Starting phenix.real_space_refine on Sat Jul 4 06:09:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9faw_50284/07_2026/9faw_50284.cif Found real_map, /net/cci-nas-00/data/ceres_data/9faw_50284/07_2026/9faw_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_50284/07_2026/9faw_50284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9faw_50284/07_2026/9faw_50284.map" model { file = "/net/cci-nas-00/data/ceres_data/9faw_50284/07_2026/9faw_50284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9faw_50284/07_2026/9faw_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 Unresolved non-hydrogen dihedrals: 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 Unresolved non-hydrogen dihedrals: 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: 5.60, per 1000 atoms: 0.30 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.58 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: 3.58 Time building geometry restraints manager: 2.74 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 - 4.08: 26178 4.08 - 8.15: 182 8.15 - 12.23: 6 12.23 - 16.30: 2 16.30 - 20.38: 3 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 102.31 122.69 -20.38 3.00e+00 1.11e-01 4.61e+01 angle pdb=" CB P1L C 385 " pdb=" SG P1L C 385 " pdb=" C7 P1L C 385 " ideal model delta sigma weight residual 102.31 118.97 -16.66 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CB P1L C 380 " pdb=" SG P1L C 380 " pdb=" C7 P1L C 380 " ideal model delta sigma weight residual 102.31 118.94 -16.63 3.00e+00 1.11e-01 3.07e+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 ... (remaining 26366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 11475 29.19 - 58.38: 308 58.38 - 87.57: 80 87.57 - 116.77: 66 116.77 - 145.96: 5 Dihedral angle restraints: 11934 sinusoidal: 5323 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 11931 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: 3209 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 3206 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: 10.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.790 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 1.255 45.379 26513 Z= 0.514 Chirality : 0.072 1.142 3040 Planarity : 0.005 0.121 3198 Dihedral : 17.519 145.957 7677 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 are 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/Z covalent geometry : bond 0.00471 / 0.23 (19417) covalent geometry : angle 0.84143 / 0.41 (26371) SS BOND : bond 0.00606 / 0.33 ( 11) SS BOND : angle 1.98464 / 1.22 ( 22) hydrogen bonds : bond 0.12269 / 8.22 ( 923) hydrogen bonds : angle 5.91589 / 4.16 ( 2904) link_ALPHA1-3 : bond 0.03119 / 1.59 ( 7) link_ALPHA1-3 : angle 8.07241 / 5.33 ( 21) link_ALPHA1-6 : bond 0.02917 / 1.80 ( 5) link_ALPHA1-6 : angle 8.55264 / 4.82 ( 15) link_BETA1-4 : bond 0.02983 / 1.48 ( 17) link_BETA1-4 : angle 14.90439 / 10.39 ( 51) link_NAG-ASN : bond 0.08981 / 5.21 ( 11) link_NAG-ASN : angle 16.73094 / 12.46 ( 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 : 0.714 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: 0.7655 (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: 0.8028 (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: 0.5148 time to fit residues: 237.7623 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 : 0.648 ------------------------------------------------------------------------------- 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... 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 = 0.110888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073670 restraints weight = 38625.070| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.73 r_work: 0.2801 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 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 = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19468 Z= 0.163 Angle : 0.686 11.627 26513 Z= 0.330 Chirality : 0.046 0.248 3040 Planarity : 0.004 0.041 3198 Dihedral : 15.274 144.824 3543 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.97 % Allowed : 10.75 % Favored : 87.28 % 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 are not related in a simple way. whole: 0.57 (0.18), residues: 2212 helix: 1.59 (0.19), residues: 709 sheet: 0.40 (0.22), residues: 538 loop : -0.49 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 250 TYR 0.030 0.002 TYR E 299 PHE 0.028 0.002 PHE A 307 TRP 0.021 0.001 TRP E 237 HIS 0.011 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (19417) covalent geometry : angle 0.65033 / 0.32 (26371) SS BOND : bond 0.00226 / 0.12 ( 11) SS BOND : angle 0.81786 / 0.50 ( 22) hydrogen bonds : bond 0.04200 / 2.82 ( 923) hydrogen bonds : angle 4.69390 / 3.26 ( 2904) link_ALPHA1-3 : bond 0.00829 / 0.44 ( 7) link_ALPHA1-3 : angle 2.32330 / 1.69 ( 21) link_ALPHA1-6 : bond 0.00537 / 0.27 ( 5) link_ALPHA1-6 : angle 2.19606 / 1.45 ( 15) link_BETA1-4 : bond 0.00583 / 0.29 ( 17) link_BETA1-4 : angle 2.81999 / 2.07 ( 51) link_NAG-ASN : bond 0.00746 / 0.41 ( 11) link_NAG-ASN : angle 4.67338 / 3.76 ( 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 367 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 328 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 421 ASN cc_start: 0.6326 (t0) cc_final: 0.5838 (p0) REVERT: E 299 TYR cc_start: 0.8324 (t80) cc_final: 0.8054 (t80) REVERT: D 307 PHE cc_start: 0.7384 (t80) cc_final: 0.6746 (t80) REVERT: D 444 LEU cc_start: 0.8749 (tt) cc_final: 0.8350 (mt) REVERT: C 415 CYS cc_start: 0.8275 (m) cc_final: 0.7903 (m) REVERT: L 30 THR cc_start: 0.8045 (m) cc_final: 0.7794 (t) REVERT: L 64 TYR cc_start: 0.7180 (p90) cc_final: 0.6651 (p90) REVERT: L 83 ASP cc_start: 0.7901 (t0) cc_final: 0.7631 (t0) REVERT: L 126 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8464 (mttm) REVERT: L 153 GLU cc_start: 0.8232 (tp30) cc_final: 0.7974 (pt0) REVERT: K 3 GLN cc_start: 0.8053 (mp10) cc_final: 0.7448 (mp10) REVERT: K 474 LYS cc_start: 0.8081 (mmtm) cc_final: 0.7796 (mptt) REVERT: O 3 GLN cc_start: 0.8381 (mp10) cc_final: 0.8162 (mp10) REVERT: O 5 VAL cc_start: 0.9212 (p) cc_final: 0.8869 (t) REVERT: O 6 GLU cc_start: 0.8385 (pm20) cc_final: 0.7892 (pm20) REVERT: O 432 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.6759 (mtp180) REVERT: O 474 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8045 (mptt) REVERT: O 504 GLN cc_start: 0.7842 (pm20) cc_final: 0.7282 (pm20) REVERT: F 460 ASP cc_start: 0.8326 (t0) cc_final: 0.8117 (t70) REVERT: F 464 ASN cc_start: 0.8471 (t0) cc_final: 0.7792 (t0) REVERT: F 469 GLU cc_start: 0.8226 (pm20) cc_final: 0.7743 (pm20) REVERT: F 472 ASN cc_start: 0.8521 (p0) cc_final: 0.8116 (p0) outliers start: 39 outliers final: 23 residues processed: 340 average time/residue: 0.4795 time to fit residues: 187.6342 Evaluate side-chains 332 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 160 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 265 ASN A 224 GLN C 128 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 = 0.3597 r_free = 0.3597 target = 0.111478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.073256 restraints weight = 56064.554| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.27 r_work: 0.2774 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19468 Z= 0.133 Angle : 0.638 11.209 26513 Z= 0.307 Chirality : 0.045 0.255 3040 Planarity : 0.003 0.034 3198 Dihedral : 12.576 147.061 3541 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.07 % Allowed : 12.72 % Favored : 85.21 % 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 are not related in a simple way. whole: 0.69 (0.18), residues: 2212 helix: 1.65 (0.20), residues: 710 sheet: 0.57 (0.22), residues: 540 loop : -0.47 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 78 TYR 0.024 0.001 TYR E 299 PHE 0.025 0.001 PHE C 304 TRP 0.018 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (19417) covalent geometry : angle 0.60653 / 0.30 (26371) SS BOND : bond 0.00278 / 0.16 ( 11) SS BOND : angle 0.68796 / 0.43 ( 22) hydrogen bonds : bond 0.03815 / 2.54 ( 923) hydrogen bonds : angle 4.46337 / 3.10 ( 2904) link_ALPHA1-3 : bond 0.00925 / 0.50 ( 7) link_ALPHA1-3 : angle 1.91731 / 1.47 ( 21) link_ALPHA1-6 : bond 0.00597 / 0.33 ( 5) link_ALPHA1-6 : angle 2.09025 / 1.38 ( 15) link_BETA1-4 : bond 0.00472 / 0.23 ( 17) link_BETA1-4 : angle 2.56244 / 1.87 ( 51) link_NAG-ASN : bond 0.00766 / 0.41 ( 11) link_NAG-ASN : angle 4.22407 / 3.40 ( 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 364 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 323 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7745 (mmt) REVERT: B 268 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 421 ASN cc_start: 0.6308 (t0) cc_final: 0.5891 (p0) REVERT: E 269 ARG cc_start: 0.7511 (ptt180) cc_final: 0.7254 (ptt180) REVERT: A 224 GLN cc_start: 0.8596 (tp40) cc_final: 0.8312 (tp40) REVERT: A 285 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8058 (mm) REVERT: D 294 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7539 (mp) REVERT: D 307 PHE cc_start: 0.7443 (t80) cc_final: 0.6712 (t80) REVERT: D 444 LEU cc_start: 0.8683 (tt) cc_final: 0.8314 (tp) REVERT: C 415 CYS cc_start: 0.8179 (m) cc_final: 0.7794 (m) REVERT: L 30 THR cc_start: 0.8076 (m) cc_final: 0.7850 (t) REVERT: L 64 TYR cc_start: 0.7533 (p90) cc_final: 0.7320 (p90) REVERT: L 101 LEU cc_start: 0.9113 (mp) cc_final: 0.8895 (mp) REVERT: L 126 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8450 (mttm) REVERT: L 154 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7916 (t) REVERT: L 158 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6649 (pmm) REVERT: K 3 GLN cc_start: 0.8040 (mp10) cc_final: 0.7421 (mp10) REVERT: K 433 GLU cc_start: 0.8642 (pt0) cc_final: 0.8416 (pt0) REVERT: K 474 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7781 (mptt) REVERT: K 477 ASP cc_start: 0.7313 (m-30) cc_final: 0.7078 (m-30) REVERT: O 3 GLN cc_start: 0.8355 (mp10) cc_final: 0.8123 (mp10) REVERT: O 5 VAL cc_start: 0.9179 (p) cc_final: 0.8831 (t) REVERT: O 6 GLU cc_start: 0.8376 (pm20) cc_final: 0.7732 (pm20) REVERT: O 406 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.7052 (ttp80) REVERT: O 432 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6693 (mtp180) REVERT: O 474 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7893 (mptt) REVERT: O 504 GLN cc_start: 0.7850 (pm20) cc_final: 0.7256 (pm20) REVERT: F 464 ASN cc_start: 0.8409 (t0) cc_final: 0.7773 (t0) REVERT: F 469 GLU cc_start: 0.8252 (pm20) cc_final: 0.7776 (pm20) REVERT: F 472 ASN cc_start: 0.8397 (p0) cc_final: 0.8119 (p0) outliers start: 41 outliers