Starting phenix.real_space_refine on Sun Aug 24 09:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9faw_50284/08_2025/9faw_50284.cif Found real_map, /net/cci-nas-00/data/ceres_data/9faw_50284/08_2025/9faw_50284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9faw_50284/08_2025/9faw_50284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9faw_50284/08_2025/9faw_50284.map" model { file = "/net/cci-nas-00/data/ceres_data/9faw_50284/08_2025/9faw_50284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9faw_50284/08_2025/9faw_50284.cif" } resolution = 2.9 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= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 114 5.16 5 C 12313 2.51 5 N 3019 2.21 5 O 3487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18934 Number of models: 1 Model: "" Number of chains: 23 Chain: "B" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain breaks: 1 bond proxies already assigned to first conformer: 2790 Chain: "A" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2724 Classifications: {'peptide': 332} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2720 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2983 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 356, 2967 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'P1L:plan-1': 3} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 356, 2967 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'P1L:plan-1': 3} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 3027 Chain: "H" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 255 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "L" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1439 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "K" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 912 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Chain: "O" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 1 Chain: "F" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 912 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {'EPE': 1, 'HEX': 1, 'PGW': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'EPE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'EPE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.26 Number of scatterers: 18934 At special positions: 0 Unit cell: (119.556, 115.911, 142.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 1 15.00 O 3487 8.00 N 3019 7.00 C 12313 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 77 " distance=2.03 Simple disulfide: pdb=" SG CYS L 109 " - pdb=" SG CYS L 128 " distance=2.05 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 171 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.03 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " 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 Atom "HETATM18477 O5 NAG M 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM18549 O5 NAG N 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM18316 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA P 3 " - " MAN P 6 " " MAN P 4 " - " MAN P 5 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A 502 " - " ASN A 8 " " NAG E 502 " - " ASN E 8 " " NAG G 1 " - " ASN B 80 " " NAG I 1 " - " ASN B 149 " " NAG J 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 149 " " NAG N 1 " - " ASN A 80 " " NAG P 1 " - " ASN A 149 " " NAG Q 1 " - " ASN D 80 " " NAG R 1 " - " ASN D 149 " " NAG S 1 " - " ASN C 208 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 771.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 25 sheets defined 38.8% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.335A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 268 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.538A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 447 Proline residue: B 432 - end of helix Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.616A pdb=" N ALA E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 225 through 242 removed outlier: 4.029A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 269 removed outlier: 3.589A pdb=" N ALA E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG E 269 " --> pdb=" O ASN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.549A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 429 removed outlier: 3.975A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 446 removed outlier: 3.701A pdb=" N PHE E 433 " --> pdb=" O ILE E 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.616A pdb=" N LEU A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 246 through 270 removed outlier: 3.500A pdb=" N LEU A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 307 removed outlier: 3.663A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 446 Proline residue: A 432 - end of helix Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.590A pdb=" N ASP D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 170 through 173 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 225 through 238 Processing helix chain 'D' and resid 246 through 268 Processing helix chain 'D' and resid 279 through 308 Processing helix chain 'D' and resid 422 through 447 removed outlier: 4.784A pdb=" N ARG D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'C' and resid 23 through 36 removed outlier: 3.579A pdb=" N VAL C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 88 Processing helix chain 'C' and resid 99 through 104 removed outlier: 3.738A pdb=" N VAL C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 104' Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 240 through 254 removed outlier: 3.973A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 257 No H-bonds generated for 'chain 'C' and resid 255 through 257' Processing helix chain 'C' and resid 261 through 285 Processing helix chain 'C' and resid 294 through 323 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 398 through 400 No H-bonds generated for 'chain 'C' and resid 398 through 400' Processing helix chain 'C' and resid 401 through 428 removed outlier: 3.671A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.858A pdb=" N TYR C 427 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'H' and resid 672 through 699 removed outlier: 3.596A pdb=" N TYR H 699 " --> pdb=" O ALA H 695 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 43 removed outlier: 4.220A pdb=" N VAL L 24 " --> pdb=" O ARG L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 89 through 113 Processing helix chain 'L' and resid 114 through 118 removed outlier: 3.530A pdb=" N PHE L 117 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 146 removed outlier: 3.542A pdb=" N VAL L 124 " --> pdb=" O ASN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 150 Processing helix chain 'L' and resid 152 through 159 Processing helix chain 'L' and resid 174 through 203 removed outlier: 3.930A pdb=" N ILE L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR L 202 " --> pdb=" O GLY L 198 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP L 203 " --> pdb=" O ASN L 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 499 Processing helix chain 'O' and resid 461 through 463 No H-bonds generated for 'chain 'O' and resid 461 through 463' Processing helix chain 'O' and resid 474 through 478 removed outlier: 3.617A pdb=" N ASP O 477 " --> pdb=" O LYS O 474 