 251 TYR 0.023 0.001 TYR K 184 ARG 0.005 0.000 ARG G 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 2.259 Fit side-chains REVERT: A 117 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7034 (mp0) REVERT: A 375 ARG cc_start: 0.8065 (mtt-85) cc_final: 0.7569 (mtp85) REVERT: B 9 ARG cc_start: 0.8496 (mmt-90) cc_final: 0.7893 (mpt180) REVERT: B 11 HIS cc_start: 0.8289 (m-70) cc_final: 0.8019 (m90) REVERT: B 23 TRP cc_start: 0.7037 (m-10) cc_final: 0.6802 (m100) REVERT: B 160 ASN cc_start: 0.8364 (m-40) cc_final: 0.8035 (m110) REVERT: B 178 MET cc_start: 0.8628 (mtp) cc_final: 0.8225 (mtp) REVERT: B 199 MET cc_start: 0.6988 (mtp) cc_final: 0.6257 (mtp) REVERT: B 205 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6139 (mm) REVERT: B 210 LYS cc_start: 0.8174 (mtmm) cc_final: 0.7261 (tptt) REVERT: B 237 TRP cc_start: 0.7505 (t60) cc_final: 0.7238 (t60) REVERT: E 117 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7032 (mp0) REVERT: I 108 GLN cc_start: 0.7267 (tt0) cc_final: 0.6971 (tt0) REVERT: I 117 GLU cc_start: 0.7756 (mm-30) cc_final: 0.6985 (mp0) REVERT: I 176 GLN cc_start: 0.8096 (mt0) cc_final: 0.7704 (mm-40) REVERT: I 375 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7635 (mtp85) REVERT: F 9 ARG cc_start: 0.8524 (mmt-90) cc_final: 0.8021 (mpt180) REVERT: F 11 HIS cc_start: 0.8241 (m-70) cc_final: 0.7952 (m90) REVERT: F 23 TRP cc_start: 0.7054 (m-10) cc_final: 0.6827 (m100) REVERT: F 178 MET cc_start: 0.8616 (mtp) cc_final: 0.8023 (mtm) REVERT: F 199 MET cc_start: 0.6999 (mtp) cc_final: 0.6153 (mtm) REVERT: F 210 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7275 (tptt) REVERT: F 230 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6963 (ptt) REVERT: J 9 ARG cc_start: 0.8538 (mmt-90) cc_final: 0.8013 (mpt180) REVERT: J 11 HIS cc_start: 0.8249 (m-70) cc_final: 0.8005 (m90) REVERT: J 23 TRP cc_start: 0.7051 (m-10) cc_final: 0.6826 (m100) REVERT: J 178 MET cc_start: 0.8663 (mtp) cc_final: 0.8247 (mtp) REVERT: J 199 MET cc_start: 0.6980 (mtp) cc_final: 0.5998 (mtt) REVERT: J 205 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5968 (mm) REVERT: J 210 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7212 (tptt) REVERT: J 230 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6987 (ptt) REVERT: G 177 PHE cc_start: 0.8267 (m-80) cc_final: 0.8034 (t80) REVERT: K 90 MET cc_start: 0.6019 (mmt) cc_final: 0.5375 (mmt) REVERT: K 113 LYS cc_start: 0.8088 (mptt) cc_final: 0.7848 (mptt) outliers start: 47 outliers final: 27 residues processed: 255 average time/residue: 0.3900 time to fit residues: 155.0208 Evaluate side-chains 248 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21609 Z= 0.253 Angle : 0.545 9.499 29505 Z= 0.283 Chirality : 0.044 0.164 3171 Planarity : 0.004 0.047 3660 Dihedral : 5.052 52.274 2839 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 1.92 % Allowed : 15.64 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.70 (0.17), residues: 2559 helix: 1.30 (0.15), residues: 1188 sheet: 0.31 (0.27), residues: 387 loop : -0.40 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 54 HIS 0.003 0.001 HIS J 232 PHE 0.017 0.001 PHE K 251 TYR 0.024 0.001 TYR C 184 ARG 0.005 0.000 ARG G 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 2.333 Fit side-chains REVERT: A 117 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7031 (mp0) REVERT: A 176 GLN cc_start: 0.8141 (mt0) cc_final: 0.7755 (mm-40) REVERT: A 375 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7552 (mtp85) REVERT: B 9 ARG cc_start: 0.8530 (mmt-90) cc_final: 0.7909 (mpt180) REVERT: B 11 HIS cc_start: 0.8322 (m-70) cc_final: 0.8057 (m90) REVERT: B 199 MET cc_start: 0.6940 (mtp) cc_final: 0.6211 (mtp) REVERT: B 205 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6147 (mm) REVERT: B 210 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7193 (tptt) REVERT: B 237 TRP cc_start: 0.7503 (t60) cc_final: 0.7234 (t60) REVERT: C 154 GLU cc_start: 0.5703 (mm-30) cc_final: 0.5435 (mm-30) REVERT: C 219 MET cc_start: 0.6652 (tpp) cc_final: 0.6254 (ttm) REVERT: E 117 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7038 (mp0) REVERT: E 375 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7710 (mtp85) REVERT: I 117 GLU cc_start: 0.7761 (mm-30) cc_final: 0.6989 (mp0) REVERT: I 176 GLN cc_start: 0.8127 (mt0) cc_final: 0.7748 (mm-40) REVERT: I 375 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7712 (mtp85) REVERT: F 9 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.7969 (mpt180) REVERT: F 11 HIS cc_start: 0.8248 (m-70) cc_final: 0.7958 (m90) REVERT: F 23 TRP cc_start: 0.7053 (m-10) cc_final: 0.6826 (m100) REVERT: F 178 MET cc_start: 0.8616 (mtp) cc_final: 0.8077 (mtm) REVERT: F 199 MET cc_start: 0.6919 (mtp) cc_final: 0.6103 (mtp) REVERT: F 210 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7321 (tptt) REVERT: F 230 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6950 (ptt) REVERT: J 9 ARG cc_start: 0.8573 (mmt-90) cc_final: 0.7969 (mpt180) REVERT: J 11 HIS cc_start: 0.8251 (m-70) cc_final: 0.8016 (m90) REVERT: J 23 TRP cc_start: 0.7073 (m-10) cc_final: 0.6870 (m100) REVERT: J 199 MET cc_start: 0.7000 (mtp) cc_final: 0.6016 (mtt) REVERT: J 205 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5951 (mm) REVERT: J 210 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7280 (tptt) REVERT: J 230 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6967 (ptt) REVERT: G 154 GLU cc_start: 0.5615 (mm-30) cc_final: 0.5388 (mm-30) REVERT: K 90 MET cc_start: 0.6053 (mmt) cc_final: 0.5413 (mmt) REVERT: K 113 LYS cc_start: 0.8082 (mptt) cc_final: 0.7850 (mptt) outliers start: 42 outliers final: 30 residues processed: 249 average time/residue: 0.3555 time to fit residues: 134.6265 Evaluate side-chains 247 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 211 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21609 Z= 0.189 Angle : 0.523 8.277 29505 Z= 0.271 Chirality : 0.043 0.172 3171 Planarity : 0.004 0.046 3660 Dihedral : 4.850 48.087 2836 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.08 % Favored : 94.80 % Rotamer: Outliers : 2.01 % Allowed : 15.64 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.80 (0.17), residues: 2559 helix: 1.36 (0.15), residues: 1191 sheet: 0.36 (0.28), residues: 387 loop : -0.34 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 54 HIS 0.003 0.001 HIS F 232 PHE 0.018 0.001 PHE K 251 TYR 0.023 0.001 TYR C 184 ARG 0.006 0.000 ARG G 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7038 (mp0) REVERT: A 176 GLN cc_start: 0.8127 (mt0) cc_final: 0.7757 (mm-40) REVERT: A 375 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7544 (mtp85) REVERT: B 9 ARG cc_start: 0.8528 (mmt-90) cc_final: 0.7891 (mpt180) REVERT: B 11 HIS cc_start: 0.8311 (m-70) cc_final: 0.7996 (m170) REVERT: B 199 MET cc_start: 0.6814 (mtp) cc_final: 0.5964 (mtp) REVERT: B 205 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6066 (mm) REVERT: B 210 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7175 (tptt) REVERT: B 237 TRP cc_start: 0.7522 (t60) cc_final: 0.7271 (t60) REVERT: C 219 MET cc_start: 0.6577 (tpp) cc_final: 0.6268 (ttm) REVERT: E 117 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7058 (mp0) REVERT: E 375 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7724 (mtp85) REVERT: I 108 GLN cc_start: 0.7223 (tt0) cc_final: 0.6938 (tt0) REVERT: I 117 GLU cc_start: 0.7761 (mm-30) cc_final: 0.6985 (mp0) REVERT: I 176 GLN cc_start: 0.8096 (mt0) cc_final: 0.7735 (mm-40) REVERT: I 375 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7711 (mtp85) REVERT: F 9 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.7946 (mpt180) REVERT: F 11 HIS cc_start: 0.8243 (m-70) cc_final: 0.7973 (m90) REVERT: F 199 MET cc_start: 0.6882 (mtp) cc_final: 0.6139 (mtp) REVERT: F 210 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7300 (tptt) REVERT: F 230 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6965 (ptt) REVERT: J 9 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.7962 (mpt180) REVERT: J 199 MET cc_start: 0.6890 (mtp) cc_final: 0.5880 (mtt) REVERT: J 210 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7209 (tptt) REVERT: J 230 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6951 (ptt) REVERT: K 113 LYS cc_start: 0.8053 (mptt) cc_final: 0.7828 (mptt) outliers start: 44 outliers final: 32 residues processed: 249 average time/residue: 0.3642 time to fit residues: 137.1906 Evaluate side-chains 248 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 155 GLN Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 229 optimal weight: 0.8980 chunk 137 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21609 Z= 0.339 Angle : 0.584 7.942 29505 Z= 0.304 Chirality : 0.045 0.142 3171 Planarity : 0.004 0.046 3660 Dihedral : 4.974 48.695 2835 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 2.10 % Allowed : 15.82 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.71 (0.17), residues: 2559 helix: 1.23 (0.15), residues: 1203 sheet: 0.34 (0.27), residues: 387 loop : -0.34 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 54 HIS 0.004 0.001 HIS E 72 PHE 0.018 0.002 PHE K 251 TYR 0.024 0.002 TYR K 184 ARG 0.006 0.000 ARG G 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 223 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7000 (mp0) REVERT: A 176 GLN cc_start: 0.8155 (mt0) cc_final: 0.7779 (mm-40) REVERT: A 375 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7817 (mtt-85) REVERT: B 9 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.7898 (mpt180) REVERT: B 11 HIS cc_start: 0.8319 (m-70) cc_final: 0.8047 (m-70) REVERT: B 199 MET cc_start: 0.7018 (mtp) cc_final: 0.6307 (mtp) REVERT: B 205 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6168 (mm) REVERT: B 210 LYS cc_start: 0.8319 (mtmm) cc_final: 0.7226 (tptt) REVERT: B 237 TRP cc_start: 0.7498 (t60) cc_final: 0.7218 (t60) REVERT: C 219 MET cc_start: 0.6637 (tpp) cc_final: 0.6344 (ttm) REVERT: E 117 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7038 (mp0) REVERT: E 176 GLN cc_start: 0.8168 (mt0) cc_final: 0.7785 (mm-40) REVERT: E 375 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7694 (mtp85) REVERT: I 117 GLU cc_start: 0.7742 (mm-30) cc_final: 0.6976 (mp0) REVERT: I 176 GLN cc_start: 0.8126 (mt0) cc_final: 0.7759 (mm-40) REVERT: I 375 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7676 (mtp85) REVERT: F 9 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.7906 (mpt180) REVERT: F 11 HIS cc_start: 0.8293 (m-70) cc_final: 0.7972 (m-70) REVERT: F 199 MET cc_start: 0.7020 (mtp) cc_final: 0.6281 (mtp) REVERT: F 210 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7264 (tptt) REVERT: F 230 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6966 (ptt) REVERT: J 9 ARG cc_start: 0.8581 (mmt-90) cc_final: 0.7883 (mpt180) REVERT: J 100 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6978 (mt-10) REVERT: J 199 MET cc_start: 0.7038 (mtp) cc_final: 0.6341 (mtp) REVERT: J 210 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7304 (tptt) REVERT: J 230 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6966 (ptt) REVERT: K 113 LYS cc_start: 0.8051 (mptt) cc_final: 0.7816 (mptt) outliers start: 46 outliers final: 29 residues processed: 254 average time/residue: 0.3556 time to fit residues: 136.2379 Evaluate side-chains 248 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 147 optimal weight: 0.0770 chunk 114 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 254 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21609 Z= 0.194 Angle : 0.536 8.091 29505 Z= 0.277 Chirality : 0.043 0.135 3171 Planarity : 0.004 0.046 3660 Dihedral : 4.830 46.878 2835 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.16 % Favored : 94.72 % Rotamer: Outliers : 