final: 15 residues processed: 339 average time/residue: 0.4951 time to fit residues: 193.8002 Evaluate side-chains 329 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 307 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 201 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 136 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN E 265 ASN D 41 ASN C 128 ASN H 690 ASN L 186 ASN L 199 ASN O 471 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.111206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.073100 restraints weight = 56623.591| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.24 r_work: 0.2787 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19468 Z= 0.127 Angle : 0.608 9.799 26513 Z= 0.298 Chirality : 0.045 0.251 3040 Planarity : 0.003 0.034 3198 Dihedral : 10.716 146.198 3541 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.17 % Allowed : 13.68 % Favored : 84.15 % 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 are not related in a simple way. whole: 0.80 (0.18), residues: 2212 helix: 1.64 (0.20), residues: 710 sheet: 0.76 (0.22), residues: 534 loop : -0.40 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 180 TYR 0.026 0.001 TYR E 299 PHE 0.021 0.001 PHE C 304 TRP 0.021 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (19417) covalent geometry : angle 0.58229 / 0.29 (26371) SS BOND : bond 0.00897 / 0.48 ( 11) SS BOND : angle 1.43383 / 0.75 ( 22) hydrogen bonds : bond 0.03699 / 2.44 ( 923) hydrogen bonds : angle 4.34702 / 3.01 ( 2904) link_ALPHA1-3 : bond 0.00953 / 0.53 ( 7) link_ALPHA1-3 : angle 1.87547 / 1.40 ( 21) link_ALPHA1-6 : bond 0.00683 / 0.41 ( 5) link_ALPHA1-6 : angle 2.00656 / 1.30 ( 15) link_BETA1-4 : bond 0.00473 / 0.24 ( 17) link_BETA1-4 : angle 2.19858 / 1.60 ( 51) link_NAG-ASN : bond 0.00714 / 0.39 ( 11) link_NAG-ASN : angle 3.57851 / 2.90 ( 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 363 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 320 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7765 (mmt) REVERT: B 268 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8054 (mm) REVERT: B 421 ASN cc_start: 0.6236 (t0) cc_final: 0.5992 (p0) REVERT: A 14 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8529 (tp30) REVERT: A 215 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8622 (mtpp) REVERT: A 285 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8114 (mm) REVERT: D 444 LEU cc_start: 0.8664 (tt) cc_final: 0.8307 (tp) REVERT: C 415 CYS cc_start: 0.8160 (m) cc_final: 0.7777 (m) REVERT: L 78 ARG cc_start: 0.7266 (ppt170) cc_final: 0.7055 (ppt170) REVERT: L 83 ASP cc_start: 0.7940 (t0) cc_final: 0.7677 (t0) REVERT: L 126 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8429 (mttm) REVERT: L 153 GLU cc_start: 0.8140 (tp30) cc_final: 0.7878 (pt0) REVERT: L 154 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7930 (t) REVERT: L 158 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6667 (pmm) REVERT: K 3 GLN cc_start: 0.8011 (mp10) cc_final: 0.7359 (mp10) REVERT: K 474 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7819 (mptt) REVERT: O 3 GLN cc_start: 0.8356 (mp10) cc_final: 0.8092 (mp10) REVERT: O 5 VAL cc_start: 0.9170 (p) cc_final: 0.8853 (t) REVERT: O 6 GLU cc_start: 0.8332 (pm20) cc_final: 0.7662 (pm20) REVERT: O 406 ARG cc_start: 0.7648 (ttp-170) cc_final: 0.7057 (ttp80) REVERT: O 432 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6671 (mtp180) REVERT: O 447 TYR cc_start: 0.8880 (m-80) cc_final: 0.8666 (m-80) REVERT: O 472 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8032 (t0) REVERT: O 474 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7872 (mptt) REVERT: O 504 GLN cc_start: 0.7825 (pm20) cc_final: 0.7174 (pm20) REVERT: F 464 ASN cc_start: 0.8477 (t0) cc_final: 0.7818 (t0) REVERT: F 469 GLU cc_start: 0.8204 (pm20) cc_final: 0.7720 (pm20) REVERT: F 472 ASN cc_start: 0.8358 (p0) cc_final: 0.8048 (p0) outliers start: 43 outliers final: 13 residues processed: 332 average time/residue: 0.4720 time to fit residues: 180.6379 Evaluate side-chains 315 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 295 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 8 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 285 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 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 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 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: 1.9990 chunk 40 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 186 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN E 265 ASN C 128 ASN 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 = 0.3606 r_free = 0.3606 target = 0.112020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.074059 restraints weight = 51825.501| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.15 r_work: 0.2795 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19468 Z= 0.124 Angle : 0.599 9.437 26513 Z= 0.295 Chirality : 0.044 0.246 3040 Planarity : 0.003 0.035 3198 Dihedral : 9.742 145.756 3541 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.87 % Allowed : 15.19 % Favored : 82.94 % 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 are not related in a simple way. whole: 0.85 (0.18), residues: 2212 