Starting phenix.real_space_refine on Fri Feb 6 15:07:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rbq_53902/02_2026/9rbq_53902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rbq_53902/02_2026/9rbq_53902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rbq_53902/02_2026/9rbq_53902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rbq_53902/02_2026/9rbq_53902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rbq_53902/02_2026/9rbq_53902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rbq_53902/02_2026/9rbq_53902.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 207 5.16 5 C 16095 2.51 5 N 4400 2.21 5 O 4882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25585 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 312 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "D" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 415 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "E" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 415 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "F" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 415 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "G" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "H" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "I" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "J" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3282 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "K" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3282 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "L" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3282 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "M" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "N" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "O" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "g" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.61, per 1000 atoms: 0.22 Number of scatterers: 25585 At special positions: 0 Unit cell: (169.56, 155.52, 191.16, 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) Ca 1 19.99 S 207 16.00 O 4882 8.00 N 4400 7.00 C 16095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=49, symmetry=0 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 18 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 27 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 18 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 18 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 27 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.03 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 68 " - pdb=" SG CYS I 78 " distance=2.03 Simple disulfide: pdb=" SG CYS I 259 " - pdb=" SG CYS I 271 " distance=2.03 Simple disulfide: pdb=" SG CYS I 301 " - pdb=" SG CYS I 376 " distance=2.03 Simple disulfide: pdb=" SG CYS I 306 " - pdb=" SG CYS I 380 " distance=2.03 Simple disulfide: pdb=" SG CYS I 328 " - pdb=" SG CYS I 370 " distance=2.04 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 28 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.04 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 28 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 225 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 125 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 28 " distance=2.03 Simple disulfide: pdb=" SG CYS L 91 " - pdb=" SG CYS L 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 201 " - pdb=" SG CYS L 225 " distance=2.04 Simple disulfide: pdb=" SG CYS L 203 " - pdb=" SG CYS L 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " NAG B 1 " - " MAN B 4 " " NAG R 1 " - " MAN R 4 " " NAG V 1 " - " MAN V 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " NAG Z 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " NAG c 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " NAG g 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " NAG j 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " NAG n 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " NAG q 3 " BETA1-6 " NAG c 3 " - " NAG c 4 " " NAG j 3 " - " NAG j 4 " " NAG q 3 " - " NAG q 4 " NAG-ASN " NAG B 1 " - " ASN G 141 " " NAG R 1 " - " ASN H 141 " " NAG V 1 " - " ASN I 141 " " NAG Z 1 " - " ASN J 200 " " NAG c 1 " - " ASN J 262 " " NAG g 1 " - " ASN K 200 " " NAG j 1 " - " ASN K 262 " " NAG n 1 " - " ASN L 200 " " NAG q 1 " - " ASN L 262 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 852.6 milliseconds 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6058 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 63 sheets defined 17.3% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 47 through 56 Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.535A pdb=" N LYS G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 259 Processing helix chain 'G' and resid 283 through 287 Processing helix chain 'G' and resid 404 through 438 Processing helix chain 'H' and resid 238 through 247 Processing helix chain 'H' and resid 250 through 254 Processing helix chain 'H' and resid 255 through 259 removed outlier: 4.119A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 438 Processing helix chain 'I' and resid 238 through 246 Processing helix chain 'I' and resid 250 through 255 removed outlier: 3.525A pdb=" N LYS I 254 " --> pdb=" O ALA I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 259 Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 404 through 438 Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.774A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 350 through 362 Processing helix chain 'J' and resid 365 through 402 Proline residue: J 398 - end of helix Processing helix chain 'J' and resid 408 through 414 removed outlier: 3.653A pdb=" N LEU J 414 " --> pdb=" O THR J 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 7 through 12 removed outlier: 3.630A pdb=" N ALA K 11 " --> pdb=" O VAL K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 350 through 362 Processing helix chain 'K' and resid 365 through 402 Proline residue: K 398 - end of helix Processing helix chain 'K' and resid 408 through 415 Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 8 through 12 removed outlier: 3.854A pdb=" N ALA L 11 " --> pdb=" O VAL L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 177 through 179 No H-bonds generated for 'chain 'L' and resid 177 through 179' Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 350 through 360 Processing helix chain 'L' and resid 362 through 402 Proline residue: L 398 - end of helix removed outlier: 3.539A pdb=" N THR L 402 " --> pdb=" O PRO L 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 415 Processing helix chain 'M' and resid 107 through 120 removed outlier: 3.742A pdb=" N ASP M 118 " --> pdb=" O LYS M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 157 Processing helix chain 'M' and resid 174 through 181 removed outlier: 5.709A pdb=" N SER M 179 " --> pdb=" O HIS M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 119 removed outlier: 4.549A pdb=" N ASP N 118 " --> pdb=" O LYS N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 157 Processing helix chain 'N' and resid 174 through 178 removed outlier: 3.642A pdb=" N ARG N 178 " --> pdb=" O VAL N 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 119 removed outlier: 4.265A pdb=" N MET O 111 " --> pdb=" O LYS O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 157 removed outlier: 3.518A pdb=" N LYS O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 178 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 Processing sheet with id=AA2, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AA3, first strand: chain 'E' and resid 8 through 11 Processing sheet with id=AA4, first strand: chain 'F' and resid 8 through 9 removed outlier: 3.554A pdb=" N PHE F 16 " --> pdb=" O CYS F 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AA6, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.435A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU G 35 " --> pdb=" O LYS G 132 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 140 through 147 current: chain 'G' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 185 current: chain 'G' and resid 267 