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR O 478 " --> pdb=" O PRO O 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 474 through 478' Processing helix chain 'O' and resid 495 through 497 No H-bonds generated for 'chain 'O' and resid 495 through 497' Processing helix chain 'F' and resid 449 through 452 removed outlier: 3.826A pdb=" N LYS F 452 " --> pdb=" O ASP F 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 449 through 452' Processing helix chain 'F' and resid 474 through 478 removed outlier: 3.521A pdb=" N THR F 478 " --> pdb=" O PRO F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'B' and resid 81 through 83 removed outlier: 4.576A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.562A pdb=" N ASP B 101 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ALA B 135 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 103 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.180A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.379A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.526A pdb=" N ASP E 101 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA E 135 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS E 103 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 96 through 98 removed outlier: 4.013A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR E 205 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASN E 197 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG E 207 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER E 195 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU E 193 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER E 211 " --> pdb=" O HIS E 191 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N HIS E 191 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG E 213 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83 removed outlier: 4.708A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.900A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A 106 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG A 129 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASP A 56 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 49 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 96 through 98 removed outlier: 4.030A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 81 through 83 removed outlier: 4.640A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP D 56 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL D 50 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR D 58 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR D 62 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE D 44 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN D 64 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE D 42 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 66 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET D 40 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ARG D 68 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL D 38 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.520A pdb=" N ASP D 101 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA D 135 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 103 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP D 56 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL D 50 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR D 58 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR D 62 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE D 44 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN D 64 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE D 42 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 66 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N MET D 40 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ARG D 68 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N VAL D 38 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 96 through 98 removed outlier: 4.340A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.319A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 118 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU C 150 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER C 116 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 95 through 98 removed outlier: 4.319A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU C 71 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL C 65 " --> pdb=" O GLU C 71 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR C 73 " --> pdb=" O GLY C 63 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE C 77 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL C 59 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA C 79 " --> pdb=" O MET C 57 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N MET C 57 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR C 81 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR C 55 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N TYR C 83 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE C 53 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N THR C 51 " --> pdb=" O TYR C 181 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N TRP C 183 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N ILE C 53 " --> pdb=" O TRP C 183 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N ARG C 185 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N THR C 55 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SER C 187 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.580A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 205 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 47 through 49 Processing sheet with id=AB8, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AB9, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AC1, first strand: chain 'K' and resid 445 through 447 removed outlier: 6.662A pdb=" N TRP K 423 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA K 437 " --> pdb=" O MET K 421 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET K 421 " --> pdb=" O ALA K 437 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 445 through 447 removed outlier: 6.662A pdb=" N TRP K 423 " --> pdb=" O VAL K 435 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA K 437 " --> pdb=" O MET K 421 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET K 421 " --> pdb=" O ALA K 437 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 2 through 7 Processing sheet with id=AC4, first strand: chain 'O' and resid 445 through 447 removed outlier: 6.530A pdb=" N TRP O 423 " --> pdb=" O VAL O 435 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA O 437 " --> pdb=" O MET O 421 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET O 421 " --> pdb=" O ALA O 437 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR O 501 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 445 through 447 removed outlier: 6.530A pdb=" N TRP O 423 " --> pdb=" O VAL O 435 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA O 437 " --> pdb=" O MET O 421 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET O 421 " --> pdb=" O ALA O 437 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR O 506 " --> pdb=" O TYR O 481 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AC7, first strand: chain 'F' and resid 445 through 447 removed outlier: 6.600A pdb=" N