helix: 1.63 (0.19), residues: 712 sheet: 0.91 (0.22), residues: 530 loop : -0.39 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 213 TYR 0.027 0.001 TYR E 299 PHE 0.024 0.001 PHE L 29 TRP 0.024 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (19417) covalent geometry : angle 0.57652 / 0.29 (26371) SS BOND : bond 0.00413 / 0.23 ( 11) SS BOND : angle 0.87899 / 0.49 ( 22) hydrogen bonds : bond 0.03591 / 2.39 ( 923) hydrogen bonds : angle 4.23754 / 2.94 ( 2904) link_ALPHA1-3 : bond 0.00975 / 0.55 ( 7) link_ALPHA1-3 : angle 1.82901 / 1.36 ( 21) link_ALPHA1-6 : bond 0.00784 / 0.47 ( 5) link_ALPHA1-6 : angle 2.00081 / 1.39 ( 15) link_BETA1-4 : bond 0.00456 / 0.23 ( 17) link_BETA1-4 : angle 1.94846 / 1.43 ( 51) link_NAG-ASN : bond 0.00686 / 0.37 ( 11) link_NAG-ASN : angle 3.45683 / 2.80 ( 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: 37 poor density : 316 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 185 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8425 (mt0) REVERT: B 227 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7789 (mmt) REVERT: B 268 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8068 (mm) REVERT: E 61 MET cc_start: 0.9318 (ptt) cc_final: 0.8929 (ptt) REVERT: E 190 GLU cc_start: 0.8316 (tt0) cc_final: 0.8003 (tt0) REVERT: A 14 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8515 (tp30) REVERT: A 215 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8632 (mtpp) REVERT: A 285 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8162 (mm) REVERT: D 294 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7442 (mp) REVERT: D 444 LEU cc_start: 0.8680 (tt) cc_final: 0.8325 (tp) REVERT: C 415 CYS cc_start: 0.8174 (m) cc_final: 0.7785 (m) REVERT: L 86 THR cc_start: 0.6510 (p) cc_final: 0.6307 (p) REVERT: L 126 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8518 (mttm) REVERT: L 153 GLU cc_start: 0.8144 (tp30) cc_final: 0.7852 (pt0) REVERT: L 154 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7947 (t) REVERT: L 158 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6648 (pmm) REVERT: K 3 GLN cc_start: 0.8072 (mp10) cc_final: 0.7372 (mp10) REVERT: K 474 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7872 (mptt) REVERT: O 3 GLN cc_start: 0.8328 (mp10) cc_final: 0.8030 (mp10) REVERT: O 5 VAL cc_start: 0.9187 (p) cc_final: 0.8886 (t) REVERT: O 6 GLU cc_start: 0.8303 (pm20) cc_final: 0.7675 (pm20) REVERT: O 406 ARG cc_start: 0.7675 (ttp-170) cc_final: 0.7098 (ttp80) REVERT: O 432 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6701 (mtp180) REVERT: O 447 TYR cc_start: 0.8902 (m-80) cc_final: 0.8663 (m-80) REVERT: O 460 ASP cc_start: 0.6640 (p0) cc_final: 0.6424 (p0) REVERT: O 472 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8066 (t0) REVERT: O 504 GLN cc_start: 0.7955 (pm20) cc_final: 0.7290 (pm20) REVERT: F 464 ASN cc_start: 0.8442 (t0) cc_final: 0.7797 (t0) REVERT: F 469 GLU cc_start: 0.8195 (pm20) cc_final: 0.7740 (pm20) REVERT: F 472 ASN cc_start: 0.8327 (p0) cc_final: 0.8009 (p0) REVERT: F 504 GLN cc_start: 0.7607 (mp10) cc_final: 0.7302 (pm20) outliers start: 37 outliers final: 18 residues processed: 330 average time/residue: 0.4913 time to fit residues: 187.7896 Evaluate side-chains 327 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 115 MET 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 235 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 O residue 432 ARG 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: 0.6980 chunk 159 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3586 r_free = 0.3586 target = 0.110714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.072232 restraints weight = 60062.713| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.37 r_work: 0.2756 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 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 = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19468 Z= 0.156 Angle : 0.599 8.833 26513 Z= 0.300 Chirality : 0.045 0.239 3040 Planarity : 0.003 0.037 3198 Dihedral : 9.355 145.014 3541 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.42 % Allowed : 15.04 % Favored : 82.53 % 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 are not related in a simple way. whole: 0.85 (0.18), residues: 2212 helix: 1.62 (0.20), residues: 712 sheet: 0.80 (0.22), residues: 546 loop : -0.33 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 213 TYR 0.027 0.002 TYR E 299 PHE 0.021 0.001 PHE E 289 TRP 0.024 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (19417) covalent geometry : angle 0.57955 / 0.30 (26371) SS BOND : bond 0.00326 / 0.19 ( 11) SS BOND : angle 0.74583 / 0.45 ( 22) hydrogen bonds : bond 0.03704 / 2.46 ( 923) hydrogen bonds : angle 4.27839 / 2.97 ( 2904) link_ALPHA1-3 : bond 0.00913 / 0.52 ( 7) link_ALPHA1-3 : angle 1.81238 / 1.34 ( 21) link_ALPHA1-6 : bond 0.00775 / 0.47 ( 5) link_ALPHA1-6 : angle 1.47970 / 0.96 ( 15) link_BETA1-4 : bond 0.00438 / 0.21 ( 17) link_BETA1-4 : angle 1.92716 / 1.44 ( 51) link_NAG-ASN : bond 0.00663 / 0.36 ( 11) link_NAG-ASN : angle 3.33353 / 2.73 ( 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 358 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 310 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7867 (mmt) REVERT: B 268 