through 269 Processing sheet with id=AA7, first strand: chain 'G' and resid 24 through 25 removed outlier: 4.680A pdb=" N THR G 288 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 100 through 110 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AB1, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AB2, first strand: chain 'G' and resid 297 through 306 removed outlier: 5.394A pdb=" N ASP G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS G 321 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AB4, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AB5, first strand: chain 'H' and resid 2 through 8 Processing sheet with id=AB6, first strand: chain 'H' and resid 15 through 19 removed outlier: 5.431A pdb=" N MET H 31 " --> pdb=" O MET H 136 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET H 136 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL H 33 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG H 134 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU H 35 " --> pdb=" O LYS H 132 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 41 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR H 126 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASN H 43 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ALA H 124 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU H 45 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR H 122 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE H 47 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER H 120 " --> pdb=" O ILE H 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 147 current: chain 'H' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 183 through 185 current: chain 'H' and resid 267 through 269 Processing sheet with id=AB7, first strand: chain 'H' and resid 24 through 25 removed outlier: 4.599A pdb=" N THR H 288 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 101 through 110 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AC1, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AC2, first strand: chain 'H' and resid 296 through 306 removed outlier: 5.645A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 343 through 346 Processing sheet with id=AC4, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AC5, first strand: chain 'I' and resid 2 through 8 Processing sheet with id=AC6, first strand: chain 'I' and resid 15 through 19 removed outlier: 5.390A pdb=" N MET I 31 " --> pdb=" O MET I 136 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET I 136 " --> pdb=" O MET I 31 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL I 33 " --> pdb=" O ARG I 134 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG I 134 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR I 41 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR I 126 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASN I 43 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA I 124 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU I 45 " --> pdb=" O TYR I 122 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR I 122 " --> pdb=" O GLU I 45 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE I 47 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER I 120 " --> pdb=" O ILE I 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 140 through 147 current: chain 'I' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 183 through 185 current: chain 'I' and resid 267 through 269 Processing sheet with id=AC7, first strand: chain 'I' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 51 through 54 current: chain 'I' and resid 101 through 110 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AC9, first strand: chain 'I' and resid 203 through 205 Processing sheet with id=AD1, first strand: chain 'I' and resid 220 through 221 Processing sheet with id=AD2, first strand: chain 'I' and resid 296 through 306 removed outlier: 5.364A pdb=" N ASP I 298 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS I 321 " --> pdb=" O ASP I 298 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL I 315 " --> pdb=" O ALA I 304 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 343 through 346 Processing sheet with id=AD4, first strand: chain 'I' and resid 387 through 388 Processing sheet with id=AD5, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AD6, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.541A pdb=" N GLN J 49 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL J 37 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS J 47 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N SER J 51 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA J 70 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LYS J 66 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 84 through 86 removed outlier: 4.164A pdb=" N GLU J 109 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 149 through 156 Processing sheet with id=AD9, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AE1, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AE2, first strand: chain 'J' and resid 181 through 184 removed outlier: 3.778A pdb=" N MET J 215 " --> pdb=" O ILE J 190 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 274 through 278 Processing sheet with id=AE4, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AE5, first strand: chain 'K' and resid 34 through 38 removed outlier: 8.476A pdb=" N ILE K 34 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER K 51 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA K 36 " --> pdb=" O GLN K 49 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N SER K 51 " --> pdb=" O ALA K 70 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA K 70 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS K 66 " --> pdb=" O GLY K 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.117A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 149 through 156 Processing sheet with id=AE8, first strand: chain 'K' and resid 166 through 167 Processing sheet with id=AE9, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AF1, first strand: chain 'K' and resid 175 through 176 Processing sheet with id=AF2, first strand: chain 'K' and resid 181 through 183 Processing sheet with id=AF3, first strand: chain 'K' and resid 274 through 278 Processing sheet with id=AF4, first strand: chain 'L' and resid 17 through 19 Processing sheet with id=AF5, first strand: chain 'L' and resid 34 through 38 removed outlier: 8.599A pdb=" N ILE L 34 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER L 51 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA L 36 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N SER L 51 " --> pdb=" O ALA L 70 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA L 70 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS L 66 " --> pdb=" O GLY L 55 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 84 through 86 removed outlier: 4.279A pdb=" N GLU L 109 " --> pdb=" O TYR L 129 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 149 through 156 Processing sheet with id=AF8, first strand: chain 'L' and resid 236 through 237 Processing sheet with id=AF9, first strand: chain 'L' and resid 181 through 184 Processing sheet with id=AG1, first strand: chain 'L' and resid 210 through 211 Processing sheet with id=AG2, first strand: chain 'L' and resid 274 through 278 Processing sheet with id=AG3, first strand: chain 'M' and resid 128 through 131 removed outlier: 5.336A pdb=" N VAL M 129 " --> pdb=" O HIS M 125 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS M 125 " --> pdb=" O VAL M 129 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY M 131 " --> pdb=" O VAL M 123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 135 through 136 Processing sheet with id=AG5, first strand: chain 'M' and resid 265 through 266 removed outlier: 6.035A pdb=" N VAL M 234 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL M 249 " --> pdb=" O VAL M 234 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE M 207 " --> pdb=" O LEU M 246 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ALA M 199 " --> pdb=" O PRO M 210 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE M 223 " --> pdb=" O VAL M 231 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 149 through 150 removed outlier: 6.494A pdb=" N PHE N 121 " --> pdb=" O TYR N 132 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR N 132 " --> pdb=" O PHE N 121 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL N 123 " --> pdb=" O THR N 130 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N TYR N 132 " --> pdb=" O PRO N 143 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 191 through 195 removed outlier: 3.538A pdb=" N GLY N 191 " --> pdb=" O TYR N 202 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ALA N 199 " --> pdb=" O PRO N 210 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 207 through 210 current: chain 'N' and resid 230 through 240 removed outlier: 8.321A pdb=" N VAL N 231 " --> pdb=" O TRP N 251 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TRP N 251 " --> pdb=" O VAL N 231 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER N 247 " --> pdb=" O LEU N 235 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY N 237 " --> pdb=" O ALA N 245 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA N 245 " --> pdb=" O GLY N 237 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN N 239 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG N 243 " --> pdb=" O ASN N 239 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 149 through 150 removed outlier: 4.296A pdb=" N VAL O 123 " --> pdb=" O GLY O 131 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY O 131 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR O 132 " --> pdb=" O PRO O 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 183 through 184 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 183 through 184 current: chain 'O' and resid 198 through 202 removed outlier: 8.504A pdb=" N ALA O 199 " --> pdb=" O PRO O 210 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 207 through 210 current: chain 'O' and resid 229 through 240 removed outlier: 7.444A pdb=" N ALA O 232 " --> pdb=" O TRP O 251 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2298 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: 4.61 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8299 1.35 - 1.47: 6513 1.47 - 1.60: 11149 1.60 - 1.72: 0 1.72 - 1.84: 279 Bond restraints: 26240 Sorted by residual: bond pdb=" C1 NAG Z 1 " pdb=" O5 NAG Z 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 NAG n 3 " pdb=" O5 NAG n 3 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C1 NAG g 3 " pdb=" O5 NAG g 3 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.77e+00 ... (remaining 26235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 35010 1.83 - 3.66: 622 3.66 - 5.49: 65 5.49 - 7.32: 26 7.32 - 9.15: 2 Bond angle restraints: 35725 Sorted by residual: angle pdb=" C ASP K 289 " pdb=" N HIS K 290 " pdb=" CA HIS K 290 " ideal model delta sigma weight residual 122.56 128.21 -5.65 1.58e+00 4.01e-01 1.28e+01 angle pdb=" N GLY K 23 " pdb=" CA GLY K 23 " pdb=" C GLY K 23 " ideal model delta sigma weight residual 112.65 108.43 4.22 1.30e+00 5.92e-01 1.06e+01 angle pdb=" N GLU N 116 " pdb=" CA GLU N 116 " pdb=" CB GLU N 116 " ideal model delta sigma weight residual 110.42 115.31 -4.89 1.62e+00 3.81e-01 9.12e+00 angle pdb=" CA CYS L 225 " pdb=" CB CYS L 225 " pdb=" SG CYS L 225 " ideal model delta sigma weight residual 114.40 121.33 -6.93 2.30e+00 1.89e-01 9.08e+00 angle pdb=" CA CYS J 225 " pdb=" CB CYS J 225 " pdb=" SG CYS J 225 " ideal model delta sigma weight residual 114.40 121.21 -6.81 2.30e+00 1.89e-01 8.77e+00 ... (remaining 35720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.91: 15356 24.91 - 49.83: 650 49.83 - 74.74: 113 74.74 - 99.65: 56 99.65 - 124.57: 42 Dihedral angle restraints: 16217 sinusoidal: 6764 harmonic: 9453 Sorted by residual: dihedral pdb=" CB CYS A 206 " pdb=" SG CYS A 206 " pdb=" SG CYS A 221 " pdb=" CB CYS A 221 " ideal model delta sinusoidal sigma weight residual 93.00 24.16 68.84 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS G 68 " pdb=" SG CYS G 68 " pdb=" SG CYS G 78 " pdb=" CB CYS G 78 " ideal model delta sinusoidal sigma weight residual -86.00 -146.80 60.80 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" CB CYS I 68 " pdb=" SG CYS I 68 " pdb=" SG CYS I 78 " pdb=" CB CYS I 78 " ideal model delta sinusoidal sigma weight residual -86.00 -146.01 60.01 1 1.00e+01 1.00e-02 4.80e+01 ... (remaining 16214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3337 0.056 - 0.111: 613 0.111 - 0.167: 100 0.167 - 0.223: 6 0.223 - 0.278: 5 Chirality restraints: 4061 Sorted by residual: chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4058 not shown) Planarity restraints: 4589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 188 " -0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO N 189 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO N 189 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO N 189 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS N 112 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C CYS N 112 " 0.035 2.00e-02 2.50e+03 pdb=" O CYS N 112 " -0.013 2.00e-02 2.50e+03 pdb=" N MET N 113 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE M 209 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO M 210 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO M 210 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO M 210 " -0.028 5.00e-02 4.00e+02 ... (remaining 4586 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 380 2.66 - 3.22: 23101 3.22 - 3.78: 40879 3.78 - 4.34: 56840 4.34 - 4.90: 92343 Nonbonded interactions: 213543 Sorted by model distance: nonbonded pdb=" O ASP K 231 " pdb=" OD1 ASP K 231 " model vdw 2.094 3.040 nonbonded pdb=" NE2 GLN N 201 " pdb=" OG1 THR N 208 " model vdw 2.132 3.120 nonbonded pdb=" OG SER G 57 " pdb=" O VAL J 242 " model vdw 2.144 3.040 nonbonded pdb=" OH TYR E 49 " pdb=" OE1 GLU K 166 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR F 49 " pdb=" OE1 GLU L 166 " model vdw 2.170 3.040 ... (remaining 213538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'Z' selection = chain 'g' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.110 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26322 Z= 0.160 Angle : 0.609 9.150 35922 Z= 0.302 Chirality : 0.045 0.278 4061 Planarity : 0.004 0.088 4580 Dihedral : 16.343 124.567 10012 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3241 helix: 1.79 (0.25), residues: 428 sheet: -0.05 (0.16), residues: 956 loop : -0.39 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 206 TYR 0.015 0.001 TYR I 59 PHE 0.030 0.001 PHE L 50 TRP 0.016 0.001 TRP O 195 HIS 0.009 0.001 HIS K 290 Details of bonding type rmsd covalent geometry : bond 0.00334 (26240) covalent geometry : angle 0.59107 (35725) SS BOND : bond 0.00354 ( 49) SS BOND : angle 1.07012 ( 98) hydrogen bonds : bond 0.12454 ( 884) hydrogen bonds : angle 6.09032 ( 2298) link_ALPHA1-6 : bond 0.00392 ( 3) link_ALPHA1-6 : angle 1.67823 ( 9) link_BETA1-4 : bond 0.00864 ( 18) link_BETA1-4 : angle 2.57570 ( 54) link_BETA1-6 : bond 0.01091 ( 3) link_BETA1-6 : angle 4.65672 ( 9) link_NAG-ASN : bond 0.00282 ( 9) link_NAG-ASN : angle 2.32991 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 136 MET cc_start: 0.8585 (mtm) cc_final: 0.8359 (mtm) REVERT: H 346 VAL cc_start: 0.8599 (t) cc_final: 0.8280 (p) REVERT: H 402 MET cc_start: 0.7178 (mmm) cc_final: 0.6893 (tpt) REVERT: J 346 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8222 (mmtm) REVERT: K 374 SER cc_start: 0.8496 (m) cc_final: 0.8164 (m) REVERT: K 416 CYS cc_start: 0.7720 (m) cc_final: 0.7372 (m) REVERT: N 111 MET cc_start: 0.6311 (ttp) cc_final: 0.5757 (ptp) REVERT: N 194 ASN cc_start: 0.7707 (m110) cc_final: 0.7437 (m-40) outliers start: 0 outliers final: 1 residues processed: 435 average time/residue: 0.6652 time to fit residues: 333.2190 Evaluate side-chains 373 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 372 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 381 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 281 ASN H 30 GLN H 260 GLN H 340 GLN I 281 ASN J 255 HIS K 157 GLN K 255 HIS ** L 