TRP F 423 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA F 437 " --> pdb=" O MET F 421 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET F 421 " --> pdb=" O ALA F 437 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 420 " --> pdb=" O LYS F 486 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2904 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: 3.55 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2833 1.31 - 1.44: 5848 1.44 - 1.57: 10549 1.57 - 1.70: 2 1.70 - 1.83: 185 Bond restraints: 19417 Sorted by residual: bond pdb=" C19 PGW B 503 " pdb=" O03 PGW B 503 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C1 PGW B 503 " pdb=" O01 PGW B 503 " ideal model delta sigma weight residual 1.332 1.415 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" N ASP C 374 " pdb=" CA ASP C 374 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.21e-02 6.83e+03 8.80e+00 bond pdb=" N LEU C 370 " pdb=" CA LEU C 370 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.13e+00 bond pdb=" C19 PGW B 503 " pdb=" C20 PGW B 503 " ideal model delta sigma weight residual 1.501 1.554 -0.053 2.00e-02 2.50e+03 6.98e+00 ... (remaining 19412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 26057 3.32 - 6.63: 294 6.63 - 9.95: 8 9.95 - 13.27: 11 13.27 - 16.59: 1 Bond angle restraints: 26371 Sorted by residual: angle pdb=" CB P1L C 381 " pdb=" SG P1L C 381 " pdb=" C7 P1L C 381 " ideal model delta sigma weight residual 106.10 122.69 -16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" N ASP C 371 " pdb=" CA ASP C 371 " pdb=" C ASP C 371 " ideal model delta sigma weight residual 111.28 105.66 5.62 1.09e+00 8.42e-01 2.66e+01 angle pdb=" CA PHE C 378 " pdb=" CB PHE C 378 " pdb=" CG PHE C 378 " ideal model delta sigma weight residual 113.80 109.10 4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" O11 PGW B 503 " pdb=" P PGW B 503 " pdb=" O12 PGW B 503 " ideal model delta sigma weight residual 98.90 111.79 -12.89 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CB P1L C 385 " pdb=" SG P1L C 385 " pdb=" C7 P1L C 385 " ideal model delta sigma weight residual 106.10 118.97 -12.87 3.00e+00 1.11e-01 1.84e+01 ... (remaining 26366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 11463 29.19 - 58.38: 302 58.38 - 87.57: 77 87.57 - 116.77: 66 116.77 - 145.96: 5 Dihedral angle restraints: 11913 sinusoidal: 5302 harmonic: 6611 Sorted by residual: dihedral pdb=" CB CYS L 159 " pdb=" SG CYS L 159 " pdb=" SG CYS L 171 " pdb=" CB CYS L 171 " ideal model delta sinusoidal sigma weight residual 93.00 179.76 -86.76 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS L 109 " pdb=" SG CYS L 109 " pdb=" SG CYS L 128 " pdb=" CB CYS L 128 " ideal model delta sinusoidal sigma weight residual -86.00 -123.42 37.42 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" O12 PGW B 503 " pdb=" C04 PGW B 503 " pdb=" C05 PGW B 503 " pdb=" OAF PGW B 503 " ideal model delta sinusoidal sigma weight residual 69.27 -144.77 -145.96 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 11910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 3011 0.228 - 0.457: 21 0.457 - 0.685: 2 0.685 - 0.913: 2 0.913 - 1.142: 4 Chirality restraints: 3040 Sorted by residual: chirality pdb=" C1 MAN M 5 " pdb=" O3 MAN M 4 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 1.26 1.14 2.00e-02 2.50e+03 3.26e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.30 -1.10 2.00e-02 2.50e+03 3.05e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-02 2.50e+03 2.89e+03 ... (remaining 3037 not shown) Planarity restraints: 3206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 80 " 0.256 2.00e-02 2.50e+03 2.61e-01 8.54e+02 pdb=" CG ASN A 80 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN A 80 " -0.121 2.00e-02 2.50e+03 pdb=" ND2 ASN A 80 " -0.371 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.337 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 8 " -0.034 2.00e-02 2.50e+03 2.24e-01 6.25e+02 pdb=" CG ASN A 8 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 8 " -0.165 2.00e-02 2.50e+03 pdb=" ND2 ASN A 8 " 0.395 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.250 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " -0.136 2.00e-02 2.50e+03 1.35e-01 2.29e+02 pdb=" CG ASN A 149 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " 0.188 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " -0.174 2.00e-02 2.50e+03 ... (remaining 3203 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 309 2.67 - 3.23: 17706 3.23 - 3.79: 28735 3.79 - 4.34: 41252 4.34 - 4.90: 67964 Nonbonded interactions: 155966 Sorted by model distance: nonbonded pdb=" OE2 GLU B 155 " pdb=" O8 EPE B 502 " model vdw 2.113 3.040 nonbonded pdb=" O LYS C 401 " pdb=" OG SER C 404 " model vdw 2.118 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" O6 NAG A 502 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP A 43 " pdb=" OG1 THR A 176 " model vdw 2.156 3.040 nonbonded pdb=" O SER C 267 " pdb=" OG1 THR C 271 " model vdw 2.177 3.040 ... (remaining 155961 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 'A' and (resid 8 through 65 or resid 67 through 308 or resid 419 through \ 447)) selection = (chain 'B' and (resid 8 through 65 or resid 67 through 308 or resid 419 through \ 447)) selection = (chain 'D' and (resid 8 through 65 or resid 67 through 308 or resid 419 through \ 447)) selection = (chain 'E' and (resid 8 through 65 or resid 67 through 447)) } ncs_group { reference = (chain 'F' and (resid 1 through 9 or resid 405 through 510)) selection = (chain 'K' and (resid 1 through 9 or resid 405 through 510)) selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = (chain 'I' and (resid 2 or resid 5 through 7)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) selection = (chain 'P' and (resid 1 or resid 4 through 6)) } 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=0.50 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: 8.810 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.240 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 19468 Z= 0.259 Angle : 1.261 45.379 26513 Z= 0.515 Chirality : 0.072 1.142 3040 Planarity : 0.005 0.121 3195 Dihedral : 17.443 145.957 7656 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.05 % Allowed : 0.20 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.29 (0.18), residues: 2212 helix: 1.25 (0.20), residues: 715 sheet: 0.09 (0.22), residues: 540 loop : -0.48 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 78 TYR 0.027 0.001 TYR D 299 PHE 0.017 0.001 PHE A 433 TRP 0.026 0.001 TRP E 237 HIS 0.010 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00471 (19417) covalent geometry : angle 0.84928 (26371) SS BOND : bond 0.00606 ( 11) SS BOND : angle 1.98464 ( 22) hydrogen bonds : bond 0.12269 ( 923) hydrogen bonds : angle 5.91589 ( 2904) link_ALPHA1-3 : bond 0.03119 ( 7) link_ALPHA1-3 : angle 8.07241 ( 21) link_ALPHA1-6 : bond 0.02917 ( 5) link_ALPHA1-6 : angle 8.55264 ( 15) link_BETA1-4 : bond 0.02983 ( 17) link_BETA1-4 : angle 14.90439 ( 51) link_NAG-ASN : bond 0.08981 ( 11) link_NAG-ASN : angle 16.73094 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 306 PHE cc_start: 0.8495 (t80) cc_final: 0.7211 (t80) REVERT: B 421 ASN cc_start: 0.6716 (t0) cc_final: 0.6363 (p0) REVERT: D 286 MET cc_start: 0.7656 (mmp) cc_final: 0.7440 (mmm) REVERT: D 307 PHE