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8072 (mm) REVERT: E 190 GLU cc_start: 0.8376 (tt0) cc_final: 0.8055 (tt0) REVERT: A 215 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8669 (mtpp) REVERT: A 285 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8202 (mm) REVERT: D 294 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7487 (mp) REVERT: D 444 LEU cc_start: 0.8680 (tt) cc_final: 0.8321 (tp) REVERT: C 415 CYS cc_start: 0.8222 (m) cc_final: 0.7822 (m) REVERT: L 83 ASP cc_start: 0.8106 (t0) cc_final: 0.7860 (t0) REVERT: L 126 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8483 (mttt) REVERT: L 153 GLU cc_start: 0.8131 (tp30) cc_final: 0.7870 (pt0) REVERT: L 154 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7929 (t) REVERT: L 158 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6729 (pmm) REVERT: L 186 ASN cc_start: 0.8163 (t0) cc_final: 0.7945 (t160) REVERT: K 3 GLN cc_start: 0.8164 (mp10) cc_final: 0.7466 (mp10) REVERT: K 474 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7847 (mptt) REVERT: O 3 GLN cc_start: 0.8327 (mp10) cc_final: 0.8036 (mp10) REVERT: O 5 VAL cc_start: 0.9169 (p) cc_final: 0.8879 (t) REVERT: O 6 GLU cc_start: 0.8300 (pm20) cc_final: 0.7583 (pm20) REVERT: O 406 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7100 (ttp80) REVERT: O 432 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6710 (mtp180) REVERT: O 460 ASP cc_start: 0.6744 (p0) cc_final: 0.6528 (p0) REVERT: O 472 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8021 (t0) REVERT: O 474 LYS cc_start: 0.7995 (mptt) cc_final: 0.7738 (mptt) REVERT: O 504 GLN cc_start: 0.7944 (pm20) cc_final: 0.7294 (pm20) REVERT: F 464 ASN cc_start: 0.8486 (t0) cc_final: 0.7820 (t0) REVERT: F 469 GLU cc_start: 0.8191 (pm20) cc_final: 0.7764 (pm20) REVERT: F 472 ASN cc_start: 0.8319 (p0) cc_final: 0.7995 (p0) REVERT: F 504 GLN cc_start: 0.7582 (mp10) cc_final: 0.7307 (pm20) outliers start: 48 outliers final: 22 residues processed: 332 average time/residue: 0.5290 time to fit residues: 201.6840 Evaluate side-chains 326 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 296 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 290 VAL Chi-restraints excluded: chain A residue 429 ILE 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 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 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 460 ASP Chi-restraints excluded: chain F residue 466 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 106 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN E 265 ASN A 224 GLN A 265 ASN K 414 HIS F 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.110728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.072443 restraints weight = 54200.711| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.22 r_work: 0.2764 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 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 = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19468 Z= 0.149 Angle : 0.609 9.783 26513 Z= 0.303 Chirality : 0.045 0.233 3040 Planarity : 0.003 0.038 3198 Dihedral : 9.129 140.115 3541 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.62 % Allowed : 15.24 % Favored : 82.13 % 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 are not related in a simple way. whole: 0.87 (0.18), residues: 2212 helix: 1.61 (0.19), residues: 712 sheet: 0.86 (0.22), residues: 544 loop : -0.34 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 213 TYR 0.026 0.002 TYR E 299 PHE 0.027 0.001 PHE L 29 TRP 0.030 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (19417) covalent geometry : angle 0.59093 / 0.30 (26371) SS BOND : bond 0.00409 / 0.23 ( 11) SS BOND : angle 0.68060 / 0.45 ( 22) hydrogen bonds : bond 0.03699 / 2.46 ( 923) hydrogen bonds : angle 4.26836 / 2.97 ( 2904) link_ALPHA1-3 : bond 0.00891 / 0.50 ( 7) link_ALPHA1-3 : angle 1.77660 / 1.32 ( 21) link_ALPHA1-6 : bond 0.00648 / 0.43 ( 5) link_ALPHA1-6 : angle 1.61036 / 1.01 ( 15) link_BETA1-4 : bond 0.00430 / 0.21 ( 17) link_BETA1-4 : angle 1.83988 / 1.38 ( 51) link_NAG-ASN : bond 0.00648 / 0.35 ( 11) link_NAG-ASN : angle 3.25198 / 2.65 ( 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 354 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7801 (mmt) REVERT: E 61 MET cc_start: 0.9328 (ptt) cc_final: 0.8956 (ptt) REVERT: E 190 GLU cc_start: 0.8372 (tt0) cc_final: 0.8053 (tt0) REVERT: A 14 GLU cc_start: 0.8840 (tp30) cc_final: 0.8585 (mm-30) REVERT: A 224 GLN cc_start: 0.8560 (tp40) cc_final: 0.8305 (tp40) REVERT: A 285 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8244 (mm) REVERT: D 294 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7499 (mp) REVERT: D 444 LEU cc_start: 0.8688 (tt) cc_final: 0.8321 (tp) REVERT: C 415 CYS cc_start: 0.8215 (m) cc_final: 0.7817 (m) REVERT: L 83 ASP cc_start: 0.8236 (t0) cc_final: 0.7941 (t0) REVERT: L 126 LYS cc_start: 0.8837 (mtmt) cc_final: 0.8522 (mttt) REVERT: L 153 GLU cc_start: 0.8127 (tp30) cc_final: 0.7868 (pt0) REVERT: L 154 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7923 (t) REVERT: L 158 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6737 (pmm) REVERT: K 3 GLN cc_start: 0.8140 (mp10) cc_final: 0.7414 (mp10) REVERT: O 3 GLN cc_start: 0.8325 (mp10) cc_final: 0.8029 (mp10) REVERT: O 5 VAL cc_start: 0.9175 (p) cc_final: 0.8888 (t) REVERT: O 6 GLU cc_start: 0.8218 (pm20) cc_final: 0.7528 (pm20) REVERT: O 406 ARG cc_start: 0.7679 (ttp-170) cc_final: 0.7119 (ttp80) REVERT: O 432 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.6699 (mtp180) REVERT: O 460 ASP cc_start: 0.6750 (p0) cc_final: 0.6539 (p0) REVERT: O 472 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7951 (t0) REVERT: O 504 GLN cc_start: 0.7919 (pm20) cc_final: 0.7224 (pm20) REVERT: F 464 ASN cc_start: 0.8478 (t0) cc_final: 0.7810 (t0) REVERT: F 469 GLU cc_start: 0.8159 (pm20) cc_final: 0.7763 (pm20) REVERT: F 472 ASN cc_start: 0.8344 (p0) cc_final: 0.8013 (p0) REVERT: F 504 GLN cc_start: 0.7558 (mp10) cc_final: 0.7333 (pm20) outliers start: 52 outliers final: 24 residues processed: 327 average time/residue: 0.4619 time to fit residues: 175.0717 Evaluate side-chains 323 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 305 ILE 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 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 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 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 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 463 LYS 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: 0.6980 chunk 203 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN E 265 ASN A 265 ASN D 243 ASN C 396 HIS L 186 ASN K 414 HIS F 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.072127 restraints weight = 54887.353| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.21 r_work: 0.2757 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 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 = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19468 Z= 0.158 Angle : 0.620 9.951 26513 Z= 0.311 Chirality : 0.045 0.256 3040 Planarity : 0.003 0.038 3198 Dihedral : 9.044 133.271 3541 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.52 % Allowed : 15.75 % Favored : 81.73 % 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 are not related in a simple way. whole: 0.81 (0.18), residues: 2212 helix: 1.52 (0.19), residues: 717 sheet: 0.86 (0.22), residues: 544 loop : -0.35 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 213 TYR 0.026 0.002 TYR E 299 PHE 0.032 0.001 PHE L 59 TRP 0.036 0.001 TRP L 150 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (19417) covalent geometry : angle 0.60080 / 0.31 (26371) SS BOND : bond 0.00313 / 0.18 ( 11) SS BOND : angle 1.62805 / 0.86 ( 22) hydrogen bonds : bond 0.03806 / 2.51 ( 923) hydrogen bonds : angle 4.34968 / 3.02 ( 2904) link_ALPHA1-3 : bond 0.00865 / 0.49 ( 7) link_ALPHA1-3 : angle 1.76286 / 1.31 ( 21) link_ALPHA1-6 : bond 0.00621 / 0.41 ( 5) link_ALPHA1-6 : angle 1.56782 / 1.02 ( 15) link_BETA1-4 : bond 0.00431 / 0.21 ( 17) link_BETA1-4 : angle 1.84387 / 1.39 ( 51) link_NAG-ASN : bond 0.00634 / 0.34 ( 11) link_NAG-ASN : angle 3.19033 / 2.62 ( 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 350 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 300 time to evaluate : 0.645 Fit side-chains revert: symmetry clash 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: 0.8366 (tt0) cc_final: 0.8046 (tt0) REVERT: A 14 GLU cc_start: 0.8862 (tp30) cc_final: 0.8569 (mm-30) REVERT: A 285 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8267 (mm) REVERT: D 294 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7490 (mp) REVERT: D 444 LEU cc_start: 0.8688 (tt) cc_final: 0.8313 (tp) REVERT: C 415 CYS cc_start: 0.8194 (m) cc_final: 0.7790 (m) REVERT: L 30 THR cc_start: 0.8197 (m) cc_final: 0.7897 (t) REVERT: L 83 ASP cc_start: 0.8254 (t0) cc_final: 0.7951 (t0) REVERT: L 126 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8515 (mttt) REVERT: L 153 GLU cc_start: 0.8130 (tp30) cc_final: 0.7878 (pt0) REVERT: L 154 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7899 (t) REVERT: L 158 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6727 (pmm) REVERT: K 3 GLN cc_start: 0.8131 (mp10) cc_final: 0.7376 (mp10) REVERT: K 463 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8465 (pttt) REVERT: O 3 GLN cc_start: 0.8315 (mp10) cc_final: 0.8011 (mp10) REVERT: O 5 VAL cc_start: 0.9183 (p) cc_final: 0.8869 (t) REVERT: O 6 GLU cc_start: 0.8216 (pm20) cc_final: 0.7576 (pm20) REVERT: O 406 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7081 (ttp80) REVERT: O 432 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6604 (mtp180) REVERT: O 460 ASP cc_start: 0.6774 (p0) cc_final: 0.6551 (p0) REVERT: O 472 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.7910 (t0) REVERT: O 504 GLN cc_start: 0.7897 (pm20) cc_final: 0.6977 (pm20) REVERT: F 464 ASN cc_start: 0.8482 (t0) cc_final: 0.7806 (t0) REVERT: F 469 GLU cc_start: 0.8176 (pm20) cc_final: 0.7893 (pm20) REVERT: F 472 ASN cc_start: 0.8361 (p0) cc_final: 0.8031 (p0) REVERT: F 504 GLN cc_start: 0.7608 (mp10) cc_final: 0.7381 (pm20) outliers start: 50 outliers final: 28 residues processed: 323 average time/residue: 0.4850 time to fit residues: 180.9087 Evaluate side-chains 325 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 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 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 463 LYS 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 