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN L 212 ASN N 176 HIS N 252 ASN O 252 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.154336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103305 restraints weight = 28581.011| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.27 r_work: 0.2726 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 26322 Z= 0.239 Angle : 0.670 10.989 35922 Z= 0.331 Chirality : 0.048 0.275 4061 Planarity : 0.005 0.066 4580 Dihedral : 12.843 104.054 4215 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.81 % Allowed : 8.73 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3241 helix: 1.75 (0.25), residues: 432 sheet: -0.08 (0.16), residues: 959 loop : -0.49 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 138 TYR 0.015 0.002 TYR J 327 PHE 0.043 0.002 PHE K 50 TRP 0.019 0.002 TRP O 195 HIS 0.013 0.001 HIS K 290 Details of bonding type rmsd covalent geometry : bond 0.00561 (26240) covalent geometry : angle 0.65280 (35725) SS BOND : bond 0.00445 ( 49) SS BOND : angle 1.29901 ( 98) hydrogen bonds : bond 0.03857 ( 884) hydrogen bonds : angle 5.53970 ( 2298) link_ALPHA1-6 : bond 0.00373 ( 3) link_ALPHA1-6 : angle 2.07360 ( 9) link_BETA1-4 : bond 0.00618 ( 18) link_BETA1-4 : angle 2.71422 ( 54) link_BETA1-6 : bond 0.01138 ( 3) link_BETA1-6 : angle 4.00402 ( 9) link_NAG-ASN : bond 0.00412 ( 9) link_NAG-ASN : angle 2.39009 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 369 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 38 MET cc_start: 0.7238 (ttp) cc_final: 0.6904 (ttp) REVERT: H 160 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7881 (tp40) REVERT: H 287 PHE cc_start: 0.8794 (m-80) cc_final: 0.8534 (m-80) REVERT: H 297 ILE cc_start: 0.8714 (pt) cc_final: 0.8456 (pp) REVERT: H 346 VAL cc_start: 0.8770 (t) cc_final: 0.8502 (p) REVERT: H 402 MET cc_start: 0.7652 (mmm) cc_final: 0.7312 (tpt) REVERT: J 166 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7784 (mt-10) REVERT: J 301 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: J 346 LYS cc_start: 0.8586 (mmtm) cc_final: 0.8254 (mmtm) REVERT: K 374 SER cc_start: 0.8582 (m) cc_final: 0.8220 (m) REVERT: K 416 CYS cc_start: 0.7986 (m) cc_final: 0.7664 (m) REVERT: L 77 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8330 (p0) REVERT: L 158 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: L 165 GLU cc_start: 0.7985 (mp0) cc_final: 0.7471 (mt-10) REVERT: M 111 MET cc_start: 0.6293 (pp-130) cc_final: 0.5966 (pmm) REVERT: M 258 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7198 (tmt90) REVERT: N 109 GLU cc_start: 0.4856 (pm20) cc_final: 0.4576 (pm20) REVERT: N 111 MET cc_start: 0.6369 (ttp) cc_final: 0.5742 (ptp) REVERT: N 122 GLU cc_start: 0.6497 (pp20) cc_final: 0.6101 (pp20) REVERT: N 124 LYS cc_start: 0.7553 (mmtm) cc_final: 0.7243 (mmtm) REVERT: N 194 ASN cc_start: 0.7774 (m110) cc_final: 0.7413 (m-40) REVERT: N 200 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7853 (p) REVERT: N 265 GLU cc_start: 0.6851 (pm20) cc_final: 0.6421 (pm20) REVERT: O 253 LYS cc_start: 0.8357 (mppt) cc_final: 0.7995 (mtpt) outliers start: 50 outliers final: 22 residues processed: 390 average time/residue: 0.6769 time to fit residues: 304.5732 Evaluate side-chains 395 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 367 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 171 MET Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 247 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 75 optimal weight: 10.0000 chunk 316 optimal weight: 30.0000 chunk 109 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 315 optimal weight: 7.9990 chunk 295 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 HIS G 281 ASN H 30 GLN H 325 ASN H 411 GLN I 3 HIS J 255 HIS K 7 ASN K 157 GLN ** K 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 HIS ** L 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN L 212 ASN N 252 ASN O 252 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.152534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.099820 restraints weight = 28758.622| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.30 r_work: 0.2669 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 26322 Z= 0.350 Angle : 0.734 10.886 35922 Z= 0.364 Chirality : 0.052 0.302 4061 Planarity : 0.005 0.058 4580 Dihedral : 11.081 99.298 4213 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.90 % Allowed : 10.54 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3241 helix: 1.52 (0.24), residues: 431 sheet: -0.15 (0.16), residues: 962 loop : -0.59 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 138 TYR 0.017 0.003 TYR J 327 PHE 0.037 0.003 PHE K 50 TRP 0.016 0.002 TRP O 195 HIS 0.011 0.002 HIS G 308 Details of bonding type rmsd covalent geometry : bond 0.00831 (26240) covalent geometry : angle 0.71565 (35725) SS BOND : bond 0.00606 ( 49) SS BOND : angle 1.37274 ( 98) hydrogen bonds : bond 0.04147 ( 884) hydrogen bonds : angle 5.63384 ( 2298) link_ALPHA1-6 : bond 0.00460 ( 3) link_ALPHA1-6 : angle 2.36741 ( 9) link_BETA1-4 : bond 0.00642 ( 18) link_BETA1-4 : angle 2.87518 ( 54) link_BETA1-6 : bond 0.01252 ( 3) link_BETA1-6 : angle 4.22182 ( 9) link_NAG-ASN : bond 0.00597 ( 9) link_NAG-ASN : angle 2.92565 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 369 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 PHE cc_start: 0.8631 (t80) cc_final: 0.8417 (t80) REVERT: G 281 ASN cc_start: 0.9271 (t0) cc_final: 0.9055 (t0) REVERT: H 160 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7898 (tp40) REVERT: H 346 VAL cc_start: 0.8780 (t) cc_final: 0.8533 (p) REVERT: H 402 MET cc_start: 0.7701 (mmm) cc_final: 0.7334 (tpt) REVERT: I 2 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: J 166 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7898 (mt-10) REVERT: J 301 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: J 346 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8290 (mmtm) REVERT: K 374 SER cc_start: 0.8591 (m) cc_final: 0.8235 (m) REVERT: K 416 CYS cc_start: 0.7978 (m) cc_final: 0.7649 (m) REVERT: L 62 HIS cc_start: 0.7762 (t70) cc_final: 0.7519 (t70) REVERT: L 77 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8394 (p0) REVERT: L 158 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7583 (mt0) REVERT: L 166 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: M 111 MET cc_start: 0.6448 (pp-130) cc_final: 0.5996 (pmm) REVERT: M 113 MET cc_start: 0.6739 (mtt) cc_final: 0.6423 (mmm) REVERT: M 122 GLU cc_start: 0.6577 (tm-30) cc_final: 0.6284 (tm-30) REVERT: M 177 MET cc_start: 0.8641 (ptp) cc_final: 0.8385 (ptt) REVERT: M 258 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.6861 (tmt90) REVERT: N 109 GLU cc_start: 0.4817 (pm20) cc_final: 0.4612 (pm20) REVERT: N 111 MET cc_start: 0.6177 (ttp) cc_final: 0.5674 (ptp) REVERT: N 122 GLU cc_start: 0.6596 (pp20) cc_final: 0.6359 (pp20) REVERT: N 194 ASN cc_start: 0.7748 (m110) cc_final: 0.7381 (m-40) REVERT: N 262 GLU cc_start: 0.7293 (mp0) cc_final: 0.7081 (mp0) REVERT: N 265 GLU cc_start: 0.7059 (pm20) cc_final: 0.6661 (pm20) REVERT: O 111 MET cc_start: 0.6421 (ppp) cc_final: 0.5882 (pmm) REVERT: O 124 LYS cc_start: 0.7650 (mmpt) cc_final: 0.7435 (mmmt) REVERT: O 126 GLU cc_start: 0.7494 (mp0) cc_final: 0.7219 (mp0) REVERT: O 194 ASN cc_start: 0.8288 (p0) cc_final: 0.7721 (p0) REVERT: O 253 LYS cc_start: 0.8442 (mppt) cc_final: 0.8021 (mppt) outliers start: 80 outliers final: 51 residues processed: 407 average time/residue: 0.6661 time to fit residues: 312.5445 Evaluate side-chains 425 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 367 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 171 MET Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 233 LYS Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 120 ASN Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 169 MET Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 381 ILE Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 247 SER Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 247 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 211 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 285 