cc_start: 0.7345 (t80) cc_final: 0.6792 (t80) REVERT: C 415 CYS cc_start: 0.8029 (m) cc_final: 0.7594 (m) REVERT: L 30 THR cc_start: 0.8061 (m) cc_final: 0.7842 (t) REVERT: L 126 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8612 (mttp) REVERT: L 153 GLU cc_start: 0.8179 (tp30) cc_final: 0.7850 (pt0) REVERT: K 3 GLN cc_start: 0.7946 (mp10) cc_final: 0.7474 (mp10) REVERT: O 5 VAL cc_start: 0.9087 (p) cc_final: 0.8875 (t) REVERT: O 6 GLU cc_start: 0.8271 (pm20) cc_final: 0.7959 (pm20) REVERT: O 467 TYR cc_start: 0.7757 (m-80) cc_final: 0.7156 (m-80) REVERT: O 504 GLN cc_start: 0.7674 (pm20) cc_final: 0.7340 (pm20) REVERT: F 464 ASN cc_start: 0.8284 (t0) cc_final: 0.7912 (t0) REVERT: F 469 GLU cc_start: 0.7858 (pm20) cc_final: 0.7546 (pm20) outliers start: 1 outliers final: 1 residues processed: 406 average time/residue: 0.5008 time to fit residues: 230.8215 Evaluate side-chains 309 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 247 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN H 690 ASN L 186 ASN ** L 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 471 ASN F 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.110845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073705 restraints weight = 38613.388| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.73 r_work: 0.2803 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19468 Z= 0.161 Angle : 0.688 10.960 26513 Z= 0.331 Chirality : 0.046 0.249 3040 Planarity : 0.004 0.041 3195 Dihedral : 15.011 145.038 3522 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.92 % Allowed : 10.75 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.57 (0.18), residues: 2212 helix: 1.59 (0.19), residues: 709 sheet: 0.41 (0.22), residues: 538 loop : -0.50 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 250 TYR 0.031 0.002 TYR E 299 PHE 0.027 0.002 PHE A 307 TRP 0.022 0.001 TRP E 237 HIS 0.008 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00370 (19417) covalent geometry : angle 0.65357 (26371) SS BOND : bond 0.00298 ( 11) SS BOND : angle 0.81295 ( 22) hydrogen bonds : bond 0.04175 ( 923) hydrogen bonds : angle 4.68135 ( 2904) link_ALPHA1-3 : bond 0.00837 ( 7) link_ALPHA1-3 : angle 2.30050 ( 21) link_ALPHA1-6 : bond 0.00526 ( 5) link_ALPHA1-6 : angle 2.20655 ( 15) link_BETA1-4 : bond 0.00546 ( 17) link_BETA1-4 : angle 2.83512 ( 51) link_NAG-ASN : bond 0.00750 ( 11) link_NAG-ASN : angle 4.57976 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 330 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 421 ASN cc_start: 0.6358 (t0) cc_final: 0.5872 (p0) REVERT: E 299 TYR cc_start: 0.8351 (t80) cc_final: 0.8071 (t80) REVERT: D 307 PHE cc_start: 0.7406 (t80) cc_final: 0.6766 (t80) REVERT: D 444 LEU cc_start: 0.8751 (tt) cc_final: 0.8350 (mt) REVERT: C 415 CYS cc_start: 0.8266 (m) cc_final: 0.7893 (m) REVERT: L 30 THR cc_start: 0.8055 (m) cc_final: 0.7797 (t) REVERT: L 64 TYR cc_start: 0.7239 (p90) cc_final: 0.6723 (p90) REVERT: L 83 ASP cc_start: 0.7935 (t0) cc_final: 0.7663 (t0) REVERT: L 101 LEU cc_start: 0.9122 (mp) cc_final: 0.8914 (mp) REVERT: L 126 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8463 (mttm) REVERT: L 153 GLU cc_start: 0.8229 (tp30) cc_final: 0.7970 (pt0) REVERT: K 3 GLN cc_start: 0.8071 (mp10) cc_final: 0.7465 (mp10) REVERT: K 433 GLU cc_start: 0.8664 (pt0) cc_final: 0.8345 (pt0) REVERT: K 474 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7837 (mptt) REVERT: K 477 ASP cc_start: 0.7328 (m-30) cc_final: 0.7098 (m-30) REVERT: O 5 VAL cc_start: 0.9217 (p) cc_final: 0.8875 (t) REVERT: O 6 GLU cc_start: 0.8420 (pm20) cc_final: 0.7935 (pm20) REVERT: O 432 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6744 (mtp180) REVERT: O 474 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8073 (mptt) REVERT: O 504 GLN cc_start: 0.7861 (pm20) cc_final: 0.7300 (pm20) REVERT: F 464 ASN cc_start: 0.8473 (t0) cc_final: 0.7810 (t0) REVERT: F 469 GLU cc_start: 0.8235 (pm20) cc_final: 0.7754 (pm20) REVERT: F 472 ASN cc_start: 0.8533 (p0) cc_final: 0.8130 (p0) outliers start: 38 outliers final: 22 residues processed: 342 average time/residue: 0.4524 time to fit residues: 178.0669 Evaluate side-chains 333 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain L residue 202 THR Chi-restraints excluded: chain O residue 432 ARG Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 509 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 157 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 185 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN A 224 GLN C 128 ASN H 690 ASN L 186 ASN ** L 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 471 ASN F 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.073057 restraints weight = 56554.281| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.24 r_work: 0.2784 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19468 Z= 0.127 Angle : 0.633 11.102 26513 Z= 0.305 Chirality : 0.045 0.256 3040 Planarity : 0.003 0.035 3195 Dihedral : 12.060 146.866 3520 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.12 % Allowed : 12.87 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.71 (0.18), residues: 2212 helix: 1.66 (0.19), residues: 710 sheet: 0.58 (0.22), residues: 540 loop : -0.45 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 78 TYR 0.023 0.001 TYR E 299 PHE 0.025 0.001 PHE C 304 TRP 0.020 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd covalent geometry : bond 0.00284 (19417) covalent geometry : angle 0.60220 (26371) SS BOND : bond 0.00261 ( 11) SS BOND : angle 0.62974 ( 22) hydrogen bonds : bond 0.03763 ( 923) hydrogen bonds : angle 4.41994 ( 2904) link_ALPHA1-3 : bond 0.00931 ( 7) link_ALPHA1-3 : angle 1.89030 ( 21) link_ALPHA1-6 : bond 0.00618 ( 5) link_ALPHA1-6 : angle 2.09752 ( 15) link_BETA1-4 : bond 0.00477 ( 17) link_BETA1-4 : angle 2.50824 ( 51) link_NAG-ASN : bond 0.00766 ( 11) link_NAG-ASN : angle 4.17073 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 323 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7755 (mmt) REVERT: B 268 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8064 (mm) REVERT: B 421 ASN cc_start: 0.6274 (t0) cc_final: 0.5886 (p0) REVERT: E 299 TYR cc_start: 0.8422 (t80) cc_final: 0.8093 (t80) REVERT: A 224 GLN cc_start: 0.8597 (tp40) cc_final: 0.8313 (tp40) REVERT: A 285 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8081 (mm) REVERT: D 294 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7565 (mp) REVERT: D 444 LEU cc_start: 0.8680 (tt) cc_final: 0.8310 (tp) REVERT: C 415 CYS cc_start: 0.8186 (m) cc_final: 0.7805 (m) REVERT: L 101 LEU cc_start: 0.9110 (mp) cc_final: 0.8902 (mp) REVERT: L 126 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8360 (mttm) REVERT: L 154 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7906 (t) REVERT: L 158 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6647 (pmm) REVERT: K 3 GLN cc_start: 0.8048 (mp10) cc_final: 0.7455 (mp10) REVERT: K 433 GLU cc_start: 0.8562 (pt0) cc_final: 0.8247 (pt0) REVERT: K 460 ASP cc_start: 0.7716 (t70) cc_final: 0.7493 (p0) REVERT: K 474 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7880 (mptt) REVERT: O 5 VAL cc_start: 0.9187 (p) cc_final: 0.8847 (t) REVERT: O 6 GLU cc_start: 0.8390 (pm20) cc_final: 0.7756 (pm20) REVERT: O 406 ARG cc_start: 0.7740 (ttp-170) cc_final: 0.7051 (ttp80) REVERT: O 407 LEU cc_start: 0.8129 (mp) cc_final: 0.7783 (mt) REVERT: O 432 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6702 (mtp180) REVERT: O 472 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8101 (t0) REVERT: O 474 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7610 (mptt) REVERT: O 477 ASP cc_start: 0.7786 (m-30) cc_final: 0.7390 (m-30) REVERT: O 504 GLN cc_start: 0.7854 (pm20) cc_final: 0.7295 (pm20) REVERT: F 460 ASP cc_start: 0.7898 (t70) cc_final: 0.7657 (t0) REVERT: F 464 ASN cc_start: 0.8456 (t0) cc_final: 0.7827 (t0) REVERT: F 469 GLU cc_start: 0.8228 (pm20) cc_final: 0.7768 (pm20) REVERT: F 472 ASN cc_start: 0.8387 (p0) cc_final: 0.8107 (p0) outliers start: 42 outliers final: 16 residues processed: 340 average time/residue: 0.4276 time to fit residues: 168.4120 Evaluate side-chains 329 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain K residue 421 MET Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain O residue 432 ARG Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 421 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 201 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 217 optimal weight: 10.0000 chunk 136 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN D 41 ASN L 186 ASN L 199 ASN K 414 HIS O 471 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.111476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.073472 restraints weight = 57409.616| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.26 r_work: 0.2792 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19468 Z= 0.122 Angle : 0.612 9.704 26513 Z= 0.300 Chirality : 0.045 0.251 3040 Planarity : 0.003 0.035 3195 Dihedral : 10.306 145.639 3520 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.42 % Allowed : 13.58 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.80 (0.18), residues: 2212 helix: 1.61 (0.19), residues: 710 sheet: 0.80 (0.22), residues: 534 loop : -0.40 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.023 0.001 TYR E 299 PHE 0.023 0.001 PHE L 29 TRP 0.022 0.001 TRP L 150 HIS 0.003 0.001 HIS O 414 Details of bonding type rmsd covalent geometry : bond 0.00273 (19417) covalent geometry : angle 0.58825 (26371) SS BOND : bond 0.00310 ( 11) SS BOND : angle 1.33457 ( 22) hydrogen bonds : bond 0.03696 ( 923) hydrogen bonds : angle 4.32463 ( 2904) link_ALPHA1-3 : bond 0.00986 ( 7) link_ALPHA1-3 : angle 1.87214 ( 21) link_ALPHA1-6 : bond 0.00707 ( 5) link_ALPHA1-6 : angle 2.00148 ( 15) link_BETA1-4 : bond 0.00469 ( 17) link_BETA1-4 : angle 2.12929 ( 51) link_NAG-ASN : bond 0.00711 ( 11) link_NAG-ASN : angle 3.53076 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 325 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7739 (mmt) REVERT: B 268 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8057 (mm) REVERT: B 421 ASN cc_start: 0.6204 (t0) cc_final: 0.5983 (p0) REVERT: A 14 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8527 (tp30) REVERT: A 215 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8616 (mtpp) REVERT: A 285 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8127 (mm) REVERT: D 444 LEU cc_start: 0.8668 (tt) cc_final: 0.8316 (tp) REVERT: C 415 CYS cc_start: 0.8133 (m) cc_final: 0.7768 (m) REVERT: L 83 ASP cc_start: 0.7897 (t0) cc_final: 0.7696 (t0) REVERT: L 126 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8413 (mttm) REVERT: L 153 GLU cc_start: 0.8169 (tp30) cc_final: 0.7887 (pt0) REVERT: L 154 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7910 (t) REVERT: L 158 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6628 (pmm) REVERT: K 3 GLN cc_start: 0.8026 (mp10) cc_final: 0.7407 (mp10) REVERT: K 474 LYS cc_start: 0.8166 (mmtm) cc_final: 0.7911 (mptt) REVERT: O 5 VAL cc_start: 0.9183 (p) cc_final: 0.8886 (t) REVERT: O 6 GLU cc_start: 0.8328 (pm20) cc_final: 0.7644 (pm20) REVERT: O 406 ARG cc_start: 0.7708 (ttp-170) cc_final: 0.7081 (ttp80) REVERT: O 432 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.6663 (mtp180) REVERT: O 447 TYR cc_start: 0.8888 (m-80) cc_final: 0.8669 (m-80) REVERT: O 472 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8054 (t0) REVERT: O 474 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7893 (mptt) REVERT: O 504 GLN cc_start: 0.7827 (pm20) cc_final: 0.7250 (pm20) REVERT: F 463 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8287 (tptp) REVERT: F 464 ASN cc_start: 0.8456 (t0) cc_final: 0.7815 (t0) REVERT: F 469 GLU cc_start: 0.8216 (pm20) cc_final: 0.7734 (pm20) REVERT: F 472 ASN cc_start: 0.8367 (p0) cc_final: 0.8053 (p0) outliers start: 48 outliers final: 16 residues processed: 341 average time/residue: 0.4577 time to fit residues: 178.8373 Evaluate side-chains 322 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 299 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain O residue 432 ARG Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 470 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 217 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN L 132 GLN L 186 ASN K 414 HIS O 471 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.112125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.074337 restraints weight = 52040.856| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.16 r_work: 0.2800 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19468 Z= 0.123 Angle : 0.599 9.538 26513 Z= 0.296 Chirality : 0.044 0.247 3040 Planarity : 0.003 0.036 3195 Dihedral : 9.435 144.949 3520 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.07 % Allowed : 15.19 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.86 (0.18), residues: 2212 helix: 1.61 (0.20), residues: 712 sheet: 0.93 (0.22), residues: 528 loop : -0.38 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 213 TYR 0.025 0.001 TYR E 299 PHE 0.029 0.001 PHE L 29 TRP 0.022 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd covalent geometry : bond 0.00280 (19417) covalent geometry : angle 0.57773 (26371) SS BOND : bond 0.00344 ( 11) SS BOND : angle 0.90753 ( 22) hydrogen bonds : bond 0.03564 ( 923) hydrogen bonds : angle 4.23121 ( 2904) link_ALPHA1-3 : bond 0.00925 ( 7) link_ALPHA1-3 : angle 1.79340 ( 21) link_ALPHA1-6 : bond 0.00780 ( 5) link_ALPHA1-6 : angle 1.93193 ( 15) link_BETA1-4 : bond 0.00468 ( 17) link_BETA1-4 : angle 1.91058 ( 51) link_NAG-ASN : bond 0.00685 ( 11) link_NAG-ASN : angle 3.35644 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8414 (mt0) REVERT: B 227 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7787 (mmt) REVERT: B 268 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8060 (mm) REVERT: E 61 MET cc_start: 0.9312 (ptt) cc_final: 0.8923 (ptt) REVERT: E 190 GLU cc_start: 0.8297 (tt0) cc_final: 0.7994 (tt0) REVERT: A 14 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8510 (tp30) REVERT: A 215 LYS cc_start: 0.8935 (ttmt) cc_final: 0.8644 (mtpp) REVERT: A 285 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8170 (mm) REVERT: D 294 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7457 (mp) REVERT: D 444 LEU cc_start: 0.8685 (tt) cc_final: 0.8324 (tp) REVERT: C 415 CYS cc_start: 0.8176 (m) cc_final: 0.7788 (m) REVERT: L 126 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8504 (mttm) REVERT: L 153 GLU cc_start: 0.8136 (tp30) cc_final: 0.7874 (pt0) REVERT: L 154 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7935 (t) REVERT: L 158 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6644 (pmm) REVERT: K 3 GLN cc_start: 0.8073 (mp10) cc_final: 0.7379 (mp10) REVERT: K 460 ASP cc_start: 0.6927 (p0) cc_final: 0.6432 (t70) REVERT: K 474 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7946 (mptt) REVERT: O 5 VAL cc_start: 0.9198 (p) cc_final: 0.8904 (t) REVERT: O 6 GLU cc_start: 0.8287 (pm20) cc_final: 0.7648 (pm20) REVERT: O 406 ARG cc_start: 0.7710 (ttp-170) cc_final: 0.7112 (ttp80) REVERT: O 432 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.6691 (mtp180) REVERT: O 467 TYR cc_start: 0.8536 (m-80) cc_final: 0.8190 (m-80) REVERT: O 472 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8072 (t0) REVERT: O 504 GLN cc_start: 0.7965 (pm20) cc_final: 0.7351 (pm20) REVERT: F 464 ASN cc_start: 0.8438 (t0) cc_final: 0.7823 (t0) REVERT: F 469 GLU cc_start: 0.8191 (pm20) cc_final: 0.7761 (pm20) REVERT: F 472 ASN cc_start: 0.8333 (p0) cc_final: 0.8003 (p0) outliers start: 41 outliers final: 19 residues processed: 330 average time/residue: 0.4185 time to fit residues: 159.8561 Evaluate side-chains 326 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain O residue 432 ARG Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 470 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 140 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN A 224 GLN L 186 ASN K 414 HIS O 471 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.073437 restraints weight = 60503.909| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.38 r_work: 0.2777 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19468 Z= 0.133 Angle : 0.589 8.739 26513 Z= 0.295 Chirality : 0.044 0.243 3040 Planarity : 0.003 0.037 3195 Dihedral : 9.035 143.777 3520 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.07 % Allowed : 15.60 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.89 (0.18), residues: 2212 helix: 1.62 (0.19), residues: 712 sheet: 0.92 (0.22), residues: 528 loop : -0.33 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 213 TYR 0.024 0.001 TYR E 299 PHE 0.027 0.001 PHE L 29 TRP 0.025 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd covalent geometry : bond 0.00303 (19417) covalent geometry : angle 0.56940 (26371) SS BOND : bond 0.00320 ( 11) SS BOND : angle 0.56934 ( 22) hydrogen bonds : bond 0.03566 ( 923) hydrogen bonds : angle 4.22225 ( 2904) link_ALPHA1-3 : bond 0.00926 ( 7) link_ALPHA1-3 : angle 1.78899 ( 21) link_ALPHA1-6 : bond 0.00681 ( 5) link_ALPHA1-6 : angle 1.58448 ( 15) link_BETA1-4 : bond 0.00440 ( 17) link_BETA1-4 : angle 1.84482 ( 51) link_NAG-ASN : bond 0.00657 ( 11) link_NAG-ASN : angle 3.29842 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 307 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 185 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8431 (mt0) REVERT: B 227 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7831 (mmt) REVERT: B 268 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8080 (mm) REVERT: E 61 MET cc_start: 0.9327 (ptt) cc_final: 0.8958 (ptt) REVERT: E 190 GLU cc_start: 0.8337 (tt0) cc_final: 0.8035 (tt0) REVERT: A 14 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8538 (tp30) REVERT: A 215 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8662 (mtpp) REVERT: A 285 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8205 (mm) REVERT: D 294 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7469 (mp) REVERT: D 444 LEU cc_start: 0.8677 (tt) cc_final: 0.8312 (tp) REVERT: C 415 CYS cc_start: 0.8219 (m) cc_final: 0.7820 (m) REVERT: L 83 ASP cc_start: 0.8069 (t0) cc_final: 0.7835 (t0) REVERT: L 126 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8449 (mttm) REVERT: L 153 GLU cc_start: 0.8110 (tp30) cc_final: 0.7856 (pt0) REVERT: L 154 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7927 (t) REVERT: L 158 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6703 (pmm) REVERT: K 3 GLN cc_start: 0.8109 (mp10) cc_final: 0.7403 (mp10) REVERT: K 460 ASP cc_start: 0.6925 (p0) cc_final: 0.6532 (p0) REVERT: K 461 ASN cc_start: 0.7736 (m-40) cc_final: 0.7209 (m-40) REVERT: K 474 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7869 (tppt) REVERT: O 5 VAL cc_start: 0.9171 (p) cc_final: 0.8894 (t) REVERT: O 6 GLU cc_start: 0.8275 (pm20) cc_final: 0.7611 (pm20) REVERT: O 406 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7144 (ttp80) REVERT: O 432 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6713 (mtp180) REVERT: O 472 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8020 (t0) REVERT: O 504 GLN cc_start: 0.7959 (pm20) cc_final: 0.7330 (pm20) REVERT: F 464 ASN cc_start: 0.8477 (t0) cc_final: 0.7866 (t0) REVERT: F 469 GLU cc_start: 0.8172 (pm20) cc_final: 0.7758 (pm20) REVERT: F 472 ASN cc_start: 0.8323 (p0) cc_final: 0.7987 (p0) REVERT: F 504 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7681 (mp10) outliers start: 41 outliers final: 19 residues processed: 324 average time/residue: 0.4373 time to fit residues: 162.5956 Evaluate side-chains 321 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 294 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain O residue 432 ARG Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 466 VAL Chi-restraints excluded: chain F residue 470 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 106 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN A 224 GLN L 186 ASN K 414 HIS O 471 ASN O 507 GLN F 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.071774 restraints weight = 53339.336| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.19 r_work: 0.2749 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19468 Z= 0.177 Angle : 0.626 10.262 26513 Z= 0.312 Chirality : 0.046 0.230 3040 Planarity : 0.004 0.039 3195 Dihedral : 9.036 140.212 3520 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.68 % Allowed : 15.50 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.84 (0.18), residues: 2212 helix: 1.58 (0.19), residues: 712 sheet: 0.85 (0.22), residues: 542 loop : -0.35 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.026 0.002 TYR B 244 PHE 0.024 0.002 PHE L 59 TRP 0.032 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd covalent geometry : bond 0.00415 (19417) covalent geometry : angle 0.60671 (26371) SS BOND : bond 0.00499 ( 11) SS BOND : angle 0.76562 ( 22) hydrogen bonds : bond 0.03863 ( 923) hydrogen bonds : angle 4.33180 ( 2904) link_ALPHA1-3 : bond 0.00944 ( 7) link_ALPHA1-3 : angle 1.83418 ( 21) link_ALPHA1-6 : bond 0.00602 ( 5) link_ALPHA1-6 : angle 1.63571 ( 15) link_BETA1-4 : bond 0.00439 ( 17) link_BETA1-4 : angle 1.94770 ( 51) link_NAG-ASN : bond 0.00670 ( 11) link_NAG-ASN : angle 3.26484 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7779 (mmt) REVERT: E 190 GLU cc_start: 0.8378 (tt0) cc_final: 0.8053 (tt0) REVERT: A 14 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8533 (tp30) REVERT: A 215 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8659 (mtpp) REVERT: A 224 GLN cc_start: 0.8526 (tp40) cc_final: 0.8277 (tp40) REVERT: A 285 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8233 (mm) REVERT: D 294 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7472 (mp) REVERT: D 444 LEU cc_start: 0.8672 (tt) cc_final: 0.8309 (tp) REVERT: C 415 CYS cc_start: 0.8181 (m) cc_final: 0.7773 (m) REVERT: L 83 ASP cc_start: 0.8176 (t0) cc_final: 