1.87 % Allowed : 16.00 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.83 (0.17), residues: 2559 helix: 1.37 (0.15), residues: 1191 sheet: 0.40 (0.27), residues: 387 loop : -0.31 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 54 HIS 0.003 0.001 HIS B 232 PHE 0.017 0.001 PHE K 251 TYR 0.023 0.001 TYR C 184 ARG 0.006 0.000 ARG C 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7040 (mp0) REVERT: A 176 GLN cc_start: 0.8114 (mt0) cc_final: 0.7752 (mm-40) REVERT: A 375 ARG cc_start: 0.8066 (mtt-85) cc_final: 0.7825 (mtt-85) REVERT: B 9 ARG cc_start: 0.8545 (mmt-90) cc_final: 0.7899 (mpt180) REVERT: B 11 HIS cc_start: 0.8320 (m-70) cc_final: 0.8103 (m-70) REVERT: B 111 TRP cc_start: 0.7854 (t60) cc_final: 0.7629 (t60) REVERT: B 199 MET cc_start: 0.6799 (mtp) cc_final: 0.6250 (mtp) REVERT: B 205 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6065 (mm) REVERT: B 210 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7224 (tptt) REVERT: B 237 TRP cc_start: 0.7511 (t60) cc_final: 0.7263 (t60) REVERT: E 117 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7056 (mp0) REVERT: E 176 GLN cc_start: 0.8146 (mt0) cc_final: 0.7783 (mm-40) REVERT: E 375 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7721 (mtp85) REVERT: I 108 GLN cc_start: 0.7180 (tt0) cc_final: 0.6880 (tt0) REVERT: I 117 GLU cc_start: 0.7766 (mm-30) cc_final: 0.6977 (mp0) REVERT: I 176 GLN cc_start: 0.8086 (mt0) cc_final: 0.7733 (mm-40) REVERT: I 375 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7742 (mtp85) REVERT: F 9 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.7913 (mpt180) REVERT: F 11 HIS cc_start: 0.8268 (m-70) cc_final: 0.7919 (m170) REVERT: F 111 TRP cc_start: 0.7935 (t60) cc_final: 0.7629 (t60) REVERT: F 199 MET cc_start: 0.6849 (mtp) cc_final: 0.6083 (mtp) REVERT: F 210 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7258 (tptt) REVERT: F 230 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6921 (ptt) REVERT: J 9 ARG cc_start: 0.8536 (mmt-90) cc_final: 0.7844 (mpt180) REVERT: J 172 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8125 (tm-30) REVERT: J 178 MET cc_start: 0.8636 (mtp) cc_final: 0.8114 (mtp) REVERT: J 199 MET cc_start: 0.6863 (mtp) cc_final: 0.6140 (mtp) REVERT: J 210 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7289 (tptt) REVERT: J 230 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6942 (ptt) REVERT: K 90 MET cc_start: 0.6164 (mmt) cc_final: 0.5485 (mmt) REVERT: K 113 LYS cc_start: 0.8023 (mptt) cc_final: 0.7790 (mptt) outliers start: 41 outliers final: 31 residues processed: 248 average time/residue: 0.3989 time to fit residues: 152.1071 Evaluate side-chains 251 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 382 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 210 LYS Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 245 HIS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 245 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 186 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 208 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.091119 restraints weight = 30163.957| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.71 r_work: 0.2947 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 21609 Z= 0.209 Angle : 0.720 59.199 29505 Z= 0.397 Chirality : 0.043 0.221 3171 Planarity : 0.004 0.046 3660 Dihedral : 4.829 46.884 2835 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 1.74 % Allowed : 16.37 % Favored : 81.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.84 (0.17), residues: 2559 helix: 1.38 (0.15), residues: 1191 sheet: 0.41 (0.27), residues: 387 loop : -0.31 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 206 HIS 0.003 0.001 HIS B 232 PHE 0.016 0.001 PHE K 251 TYR 0.022 0.001 TYR C 184 ARG 0.004 0.000 ARG C 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5012.76 seconds wall clock time: 92 minutes 59.09 seconds (5579.09 seconds total)