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN J 255 HIS K 157 GLN K 183 GLN K 255 HIS L 77 ASN L 212 ASN N 176 HIS N 186 HIS N 252 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103015 restraints weight = 28404.199| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.02 r_work: 0.2722 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26322 Z= 0.152 Angle : 0.616 10.868 35922 Z= 0.300 Chirality : 0.046 0.265 4061 Planarity : 0.004 0.050 4580 Dihedral : 9.481 97.443 4213 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.06 % Allowed : 12.75 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3241 helix: 1.69 (0.25), residues: 434 sheet: -0.14 (0.16), residues: 955 loop : -0.52 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 258 TYR 0.015 0.002 TYR I 122 PHE 0.023 0.002 PHE L 50 TRP 0.011 0.001 TRP O 195 HIS 0.007 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00345 (26240) covalent geometry : angle 0.60002 (35725) SS BOND : bond 0.00376 ( 49) SS BOND : angle 0.92947 ( 98) hydrogen bonds : bond 0.03369 ( 884) hydrogen bonds : angle 5.39881 ( 2298) link_ALPHA1-6 : bond 0.00560 ( 3) link_ALPHA1-6 : angle 1.99115 ( 9) link_BETA1-4 : bond 0.00693 ( 18) link_BETA1-4 : angle 2.65291 ( 54) link_BETA1-6 : bond 0.01099 ( 3) link_BETA1-6 : angle 3.98165 ( 9) link_NAG-ASN : bond 0.00173 ( 9) link_NAG-ASN : angle 2.23884 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 281 ASN cc_start: 0.9245 (t0) cc_final: 0.9028 (t0) REVERT: H 160 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7863 (tp40) REVERT: H 287 PHE cc_start: 0.8898 (m-80) cc_final: 0.8683 (m-80) REVERT: H 346 VAL cc_start: 0.8737 (t) cc_final: 0.8494 (p) REVERT: H 402 MET cc_start: 0.7632 (mmm) cc_final: 0.7247 (tpt) REVERT: I 2 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8053 (mm-30) REVERT: J 166 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7707 (mt-10) REVERT: J 212 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8246 (m110) REVERT: J 301 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: J 346 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8362 (mmtm) REVERT: K 374 SER cc_start: 0.8596 (m) cc_final: 0.8234 (m) REVERT: K 416 CYS cc_start: 0.7973 (m) cc_final: 0.7663 (m) REVERT: L 62 HIS cc_start: 0.7781 (t70) cc_final: 0.7011 (t70) REVERT: L 158 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: M 111 MET cc_start: 0.6406 (pp-130) cc_final: 0.6029 (pmm) REVERT: M 113 MET cc_start: 0.6774 (mtt) cc_final: 0.6141 (tmm) REVERT: M 122 GLU cc_start: 0.6478 (tm-30) cc_final: 0.6247 (tm-30) REVERT: M 141 MET cc_start: 0.8469 (mtt) cc_final: 0.7985 (mtp) REVERT: M 258 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8012 (tmm-80) REVERT: N 109 GLU cc_start: 0.4941 (pm20) cc_final: 0.4732 (pm20) REVERT: N 111 MET cc_start: 0.6232 (ttp) cc_final: 0.5690 (ptp) REVERT: N 122 GLU cc_start: 0.6663 (pp20) cc_final: 0.6423 (pp20) REVERT: N 186 HIS cc_start: 0.8385 (p90) cc_final: 0.8093 (p-80) REVERT: N 194 ASN cc_start: 0.7775 (m110) cc_final: 0.7480 (m-40) REVERT: N 262 GLU cc_start: 0.7234 (mp0) cc_final: 0.7021 (mp0) REVERT: N 265 GLU cc_start: 0.7004 (pm20) cc_final: 0.6425 (pm20) REVERT: O 126 GLU cc_start: 0.7572 (mp0) cc_final: 0.7321 (mp0) REVERT: O 194 ASN cc_start: 0.8435 (p0) cc_final: 0.7912 (p0) REVERT: O 253 LYS cc_start: 0.8387 (mppt) cc_final: 0.8018 (mppt) REVERT: O 265 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7610 (pt0) outliers start: 57 outliers final: 29 residues processed: 395 average time/residue: 0.6571 time to fit residues: 299.4101 Evaluate side-chains 394 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 358 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 171 MET Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 201 GLN Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 247 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 265 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 296 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 267 optimal weight: 4.9990 chunk 26 optimal weight: 0.0040 chunk 237 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN J 255 HIS K 157 GLN K 255 HIS L 77 ASN L 212 ASN N 252 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104648 restraints weight = 28530.681| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.17 r_work: 0.2760 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26322 Z= 0.112 Angle : 0.583 11.730 35922 Z= 0.282 Chirality : 0.044 0.254 4061 Planarity : 0.004 0.048 4580 Dihedral : 8.287 95.066 4213 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.10 % Allowed : 13.40 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3241 helix: 1.87 (0.25), residues: 432 sheet: -0.11 (0.16), residues: 960 loop : -0.46 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 258 TYR 0.013 0.001 TYR F 49 PHE 0.017 0.001 PHE L 50 TRP 0.009 0.001 TRP O 195 HIS 0.007 0.001 HIS J 170 Details of bonding type rmsd covalent geometry : bond 0.00249 (26240) covalent geometry : angle 0.56701 (35725) SS BOND : bond 0.00323 ( 49) SS BOND : angle 0.85199 ( 98) hydrogen bonds : bond 0.03078 ( 884) hydrogen bonds : angle 5.22037 ( 2298) link_ALPHA1-6 : bond 0.00630 ( 3) link_ALPHA1-6 : angle 1.77054 ( 9) link_BETA1-4 : bond 0.00709 ( 18) link_BETA1-4 : angle 2.58488 ( 54) link_BETA1-6 : bond 0.01013 ( 3) link_BETA1-6 : angle 3.84706 ( 9) link_NAG-ASN : bond 0.00131 ( 9) link_NAG-ASN : angle 2.35379 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 370 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9074 (tt) REVERT: G 95 PHE cc_start: 0.8481 (t80) cc_final: 0.8210 (t80) REVERT: H 346 VAL cc_start: 0.8699 (t) cc_final: 0.8444 (p) REVERT: H 402 MET cc_start: 0.7641 (mmm) cc_final: 0.7261 (tpt) REVERT: I 75 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: J 166 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7613 (mt-10) REVERT: J 212 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8140 (m110) REVERT: J 301 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: J 344 GLU cc_start: 0.7982 (mp0) cc_final: 0.7711 (mp0) REVERT: J 346 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8257 (mmtm) REVERT: K 374 SER cc_start: 0.8595 (m) cc_final: 0.8256 (m) REVERT: K 416 CYS cc_start: 0.7988 (m) cc_final: 0.7670 (m) REVERT: L 62 HIS cc_start: 0.7725 (t70) cc_final: 0.6988 (t70) REVERT: L 158 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: M 111 MET cc_start: 0.6487 (pp-130) cc_final: 0.6103 (pmm) REVERT: M 113 MET cc_start: 0.6803 (mtt) cc_final: 0.6032 (tmm) REVERT: M 122 GLU cc_start: 0.6480 (tm-30) cc_final: 0.6271 (tm-30) REVERT: M 141 MET cc_start: 0.8377 (mtt) cc_final: 0.7949 (mtp) REVERT: M 218 ASP cc_start: 0.7781 (m-30) cc_final: 0.7445 (m-30) REVERT: M 258 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7974 (tmm-80) REVERT: N 109 GLU cc_start: 0.4887 (pm20) cc_final: 0.4575 (pm20) REVERT: N 111 MET cc_start: 0.6283 (ttp) cc_final: 0.5739 (ptp) REVERT: N 122 GLU cc_start: 0.6695 (pp20) cc_final: 0.6242 (pp20) REVERT: N 186 HIS cc_start: 0.8233 (p90) cc_final: 0.8033 (p-80) REVERT: N 194 ASN cc_start: 0.7735 (m110) cc_final: 0.7422 (m-40) REVERT: N 200 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7839 (p) REVERT: N 252 ASN cc_start: 0.7373 (t0) cc_final: 0.7117 (t160) REVERT: N 262 GLU cc_start: 0.7213 (mp0) cc_final: 0.6994 (mp0) REVERT: N 265 GLU cc_start: 0.6954 (pm20) cc_final: 0.6243 (pm20) REVERT: O 111 MET cc_start: 0.6772 (pmm) cc_final: 0.6439 (ppp) REVERT: O 113 MET cc_start: 0.7221 (tpt) cc_final: 0.6910 (mtp) REVERT: O 116 GLU cc_start: 0.6282 (tm-30) cc_final: 0.6081 (tt0) REVERT: O 194 ASN cc_start: 0.8440 (p0) cc_final: 0.7919 (p0) REVERT: O 253 LYS cc_start: 0.8335 (mppt) cc_final: 0.8043 (mtpt) REVERT: O 265 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7613 (pt0) outliers start: 58 outliers final: 25 residues processed: 403 average time/residue: 0.5909 time to fit residues: 276.2170 Evaluate side-chains 403 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 201 GLN Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 265 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 319 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 