0.7911 (t0) REVERT: L 126 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8443 (mttm) REVERT: L 153 GLU cc_start: 0.8119 (tp30) cc_final: 0.7857 (pt0) REVERT: L 154 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7906 (t) REVERT: L 158 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6708 (pmm) REVERT: K 3 GLN cc_start: 0.8152 (mp10) cc_final: 0.7433 (mp10) REVERT: K 463 LYS cc_start: 0.8722 (pttt) cc_final: 0.8027 (tttp) REVERT: O 5 VAL cc_start: 0.9220 (p) cc_final: 0.8923 (t) REVERT: O 6 GLU cc_start: 0.8300 (pm20) cc_final: 0.7495 (pm20) REVERT: O 406 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7224 (ttp80) REVERT: O 432 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6624 (mtp180) REVERT: O 460 ASP cc_start: 0.6605 (p0) cc_final: 0.6166 (p0) REVERT: O 467 TYR cc_start: 0.8682 (m-80) cc_final: 0.8007 (m-80) REVERT: O 472 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7885 (t0) REVERT: O 504 GLN cc_start: 0.7955 (pm20) cc_final: 0.7121 (pm20) REVERT: F 464 ASN cc_start: 0.8483 (t0) cc_final: 0.7818 (t0) REVERT: F 469 GLU cc_start: 0.8189 (pm20) cc_final: 0.7804 (pm20) REVERT: F 472 ASN cc_start: 0.8339 (p0) cc_final: 0.8027 (p0) REVERT: F 504 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7647 (mp10) outliers start: 53 outliers final: 23 residues processed: 330 average time/residue: 0.4522 time to fit residues: 171.7285 Evaluate side-chains 320 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain O residue 432 ARG Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 465 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 466 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 18 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 217 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN A 265 ASN D 243 ASN C 396 HIS L 132 GLN L 186 ASN K 414 HIS O 414 HIS O 471 ASN F 3 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.072462 restraints weight = 55193.330| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.26 r_work: 0.2762 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19468 Z= 0.145 Angle : 0.620 14.624 26513 Z= 0.309 Chirality : 0.045 0.227 3040 Planarity : 0.003 0.038 3195 Dihedral : 8.787 132.439 3520 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.37 % Allowed : 16.36 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.84 (0.18), residues: 2212 helix: 1.56 (0.19), residues: 712 sheet: 0.86 (0.22), residues: 542 loop : -0.33 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.024 0.002 TYR E 299 PHE 0.033 0.001 PHE L 59 TRP 0.035 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd covalent geometry : bond 0.00335 (19417) covalent geometry : angle 0.60287 (26371) SS BOND : bond 0.00285 ( 11) SS BOND : angle 0.59086 ( 22) hydrogen bonds : bond 0.03698 ( 923) hydrogen bonds : angle 4.28696 ( 2904) link_ALPHA1-3 : bond 0.00881 ( 7) link_ALPHA1-3 : angle 1.75272 ( 21) link_ALPHA1-6 : bond 0.00665 ( 5) link_ALPHA1-6 : angle 1.54934 ( 15) link_BETA1-4 : bond 0.00433 ( 17) link_BETA1-4 : angle 1.78802 ( 51) link_NAG-ASN : bond 0.00631 ( 11) link_NAG-ASN : angle 3.15843 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7798 (mmt) REVERT: E 190 GLU cc_start: 0.8376 (tt0) cc_final: 0.8052 (tt0) REVERT: A 285 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8247 (mm) REVERT: D 294 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7481 (mp) REVERT: D 444 LEU cc_start: 0.8702 (tt) cc_final: 0.8326 (tp) REVERT: C 415 CYS cc_start: 0.8235 (m) cc_final: 0.7832 (m) REVERT: L 53 THR cc_start: 0.6544 (p) cc_final: 0.6249 (p) REVERT: L 83 ASP cc_start: 0.8178 (t0) cc_final: 0.7908 (t0) REVERT: L 126 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8462 (mttm) REVERT: L 153 GLU cc_start: 0.8130 (tp30) cc_final: 0.7881 (pt0) REVERT: L 154 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7897 (t) REVERT: L 158 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6733 (pmm) REVERT: K 3 GLN cc_start: 0.8137 (mp10) cc_final: 0.7422 (mp10) REVERT: K 6 GLU cc_start: 0.7611 (pm20) cc_final: 0.7235 (pm20) REVERT: K 460 ASP cc_start: 0.6713 (p0) cc_final: 0.6447 (p0) REVERT: K 467 TYR cc_start: 0.8188 (m-80) cc_final: 0.7923 (m-80) REVERT: K 508 VAL cc_start: 0.7294 (t) cc_final: 0.6963 (p) REVERT: O 5 VAL cc_start: 0.9221 (p) cc_final: 0.8922 (t) REVERT: O 6 GLU cc_start: 0.8224 (pm20) cc_final: 0.7557 (pm20) REVERT: O 406 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7226 (ttp80) REVERT: O 432 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6621 (mtp180) REVERT: O 460 ASP cc_start: 0.6525 (p0) cc_final: 0.6000 (p0) REVERT: O 467 TYR cc_start: 0.8673 (m-80) cc_final: 0.7961 (m-80) REVERT: O 472 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7827 (t0) REVERT: O 504 GLN cc_start: 0.7894 (pm20) cc_final: 0.6972 (pm20) REVERT: F 464 ASN cc_start: 0.8500 (t0) cc_final: 0.7850 (t0) REVERT: F 469 GLU cc_start: 0.8174 (pm20) cc_final: 0.7815 (pm20) REVERT: F 472 ASN cc_start: 0.8341 (p0) cc_final: 0.8002 (p0) REVERT: F 504 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7674 (mp10) outliers start: 47 outliers final: 24 residues processed: 323 average time/residue: 0.4563 time to fit residues: 169.8376 Evaluate side-chains 324 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain O residue 432 ARG Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 466 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 124 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 210 optimal weight: 0.0980 chunk 174 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN L 132 GLN L 186 ASN K 414 HIS O 471 ASN F 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.111618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.073264 restraints weight = 55585.544| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.27 r_work: 0.2781 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19468 Z= 0.124 Angle : 0.625 14.291 26513 Z= 0.311 Chirality : 0.045 0.251 3040 Planarity : 0.003 0.038 3195 Dihedral : 8.463 125.065 3520 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.82 % Allowed : 17.31 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.87 (0.18), residues: 2212 helix: 1.55 (0.19), residues: 711 sheet: 0.93 (0.22), residues: 538 loop : -0.32 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.028 0.001 TYR B 244 PHE 0.037 0.001 PHE L 59 TRP 0.042 0.001 TRP L 150 HIS 0.003 0.001 HIS K 414 Details of bonding type rmsd covalent geometry : bond 0.00278 (19417) covalent geometry : angle 0.60684 (26371) SS BOND : bond 0.00330 ( 11) SS BOND : angle 1.84496 ( 22) hydrogen bonds : bond 0.03639 ( 923) hydrogen bonds : angle 4.26577 ( 2904) link_ALPHA1-3 : bond 0.00825 ( 7) link_ALPHA1-3 : angle 1.68465 ( 21) link_ALPHA1-6 : bond 0.00718 ( 5) link_ALPHA1-6 : angle 1.52181 ( 15) link_BETA1-4 : bond 0.00462 ( 17) link_BETA1-4 : angle 1.68427 ( 51) link_NAG-ASN : bond 0.00628 ( 11) link_NAG-ASN : angle 3.10605 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 300 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7772 (mmt) REVERT: E 190 GLU cc_start: 0.8355 (tt0) cc_final: 0.8068 (tt0) REVERT: A 14 GLU cc_start: 0.8853 (tp30) cc_final: 0.8559 (mm-30) REVERT: A 285 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8236 (mm) REVERT: D 444 LEU cc_start: 0.8696 (tt) cc_final: 0.8321 (tp) REVERT: C 415 CYS