463 LYS 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: 1.9990 chunk 104 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 210 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN E 265 ASN A 224 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN L 132 GLN K 414 HIS O 414 HIS F 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.072948 restraints weight = 54960.108| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.26 r_work: 0.2775 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- 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 = 0.22 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 = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19468 Z= 0.131 Angle : 0.624 12.405 26513 Z= 0.312 Chirality : 0.045 0.275 3040 Planarity : 0.003 0.038 3198 Dihedral : 8.764 123.486 3541 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.02 % Allowed : 16.76 % Favored : 81.22 % 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 are not related in a simple way. whole: 0.82 (0.18), residues: 2212 helix: 1.49 (0.19), residues: 717 sheet: 0.89 (0.22), residues: 542 loop : -0.35 (0.21), residues: 953 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 0.038 0.001 PHE L 59 TRP 0.042 0.001 TRP L 150 HIS 0.004 0.001 HIS O 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (19417) covalent geometry : angle 0.60681 / 0.31 (26371) SS BOND : bond 0.00567 / 0.31 ( 11) SS BOND : angle 1.48886 / 0.87 ( 22) hydrogen bonds : bond 0.03693 / 2.42 ( 923) hydrogen bonds : angle 4.33032 / 3.01 ( 2904) link_ALPHA1-3 : bond 0.00875 / 0.49 ( 7) link_ALPHA1-3 : angle 1.72293 / 1.28 ( 21) link_ALPHA1-6 : bond 0.00757 / 0.51 ( 5) link_ALPHA1-6 : angle 1.55540 / 1.01 ( 15) link_BETA1-4 : bond 0.00462 / 0.23 ( 17) link_BETA1-4 : angle 1.71093 / 1.29 ( 51) link_NAG-ASN : bond 0.00623 / 0.33 ( 11) link_NAG-ASN : angle 3.10985 / 2.52 ( 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 339 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7746 (mmt) REVERT: E 61 MET cc_start: 0.9315 (ptt) cc_final: 0.8941 (ptt) REVERT: E 190 GLU cc_start: 0.8334 (tt0) cc_final: 0.8034 (tt0) REVERT: A 14 GLU cc_start: 0.8838 (tp30) cc_final: 0.8569 (mm-30) REVERT: A 285 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8273 (mm) REVERT: D 294 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7448 (mp) REVERT: D 444 LEU cc_start: 0.8701 (tt) cc_final: 0.8325 (tp) REVERT: C 415 CYS cc_start: 0.8197 (m) cc_final: 0.7816 (m) REVERT: L 53 THR cc_start: 0.6443 (p) cc_final: 0.6134 (p) REVERT: L 83 ASP cc_start: 0.8222 (t0) cc_final: 0.7890 (t0) REVERT: L 126 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8479 (mttt) REVERT: L 153 GLU cc_start: 0.8124 (tp30) cc_final: 0.7884 (pt0) REVERT: L 154 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7920 (t) REVERT: L 158 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6737 (pmm) REVERT: K 3 GLN cc_start: 0.8177 (mp10) cc_final: 0.7471 (mp10) REVERT: K 463 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8469 (pttt) REVERT: O 3 GLN cc_start: 0.8349 (mp10) cc_final: 0.8050 (mp10) REVERT: O 5 VAL cc_start: 0.9180 (p) cc_final: 0.8902 (t) REVERT: O 6 GLU cc_start: 0.8204 (pm20) cc_final: 0.7622 (pm20) REVERT: O 406 ARG cc_start: 0.7640 (ttp-170) cc_final: 0.7090 (ttp80) REVERT: O 432 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6610 (mtp180) REVERT: O 460 ASP cc_start: 0.6794 (p0) cc_final: 0.6571 (p0) REVERT: O 472 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7927 (t0) REVERT: O 504 GLN cc_start: 0.7852 (pm20) cc_final: 0.6897 (pm20) REVERT: F 406 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7674 (tmm-80) REVERT: F 464 ASN cc_start: 0.8472 (t0) cc_final: 0.7803 (t0) REVERT: F 469 GLU cc_start: 0.8143 (pm20) cc_final: 0.7899 (pm20) REVERT: F 472 ASN cc_start: 0.8320 (p0) cc_final: 0.7971 (p0) REVERT: F 504 GLN cc_start: 0.7582 (mp10) cc_final: 0.7356 (pm20) outliers start: 40 outliers final: 24 residues processed: 314 average time/residue: 0.5056 time to fit residues: 182.5944 Evaluate side-chains 329 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 296 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 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 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 K residue 463 LYS 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 406 ARG 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: 0.0060 chunk 53 optimal weight: 0.0670 chunk 217 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 163 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 159 optimal weight: 0.2980 chunk 196 optimal weight: 5.