215 optimal weight: 0.0470 chunk 219 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN J 255 HIS K 157 GLN K 255 HIS L 212 ASN N 176 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103451 restraints weight = 28534.571| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.15 r_work: 0.2730 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26322 Z= 0.162 Angle : 0.600 9.796 35922 Z= 0.293 Chirality : 0.045 0.267 4061 Planarity : 0.004 0.045 4580 Dihedral : 7.474 91.544 4213 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.21 % Allowed : 13.47 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3241 helix: 1.85 (0.24), residues: 446 sheet: -0.07 (0.16), residues: 964 loop : -0.43 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 206 TYR 0.013 0.002 TYR J 327 PHE 0.022 0.002 PHE L 50 TRP 0.012 0.001 TRP N 251 HIS 0.008 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00376 (26240) covalent geometry : angle 0.58348 (35725) SS BOND : bond 0.00422 ( 49) SS BOND : angle 0.96639 ( 98) hydrogen bonds : bond 0.03245 ( 884) hydrogen bonds : angle 5.22557 ( 2298) link_ALPHA1-6 : bond 0.00602 ( 3) link_ALPHA1-6 : angle 1.97394 ( 9) link_BETA1-4 : bond 0.00643 ( 18) link_BETA1-4 : angle 2.66653 ( 54) link_BETA1-6 : bond 0.00946 ( 3) link_BETA1-6 : angle 3.86408 ( 9) link_NAG-ASN : bond 0.00217 ( 9) link_NAG-ASN : angle 2.29525 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 374 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9081 (tt) REVERT: G 95 PHE cc_start: 0.8553 (t80) cc_final: 0.8324 (t80) REVERT: G 281 ASN cc_start: 0.9274 (t0) cc_final: 0.9045 (t0) REVERT: H 346 VAL cc_start: 0.8702 (t) cc_final: 0.8444 (p) REVERT: H 402 MET cc_start: 0.7662 (mmm) cc_final: 0.7294 (tpt) REVERT: I 2 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: I 75 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8590 (m-30) REVERT: I 245 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8324 (mppt) REVERT: J 166 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7690 (mt-10) REVERT: J 212 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.8151 (m110) REVERT: J 301 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: J 346 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8351 (mmtm) REVERT: K 374 SER cc_start: 0.8599 (m) cc_final: 0.8249 (m) REVERT: K 416 CYS cc_start: 0.8001 (m) cc_final: 0.7688 (m) REVERT: L 62 HIS cc_start: 0.7818 (t70) cc_final: 0.7116 (t-90) REVERT: L 158 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: L 255 HIS cc_start: 0.7458 (m170) cc_final: 0.6672 (p-80) REVERT: M 111 MET cc_start: 0.6594 (pp-130) cc_final: 0.6176 (pmm) REVERT: M 113 MET cc_start: 0.6810 (mtt) cc_final: 0.6028 (tmm) REVERT: M 141 MET cc_start: 0.8444 (mtt) cc_final: 0.7930 (mtp) REVERT: M 218 ASP cc_start: 0.7829 (m-30) cc_final: 0.7523 (m-30) REVERT: M 258 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7982 (tmm-80) REVERT: N 109 GLU cc_start: 0.4896 (pm20) cc_final: 0.4628 (pm20) REVERT: N 111 MET cc_start: 0.6217 (ttp) cc_final: 0.5741 (ptp) REVERT: N 122 GLU cc_start: 0.6792 (pp20) cc_final: 0.6591 (pp20) REVERT: N 126 GLU cc_start: 0.7013 (pp20) cc_final: 0.6748 (pp20) REVERT: N 141 MET cc_start: 0.8650 (mtp) cc_final: 0.8397 (mtp) REVERT: N 194 ASN cc_start: 0.7731 (m110) cc_final: 0.7409 (m-40) REVERT: N 200 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7873 (p) REVERT: N 252 ASN cc_start: 0.7241 (t0) cc_final: 0.7014 (t160) REVERT: N 262 GLU cc_start: 0.7209 (mp0) cc_final: 0.6989 (mp0) REVERT: N 265 GLU cc_start: 0.6985 (pm20) cc_final: 0.6481 (pm20) REVERT: O 111 MET cc_start: 0.6543 (pmm) cc_final: 0.6156 (ppp) REVERT: O 113 MET cc_start: 0.6910 (tpt) cc_final: 0.6666 (mtp) REVERT: O 116 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.6076 (tt0) REVERT: O 194 ASN cc_start: 0.8428 (p0) cc_final: 0.7894 (p0) REVERT: O 253 LYS cc_start: 0.8435 (mppt) cc_final: 0.8070 (mtpt) REVERT: O 258 ARG cc_start: 0.8621 (ttt-90) cc_final: 0.8336 (ttt-90) REVERT: O 265 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7629 (pt0) outliers start: 61 outliers final: 34 residues processed: 405 average time/residue: 0.6030 time to fit residues: 283.2145 Evaluate side-chains 416 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 372 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 201 GLN Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 265 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 250 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 226 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN J 170 HIS J 255 HIS K 157 GLN K 255 HIS L 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.155293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104127 restraints weight = 28413.696| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.04 r_work: 0.2737 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26322 Z= 0.141 Angle : 0.587 9.404 35922 Z= 0.289 Chirality : 0.044 0.265 4061 Planarity : 0.004 0.043 4580 Dihedral : 7.112 89.014 4213 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.35 % Allowed : 14.23 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3241 helix: 1.89 (0.24), residues: 446 sheet: -0.05 (0.16), residues: 964 loop : -0.42 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 206 TYR 0.013 0.001 TYR I 122 PHE 0.019 0.002 PHE L 50 TRP 0.012 0.001 TRP N 251 HIS 0.008 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00323 (26240) covalent geometry : angle 0.57189 (35725) SS BOND : bond 0.00363 ( 49) SS BOND : angle 0.88264 ( 98) hydrogen bonds : bond 0.03149 ( 884) hydrogen bonds : angle 5.16828 ( 2298) link_ALPHA1-6 : bond 0.00440 ( 3) link_ALPHA1-6 : angle 1.65344 ( 9) link_BETA1-4 : bond 0.00658 ( 18) link_BETA1-4 : angle 2.50293 ( 54) link_BETA1-6 : bond 0.00914 ( 3) link_BETA1-6 : angle 3.82428 ( 9) link_NAG-ASN : bond 0.00139 ( 9) link_NAG-ASN : angle 2.15354 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 374 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9083 (tt) REVERT: G 281 ASN cc_start: 0.9269 (t0) cc_final: 0.9038 (t0) REVERT: H 160 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7735 (tp40) REVERT: H 297 ILE cc_start: 0.8657 (pt) cc_final: 0.8376 (pp) REVERT: H 346 VAL cc_start: 0.8707 (t) cc_final: 0.8459 (p) REVERT: H 402 MET cc_start: 0.7723 (mmm) cc_final: 0.7404 (tpt) REVERT: I 2 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: I 75 ASP cc_start: 0.9058 (OUTLIER) cc_final: 0.8639 (m-30) REVERT: J 166 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7734 (mt-10) REVERT: J 212 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8124 (m110) REVERT: J 301 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: J 344 GLU cc_start: 0.7986 (mp0) cc_final: 0.7762 (mp0) REVERT: J 346 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8438 (mmtm) REVERT: J 401 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8260 (mp) REVERT: K 374 SER cc_start: 0.8632 (m) cc_final: 0.8283 (m) REVERT: K 416 CYS cc_start: 0.7982 (m) cc_final: 0.7673 (m) REVERT: L 62 HIS cc_start: 0.7819 (t70) cc_final: 0.7139 (t-90) REVERT: L 158 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: M 111 MET cc_start: 0.6604 (pp-130) cc_final: 0.6160 (pmm) REVERT: M 113 MET cc_start: 0.6848 (mtt) cc_final: 0.6585 (mmm) REVERT: M 141 MET cc_start: 0.8414 (mtt) cc_final: 0.7896 (mtp) REVERT: M 218 ASP cc_start: 0.7801 (m-30) cc_final: 0.7492 (m-30) REVERT: M 258 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8019 (tmm-80) REVERT: N 109 GLU cc_start: 0.4540 (pm20) cc_final: 0.4274 (pm20) REVERT: N 111 MET cc_start: 0.6198 (ttp) cc_final: 0.5726 (ptp) REVERT: N 122 GLU cc_start: 0.6881 (pp20) cc_final: 0.6612 (pp20) REVERT: N 190 GLU cc_start: 0.7459 (tp30) cc_final: 0.6657 (tp30) REVERT: N 194 ASN cc_start: 0.7740 (m110) cc_final: 0.7437 (m-40) REVERT: N 200 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7855 (p) REVERT: N 202 TYR cc_start: 0.8218 (t80) cc_final: 0.7980 (t80) REVERT: N 247 SER cc_start: 0.8345 (p) cc_final: 0.8069 (m) REVERT: N 262 GLU cc_start: 0.7178 (mp0) cc_final: 0.6965 (mp0) REVERT: N 265 GLU cc_start: 0.7001 (pm20) cc_final: 0.6495 (pm20) REVERT: O 111 