cc_start: 0.8176 (m) cc_final: 0.7810 (m) REVERT: L 53 THR cc_start: 0.6352 (p) cc_final: 0.6052 (p) REVERT: L 83 ASP cc_start: 0.8162 (t0) cc_final: 0.7887 (t0) REVERT: L 126 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8418 (mttt) REVERT: L 153 GLU cc_start: 0.8133 (tp30) cc_final: 0.7880 (pt0) REVERT: L 154 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7932 (t) REVERT: L 158 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6731 (pmm) REVERT: K 3 GLN cc_start: 0.8168 (mp10) cc_final: 0.7457 (mp10) REVERT: O 5 VAL cc_start: 0.9218 (p) cc_final: 0.8915 (t) REVERT: O 6 GLU cc_start: 0.8179 (pm20) cc_final: 0.7529 (pm20) REVERT: O 406 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7231 (ttp80) REVERT: O 407 LEU cc_start: 0.8207 (mp) cc_final: 0.7877 (mt) REVERT: O 460 ASP cc_start: 0.6539 (p0) cc_final: 0.6001 (p0) REVERT: O 467 TYR cc_start: 0.8648 (m-80) cc_final: 0.7966 (m-80) REVERT: O 472 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7789 (t0) REVERT: O 504 GLN cc_start: 0.7863 (pm20) cc_final: 0.6919 (pm20) REVERT: F 464 ASN cc_start: 0.8472 (t0) cc_final: 0.7824 (t0) REVERT: F 469 GLU cc_start: 0.8156 (pm20) cc_final: 0.7798 (pm20) REVERT: F 472 ASN cc_start: 0.8342 (p0) cc_final: 0.8003 (p0) REVERT: F 504 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7651 (mp10) outliers start: 36 outliers final: 21 residues processed: 318 average time/residue: 0.4323 time to fit residues: 159.1262 Evaluate side-chains 318 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 101 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 217 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 105 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 GLN L 186 ASN K 414 HIS K 472 ASN O 471 ASN F 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.072444 restraints weight = 47577.429| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.01 r_work: 0.2768 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 19468 Z= 0.175 Angle : 0.651 13.667 26513 Z= 0.328 Chirality : 0.046 0.294 3040 Planarity : 0.004 0.039 3195 Dihedral : 8.495 112.923 3520 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.72 % Allowed : 17.26 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.80 (0.18), residues: 2212 helix: 1.49 (0.20), residues: 712 sheet: 0.85 (0.22), residues: 544 loop : -0.33 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.024 0.002 TYR E 299 PHE 0.035 0.002 PHE L 59 TRP 0.047 0.001 TRP L 150 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00411 (19417) covalent geometry : angle 0.63230 (26371) SS BOND : bond 0.00933 ( 11) SS BOND : angle 2.01310 ( 22) hydrogen bonds : bond 0.03894 ( 923) hydrogen bonds : angle 4.41825 ( 2904) link_ALPHA1-3 : bond 0.00816 ( 7) link_ALPHA1-3 : angle 1.73180 ( 21) link_ALPHA1-6 : bond 0.00627 ( 5) link_ALPHA1-6 : angle 1.58454 ( 15) link_BETA1-4 : bond 0.00438 ( 17) link_BETA1-4 : angle 1.85898 ( 51) link_NAG-ASN : bond 0.00625 ( 11) link_NAG-ASN : angle 3.13258 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4424 Ramachandran restraints generated. 2212 Oldfield, 0 Emsley, 2212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7777 (mmt) REVERT: B 244 TYR cc_start: 0.7749 (p90) cc_final: 0.7472 (p90) REVERT: E 190 GLU cc_start: 0.8354 (tt0) cc_final: 0.8024 (tt0) REVERT: E 229 SER cc_start: 0.8453 (m) cc_final: 0.8236 (p) REVERT: A 14 GLU cc_start: 0.8872 (tp30) cc_final: 0.8573 (mm-30) REVERT: A 285 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8276 (mm) REVERT: D 444 LEU cc_start: 0.8696 (tt) cc_final: 0.8314 (tp) REVERT: C 415 CYS cc_start: 0.8180 (m) cc_final: 0.7768 (m) REVERT: L 53 THR cc_start: 0.6390 (p) cc_final: 0.6125 (p) REVERT: L 83 ASP cc_start: 0.8253 (t0) cc_final: 0.7957 (t0) REVERT: L 153 GLU cc_start: 0.8147 (tp30) cc_final: 0.7881 (pt0) REVERT: L 154 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7869 (t) REVERT: L 158 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6760 (pmm) REVERT: K 3 GLN cc_start: 0.8187 (mp10) cc_final: 0.7467 (mp10) REVERT: K 463 LYS cc_start: 0.8686 (pttt) cc_final: 0.8193 (tttp) REVERT: O 5 VAL cc_start: 0.9216 (p) cc_final: 0.8955 (t) REVERT: O 6 GLU cc_start: 0.8165 (pm20) cc_final: 0.7342 (pm20) REVERT: O 406 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7228 (ttp80) REVERT: O 460 ASP cc_start: 0.6665 (p0) cc_final: 0.6118 (p0) REVERT: O 467 TYR cc_start: 0.8634 (m-80) cc_final: 0.7943 (m-80) REVERT: O 472 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7782 (t0) REVERT: O 477 ASP cc_start: 0.7534 (m-30) cc_final: 0.7333 (m-30) REVERT: O 504 GLN cc_start: 0.7827 (pm20) cc_final: 0.6881 (pm20) REVERT: F 406 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7694 (tmm-80) REVERT: F 464 ASN cc_start: 0.8491 (t0) cc_final: 0.7837 (t0) REVERT: F 469 GLU cc_start: 0.8163 (pm20) cc_final: 0.7845 (pm20) REVERT: F 472 ASN cc_start: 0.8328 (p0) cc_final: 0.7976 (p0) REVERT: F 504 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7662 (mp10) outliers start: 34 outliers final: 21 residues processed: 311 average time/residue: 0.4602 time to fit residues: 164.4995 Evaluate side-chains 318 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain H residue 674 THR Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 189 ILE Chi-restraints excluded: chain O residue 450 SER Chi-restraints excluded: chain O residue 456 THR Chi-restraints excluded: chain O residue 472 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 406 ARG Chi-restraints excluded: chain F residue 421 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 211 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 163 optimal weight: 0.0020 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN E 265 ASN A 224 GLN L 132 GLN L 186 ASN K 414 HIS O 471 ASN F 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.110403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.072524 restraints weight = 54690.428| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.18 r_work: 0.2774 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19468 Z= 0.140 Angle : 0.640 13.703 26513 Z= 0.322 Chirality : 0.045 0.246 3040 Planarity : 0.003 0.039 3195 Dihedral : 8.333 100.515 3520 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.36 % Allowed : 17.87 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.02 % Cis-general : 0.23 % 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 aren not related in a simple way. whole: 0.82 (0.18), residues: 2212 helix: 1.55 (0.20), residues: 699 sheet: 0.85 (0.22), residues: 544 loop : -0.33 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 428 TYR 0.023 0.001 TYR E 299 PHE 0.033 0.001 PHE L 59 TRP 0.058 0.001 TRP L 150 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00323 (19417) covalent geometry : angle 0.62370 (26371) SS BOND : bond 0.00527 ( 11) SS BOND : angle 1.63753 ( 22) hydrogen bonds : bond 0.03818 ( 923) hydrogen bonds : angle 4.36414 ( 2904) link_ALPHA1-3 : bond 0.00838 ( 7) link_ALPHA1-3 : angle 1.69417 ( 21) link_ALPHA1-6 : bond 0.00687 ( 5) link_ALPHA1-6 : angle 1.53413 ( 15) link_BETA1-4 : bond 0.00429 ( 17) link_BETA1-4 : angle 1.72515 ( 51) link_NAG-ASN : bond 0.00618 ( 11) link_NAG-ASN : angle 3.05817 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6254.64 seconds wall clock time: 107 minutes 14.47 seconds (6434.47 seconds total)