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN E 265 ASN A 224 GLN A 265 ASN L 132 GLN K 414 HIS K 472 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 = 0.3617 r_free = 0.3617 target = 0.112718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074914 restraints weight = 47563.942| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.04 r_work: 0.2823 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19468 Z= 0.115 Angle : 0.615 13.699 26513 Z= 0.308 Chirality : 0.044 0.247 3040 Planarity : 0.003 0.040 3198 Dihedral : 8.282 106.054 3541 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.62 % Allowed : 17.62 % 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 are not related in a simple way. whole: 0.92 (0.18), residues: 2212 helix: 1.64 (0.20), residues: 697 sheet: 0.93 (0.21), residues: 560 loop : -0.31 (0.21), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 213 TYR 0.023 0.001 TYR E 299 PHE 0.035 0.001 PHE L 59 TRP 0.046 0.001 TRP L 150 HIS 0.003 0.000 HIS K 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (19417) covalent geometry : angle 0.59898 / 0.31 (26371) SS BOND : bond 0.00584 / 0.32 ( 11) SS BOND : angle 1.47485 / 0.95 ( 22) hydrogen bonds : bond 0.03524 / 2.32 ( 923) hydrogen bonds : angle 4.23365 / 2.95 ( 2904) link_ALPHA1-3 : bond 0.00910 / 0.51 ( 7) link_ALPHA1-3 : angle 1.65249 / 1.23 ( 21) link_ALPHA1-6 : bond 0.00787 / 0.51 ( 5) link_ALPHA1-6 : angle 1.51120 / 0.98 ( 15) link_BETA1-4 : bond 0.00463 / 0.25 ( 17) link_BETA1-4 : angle 1.55904 / 1.17 ( 51) link_NAG-ASN : bond 0.00614 / 0.33 ( 11) link_NAG-ASN : angle 3.03232 / 2.41 ( 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 338 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 306 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.8136 (ttp) cc_final: 0.7681 (mmt) REVERT: B 268 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8103 (mm) REVERT: E 61 MET cc_start: 0.9266 (ptt) cc_final: 0.8868 (ptt) REVERT: E 190 GLU cc_start: 0.8255 (tt0) cc_final: 0.7960 (tt0) REVERT: A 244 TYR cc_start: 0.7839 (p90) cc_final: 0.7631 (p90) REVERT: A 285 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (mm) REVERT: D 294 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7345 (mp) REVERT: D 444 LEU cc_start: 0.8687 (tt) cc_final: 0.8301 (tp) REVERT: L 53 THR cc_start: 0.6437 (p) cc_final: 0.6194 (p) REVERT: L 83 ASP cc_start: 0.8164 (t0) cc_final: 0.7861 (t0) REVERT: L 126 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8448 (mttt) REVERT: L 153 GLU cc_start: 0.8136 (tp30) cc_final: 0.7845 (pt0) REVERT: L 154 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7925 (t) REVERT: L 158 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6740 (pmm) REVERT: K 3 GLN cc_start: 0.8166 (mp10) cc_final: 0.7500 (mp10) REVERT: K 6 GLU cc_start: 0.7681 (pm20) cc_final: 0.7464 (pm20) REVERT: O 3 GLN cc_start: 0.8351 (mp10) cc_final: 0.8041 (mp10) REVERT: O 5 VAL cc_start: 0.9170 (p) cc_final: 0.8886 (t) REVERT: O 6 GLU cc_start: 0.8134 (pm20) cc_final: 0.7559 (pm20) REVERT: O 406 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.7091 (ttp80) REVERT: O 407 LEU cc_start: 0.8198 (mp) cc_final: 0.7881 (mt) REVERT: O 460 ASP cc_start: 0.6820 (p0) cc_final: 0.6588 (p0) REVERT: O 472 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7868 (t0) REVERT: O 504 GLN cc_start: 0.7797 (pm20) cc_final: 0.6836 (pm20) REVERT: F 406 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7662 (tmm-80) REVERT: F 464 ASN cc_start: 0.8419 (t0) cc_final: 0.7773 (t0) REVERT: F 469 GLU cc_start: 0.8149 (pm20) cc_final: 0.7902 (pm20) REVERT: F 472 ASN cc_start: 0.8262 (p0) cc_final: 0.7950 (p0) REVERT: F 504 GLN cc_start: 0.7620 (mp10) cc_final: 0.7393 (pm20) outliers start: 32 outliers final: 16 residues processed: 320 average time/residue: 0.4885 time to fit residues: 180.9185 Evaluate side-chains 318 residues out of total 1975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 259 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 285 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 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 466 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 211 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 224 GLN A 224 GLN A 265 ASN D 41 ASN L 132 GLN K 414 HIS 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 = 0.3574 r_free = 0.3574 target = 0.109825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.071479 restraints weight = 55208.960| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.23 r_work: 0.2744 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19468 Z= 0.219 Angle : 0.665 12.437 26513 Z= 0.334 Chirality : 0.047 0.278 3040 Planarity : 0.004 0.039 3198 Dihedral : 8.567 100.662 3541 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.62 % Allowed : 18.02 % Favored : 80.36 % 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 are not related in a simple way. whole: 0.82 (0.18), residues: 2212 helix: 1.49 (0.19), residues: 712 sheet: 0.84 (0.22), residues: 547 loop : -0.30 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.025 0.002 TYR E 299 PHE 0.034 0.002 PHE L 59 TRP 0.057 0.002 TRP D 241 HIS 0.006 0.001 HIS C 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (19417) covalent geometry : angle 0.64686 / 0.33 (26371) SS BOND : bond 0.00520 / 0.29 ( 11) SS BOND : angle 1.91748 / 1.13 ( 22) hydrogen bonds : bond 0.04001 / 2.61 ( 923) hydrogen bonds : angle 4.43435 / 3.08 ( 2904) link_ALPHA1-3 : bond 0.00785 / 0.44 ( 7) link_ALPHA1-3 : angle 1.71139 / 1.26 ( 21) link_ALPHA1-6 : bond 0.00577 / 0.38 ( 5) link_ALPHA1-6 : angle 1.62461 / 1.07 ( 15) link_BETA1-4 : bond 0.00443 / 0.22 ( 17) link_BETA1-4 : angle 1.91511 / 1.45 ( 51) link_NAG-ASN : bond 0.00630 / 0.34 ( 11) link_NAG-ASN : angle 3.11650 / 2.57 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6803.24 seconds wall clock time: 116 minutes 45.20 seconds (7005.20 seconds total)