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6131 (ppp) REVERT: O 113 MET cc_start: 0.7090 (tpt) cc_final: 0.6787 (mtp) REVERT: O 116 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.6021 (tm-30) REVERT: O 194 ASN cc_start: 0.8427 (p0) cc_final: 0.7909 (p0) REVERT: O 253 LYS cc_start: 0.8440 (mppt) cc_final: 0.8077 (mtpt) REVERT: O 258 ARG cc_start: 0.8656 (ttt-90) cc_final: 0.8399 (ttt-90) REVERT: O 265 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7628 (pt0) outliers start: 65 outliers final: 34 residues processed: 405 average time/residue: 0.6209 time to fit residues: 292.0332 Evaluate side-chains 415 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 368 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 401 LEU Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 201 GLN Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 265 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 138 optimal weight: 9.9990 chunk 267 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 192 optimal weight: 0.0010 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN J 170 HIS J 255 HIS K 157 GLN K 255 HIS L 212 ASN N 252 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.156117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104812 restraints weight = 28440.733| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.05 r_work: 0.2766 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26322 Z= 0.116 Angle : 0.572 9.440 35922 Z= 0.280 Chirality : 0.044 0.258 4061 Planarity : 0.004 0.042 4580 Dihedral : 6.799 86.482 4213 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.03 % Allowed : 14.63 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3241 helix: 2.01 (0.24), residues: 446 sheet: -0.00 (0.16), residues: 964 loop : -0.40 (0.15), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 392 TYR 0.011 0.001 TYR F 49 PHE 0.017 0.001 PHE G 95 TRP 0.020 0.001 TRP N 251 HIS 0.008 0.001 HIS J 170 Details of bonding type rmsd covalent geometry : bond 0.00262 (26240) covalent geometry : angle 0.55671 (35725) SS BOND : bond 0.00382 ( 49) SS BOND : angle 0.87076 ( 98) hydrogen bonds : bond 0.03014 ( 884) hydrogen bonds : angle 5.08640 ( 2298) link_ALPHA1-6 : bond 0.00374 ( 3) link_ALPHA1-6 : angle 1.58019 ( 9) link_BETA1-4 : bond 0.00662 ( 18) link_BETA1-4 : angle 2.44903 ( 54) link_BETA1-6 : bond 0.00909 ( 3) link_BETA1-6 : angle 3.74308 ( 9) link_NAG-ASN : bond 0.00149 ( 9) link_NAG-ASN : angle 2.11377 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8197 (mt-10) REVERT: G 29 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9070 (tt) REVERT: G 75 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8851 (t0) REVERT: G 95 PHE cc_start: 0.8403 (t80) cc_final: 0.8185 (t80) REVERT: G 281 ASN cc_start: 0.9251 (t0) cc_final: 0.8999 (t0) REVERT: H 346 VAL cc_start: 0.8685 (t) cc_final: 0.8432 (p) REVERT: H 402 MET cc_start: 0.7706 (mmm) cc_final: 0.7390 (tpt) REVERT: I 2 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: I 67 GLU cc_start: 0.6494 (tp30) cc_final: 0.6102 (pm20) REVERT: I 75 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8589 (m-30) REVERT: J 166 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7672 (mt-10) REVERT: J 212 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8149 (m110) REVERT: J 301 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: J 346 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8373 (mmtm) REVERT: K 374 SER cc_start: 0.8631 (m) cc_final: 0.8288 (m) REVERT: K 416 CYS cc_start: 0.7984 (m) cc_final: 0.7674 (m) REVERT: L 60 ASP cc_start: 0.8396 (m-30) cc_final: 0.8183 (m-30) REVERT: L 62 HIS cc_start: 0.7747 (t70) cc_final: 0.7114 (t-90) REVERT: L 158 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: M 111 MET cc_start: 0.6609 (pp-130) cc_final: 0.6344 (ppp) REVERT: M 113 MET cc_start: 0.6853 (mtt) cc_final: 0.6584 (mmm) REVERT: M 218 ASP cc_start: 0.7725 (m-30) cc_final: 0.7383 (m-30) REVERT: M 258 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7964 (tmm-80) REVERT: N 109 GLU cc_start: 0.4543 (pm20) cc_final: 0.4270 (pm20) REVERT: N 111 MET cc_start: 0.6203 (ttp) cc_final: 0.5726 (ptp) REVERT: N 122 GLU cc_start: 0.6892 (pp20) cc_final: 0.6621 (pp20) REVERT: N 194 ASN cc_start: 0.7722 (m110) cc_final: 0.7421 (m-40) REVERT: N 200 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7825 (p) REVERT: N 247 SER cc_start: 0.8313 (p) cc_final: 0.8050 (m) REVERT: N 262 GLU cc_start: 0.7232 (mp0) cc_final: 0.7006 (mp0) REVERT: N 265 GLU cc_start: 0.6966 (pm20) cc_final: 0.6341 (pm20) REVERT: O 111 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6115 (ppp) REVERT: O 113 MET cc_start: 0.7089 (tpt) cc_final: 0.6788 (mtp) REVERT: O 194 ASN cc_start: 0.8371 (p0) cc_final: 0.7864 (p0) REVERT: O 253 LYS cc_start: 0.8409 (mppt) cc_final: 0.8063 (mtpt) REVERT: O 258 ARG cc_start: 0.8685 (ttt-90) cc_final: 0.8460 (ttt-90) outliers start: 56 outliers final: 34 residues processed: 399 average time/residue: 0.6315 time to fit residues: 293.0658 Evaluate side-chains 400 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 356 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 201 GLN Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 110 optimal weight: 0.0570 chunk 117 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 300 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN I 264 ASN J 170 HIS J 255 HIS K 157 GLN K 255 HIS L 212 ASN ** M 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.156308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104848 restraints weight = 28651.098| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.05 r_work: 0.2771 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26322 Z= 0.119 Angle : 0.572 9.443 35922 Z= 0.281 Chirality : 0.044 0.259 4061 Planarity : 0.004 0.041 4580 Dihedral : 6.598 83.364 4213 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.96 % Allowed : 15.10 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3241 helix: 2.10 (0.25), residues: 444 sheet: 0.00 (0.16), residues: 960 loop : -0.39 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 206 TYR 0.012 0.001 TYR I 122 PHE 0.018 0.001 PHE L 50 TRP 0.020 0.001 TRP N 251 HIS 0.007 0.001 HIS J 170 Details of bonding type rmsd covalent geometry : bond 0.00271 (26240) covalent geometry : angle 0.55675 (35725) SS BOND : bond 0.00337 ( 49) SS BOND : angle 0.88174 ( 98) hydrogen bonds : bond 0.03004 ( 884) hydrogen bonds : angle 5.04367 ( 2298) link_ALPHA1-6 : bond 0.00310 ( 3) link_ALPHA1-6 : angle 1.60337 ( 9) link_BETA1-4 : bond 0.00639 ( 18) link_BETA1-4 : angle 2.42774 ( 54) link_BETA1-6 : bond 0.00888 ( 3) link_BETA1-6 : angle 3.70958 ( 9) link_NAG-ASN : bond 0.00130 ( 9) link_NAG-ASN : angle 2.09483 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 363 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8195 (mt-10) REVERT: G 29 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9072 (tt) REVERT: G 75 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8832 (t0) REVERT: G 95 PHE cc_start: 0.8505 (t80) cc_final: 0.8302 (t80) REVERT: G 281 ASN cc_start: 0.9244 (t0) cc_final: 0.8989 (t0) REVERT: H 297 ILE cc_start: 0.8729 (pt) cc_final: 0.8288 (pp) REVERT: H 346 VAL cc_start: 0.8673 (t) cc_final: 0.8401 (p) REVERT: H 402 MET cc_start: 0.7700 (mmm) cc_final: 0.7390 (tpt) REVERT: I 2 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: I 75 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8594 (m-30) REVERT: J 166 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7666 (mt-10) REVERT: J 301 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7615 (tp30) REVERT: J 346 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8258 (mmtm) REVERT: K 374 SER cc_start: 0.8614 (m) cc_final: 0.8274 (m) REVERT: K 416 CYS cc_start: 0.8004 (m) cc_final: 0.7699 (m) REVERT: L 62 HIS cc_start: 0.7716 (t70) cc_final: 0.7076 (t-90) REVERT: L 158 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7516 (mt0) REVERT: L 255 HIS cc_start: 0.7329 (m170) cc_final: 0.6621 (p-80) REVERT: M 111 MET cc_start: 0.6650 (pp-130) cc_final: 0.6382 (ppp) REVERT: M 113 MET cc_start: 0.6863 (mtt) cc_final: 0.6586 (mmm) REVERT: M 141 MET cc_start: 0.8183 (mtt) cc_final: 0.7859 (mtp) REVERT: M 218 ASP cc_start: 0.7847 (m-30) cc_final: 0.7527 (m-30) REVERT: M 258 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7963 (tmm-80) REVERT: N 111 MET cc_start: 0.6207 (ttp) cc_final: 0.5728 (ptp) REVERT: N 122 GLU cc_start: 0.6900 (pp20) cc_final: 0.6557 (pp20) REVERT: N 176 HIS cc_start: 0.7420 (p-80) cc_final: 0.7205 (p-80) REVERT: N 190 GLU cc_start: 0.7475 (tp30) cc_final: 0.6676 (tp30) REVERT: N 194 ASN cc_start: 0.7694 (m110) cc_final: 0.7380 (m-40) REVERT: N 200 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7824 (p) REVERT: N 202 TYR cc_start: 0.8127 (t80) cc_final: 0.7844 (t80) REVERT: N 247 SER cc_start: 0.8288 (p) cc_final: 0.8009 (m) REVERT: N 265 GLU cc_start: 0.6974 (pm20) cc_final: 0.6337 (pm20) REVERT: O 111 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6114 (ppp) REVERT: O 113 MET cc_start: 0.7050 (tpt) cc_final: 0.6674 (mtp) REVERT: O 126 GLU cc_start: 0.7437 (mp0) cc_final: 0.7145 (mp0) REVERT: O 194 ASN cc_start: 0.8400 (p0) cc_final: 0.7883 (p0) REVERT: O 201 GLN cc_start: 0.8043 (mt0) cc_final: 0.7701 (pt0) REVERT: O 253 LYS cc_start: 0.8428 (mppt) cc_final: 0.8188 (mtmm) REVERT: O 258 ARG cc_start: 0.8709 (ttt-90) cc_final: 0.8493 (ttt-90) outliers start: 54 outliers final: 35 residues processed: 395 average time/residue: 0.6301 time to fit residues: 289.9343 Evaluate side-chains 402 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 358 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 339 SER Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 201 GLN Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 33 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 180 optimal weight: 0.0170 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 223 optimal weight: 9.9990 chunk 267 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN I 264 ASN J 157 GLN J 170 HIS J 255 HIS K 157 GLN K 255 HIS L 212 ASN N 186 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.154096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.102553 restraints weight = 28462.829| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.25 r_work: 0.2734 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 26322 Z= 0.228 Angle : 0.647 9.385 35922 Z= 0.321 Chirality : 0.047 0.286 4061 Planarity : 0.004 0.041 4580 Dihedral : 6.881 79.370 4213 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.99 % Allowed : 15.14 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3241 helix: 1.94 (0.24), residues: 446 sheet: -0.03 (0.16), residues: 970 loop : -0.43 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 206 TYR 0.017 0.002 TYR J 327 PHE 0.028 0.002 PHE K 50 TRP 0.022 0.001 TRP N 251 HIS 0.010 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00537 (26240) covalent geometry : angle 0.63152 (35725) SS BOND : bond 0.00476 ( 49) SS BOND : angle 1.16793 ( 98) hydrogen bonds : bond 0.03455 ( 884) hydrogen bonds : angle 5.23590 ( 2298) link_ALPHA1-6 : bond 0.00274 ( 3) link_ALPHA1-6 : angle 1.77081 ( 9) link_BETA1-4 : bond 0.00610 ( 18) link_BETA1-4 : angle 2.60358 ( 54) link_BETA1-6 : bond 0.00915 ( 3) link_BETA1-6 : angle 3.81545 ( 9) link_NAG-ASN : bond 0.00320 ( 9) link_NAG-ASN : angle 2.15080 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6482 Ramachandran restraints generated. 3241 Oldfield, 0 Emsley, 3241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 353 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 29 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9117 (tt) REVERT: H 97 ASP cc_start: 0.8319 (t0) cc_final: 0.7890 (t0) REVERT: H 297 ILE cc_start: 0.8736 (pt) cc_final: 0.8262 (pp) REVERT: H 346 VAL cc_start: 0.8672 (t) cc_final: 0.8398 (p) REVERT: H 402 MET cc_start: 0.7638 (mmm) cc_final: 0.7292 (tpt) REVERT: I 2 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: I 75 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8700 (m-30) REVERT: J 166 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7893 (mt-10) REVERT: J 301 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: J 346 LYS cc_start: 0.8598 (mmtm) cc_final: 0.8324 (mmtm) REVERT: K 374 SER cc_start: 0.8603 (m) cc_final: 0.8247 (m) REVERT: K 416 CYS cc_start: 0.8052 (m) cc_final: 0.7743 (m) REVERT: L 62 HIS cc_start: 0.7861 (t70) cc_final: 0.7075 (t70) REVERT: L 158 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: L 255 HIS cc_start: 0.7381 (m170) cc_final: 0.6651 (p-80) REVERT: M 111 MET cc_start: 0.6694 (pp-130) cc_final: 0.6404 (ppp) REVERT: M 113 MET cc_start: 0.6776 (mtt) cc_final: 0.6455 (mmm) REVERT: M 141 MET cc_start: 0.8411 (mtt) cc_final: 0.7988 (mtp) REVERT: M 218 ASP cc_start: 0.7824 (m-30) cc_final: 0.7506 (m-30) REVERT: M 258 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7995 (tmm-80) REVERT: N 109 GLU cc_start: 0.4741 (pm20) cc_final: 0.4464 (pm20) REVERT: N 111 MET cc_start: 0.6189 (ttp) cc_final: 0.5717 (ptp) REVERT: N 122 GLU cc_start: 0.6847 (pp20) cc_final: 0.6484 (pp20) REVERT: N 190 GLU cc_start: 0.7611 (tp30) cc_final: 0.6768 (tp30) REVERT: N 194 ASN cc_start: 0.7614 (m110) cc_final: 0.7284 (m-40) REVERT: N 265 GLU cc_start: 0.7077 (pm20) cc_final: 0.6499 (pm20) REVERT: O 111 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6314 (ppp) REVERT: O 113 MET cc_start: 0.7029 (tpt) cc_final: 0.6697 (mtp) REVERT: O 194 ASN cc_start: 0.8380 (p0) cc_final: 0.7803 (p0) REVERT: O 201 GLN cc_start: 0.7978 (mt0) cc_final: 0.7606 (pt0) REVERT: O 253 LYS cc_start: 0.8448 (mppt) cc_final: 0.8217 (mtmm) REVERT: O 258 ARG cc_start: 0.8727 (ttt-90) cc_final: 0.8480 (ttt-90) outliers start: 55 outliers final: 38 residues processed: 387 average time/residue: 0.6327 time to fit residues: 284.6248 Evaluate side-chains 394 residues out of total 2761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 349 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 398 VAL Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 97 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 280 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain K residue 3 SER Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 339 SER Chi-restraints excluded: chain K residue 407 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 158 GLN Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain M residue 258 ARG Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 201 GLN Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 311 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 24 optimal weight: 0.4980 chunk 241 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 310 optimal weight: 8.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN J 157 GLN J 170 HIS J 255 HIS K 157 GLN K 255 HIS L 157 GLN L 212 ASN N 186 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.154837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103341 restraints weight = 28311.847| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.05 r_work: 0.2731 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26322 Z= 0.173 Angle : 0.612 9.420 35922 Z= 0.302 Chirality : 0.045 0.274 4061 Planarity : 0.004 0.041 4580 Dihedral : 6.732 78.017 4213 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.03 % Allowed : 15.39 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3241 helix: 1.94 (0.24), residues: 446 sheet: -0.04 (0.16), residues: 970 loop : -0.43 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 206 TYR 0.014 0.002 TYR J 327 PHE 0.022 0.002 PHE L 50 TRP 0.022 0.001 TRP N 251 HIS 0.009 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00405 (26240) covalent geometry : angle 0.59689 (35725) SS BOND : bond 0.00403 ( 49) SS BOND : angle 1.03536 ( 98) hydrogen bonds : bond 0.03267 ( 884) hydrogen bonds : angle 5.18389 ( 2298) link_ALPHA1-6 : bond 0.00254 ( 3) link_ALPHA1-6 : angle 1.67356 ( 9) link_BETA1-4 : bond 0.00603 ( 18) link_BETA1-4 : angle 2.51526 ( 54) link_BETA1-6 : bond 0.00902 ( 3) link_BETA1-6 : angle 3.80998 ( 9) link_NAG-ASN : bond 0.00179 ( 9) link_NAG-ASN : angle 2.02142 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12775.40 seconds wall clock time: 217 minutes 51.02 seconds (13071.02 seconds total)