Starting phenix.real_space_refine on Wed Mar 4 19:21:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbd_13290/03_2026/7pbd_13290.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbd_13290/03_2026/7pbd_13290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pbd_13290/03_2026/7pbd_13290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbd_13290/03_2026/7pbd_13290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbd_13290/03_2026/7pbd_13290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbd_13290/03_2026/7pbd_13290.map" } resolution = 3.04 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 893 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9617 2.51 5 N 2423 2.21 5 O 2698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2749 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2709 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 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: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 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 Time building chain proxies: 2.89, per 1000 atoms: 0.19 Number of scatterers: 14822 At special positions: 0 Unit cell: (94.5, 120.75, 135.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2698 8.00 N 2423 7.00 C 9617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 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 "HETATM14820 O5 NAG D 502 .*. O " rejected from bonding due to valence issues. Atom "HETATM14777 O5 NAG A 802 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 802 " - " ASN A 111 " " NAG D 502 " - " ASN D 111 " " NAG E 501 " - " ASN E 80 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 149 " " NAG J 1 " - " ASN C 80 " " NAG K 1 " - " ASN E 149 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 461.3 milliseconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 13 sheets defined 40.6% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.608A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.866A pdb=" N SER A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 93' Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.600A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 179 removed outlier: 4.127A pdb=" N VAL A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 598 through 612 Processing helix chain 'A' and resid 619 through 645 removed outlier: 4.110A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 682 removed outlier: 4.772A pdb=" N LYS A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 715 removed outlier: 3.755A pdb=" N LYS A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Proline residue: A 698 - end of helix removed outlier: 3.678A pdb=" N ARG A 715 " --> pdb=" O THR A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.530A pdb=" N LEU B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 218 through 239 removed outlier: 5.133A pdb=" N MET B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix removed outlier: 4.024A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 246 through 269 removed outlier: 3.590A pdb=" N ARG B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 279 through 308 Processing helix chain 'B' and resid 415 through 447 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.548A pdb=" N LEU C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 242 removed outlier: 3.938A pdb=" N SER C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 268 Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 279 through 308 removed outlier: 3.703A pdb=" N ALA C 295 " --> pdb=" O PHE C 291 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 447 removed outlier: 3.798A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.550A pdb=" N LEU E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 86 through 91 removed outlier: 4.027A pdb=" N GLN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 4.356A pdb=" N ARG E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 218 through 243 removed outlier: 4.870A pdb=" N MET E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix removed outlier: 4.512A pdb=" N ASN E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 270 removed outlier: 3.954A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 416 through 447 Proline residue: E 432 - end of helix Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.753A pdb=" N SER D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.488A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 223 through 230 removed outlier: 4.157A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 247 Processing helix chain 'D' and resid 251 through 276 removed outlier: 3.598A pdb=" N ARG D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 346 removed outlier: 4.130A pdb=" N ALA D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Proline residue: D 330 - end of helix removed outlier: 3.734A pdb=" N ASN D 346 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 418 Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 474 through 478 removed outlier: 3.665A pdb=" N THR F 478 " --> pdb=" O PRO F 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 39 through 44 current: chain 'A' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.247A pdb=" N SER A 159 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 579 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY A 195 " --> pdb=" O HIS A 586 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS A 588 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU A 193 " --> pdb=" O LYS A 588 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 36 through 46 current: chain 'B' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 68 current: chain 'B' and resid 123 through 135 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.824A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR B 205 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN B 197 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG B 207 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER B 195 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER B 209 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 193 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER B 211 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS B 191 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG B 213 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 51 removed outlier: 6.622A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N MET C 49 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP C 56 " --> pdb=" O MET C 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.994A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR C 205 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN C 197 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG C 207 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER C 195 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER C 209 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 193 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER C 211 " --> pdb=" O HIS C 191 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N HIS C 191 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG C 213 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 36 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 46 current: chain 'E' and resid 56 through 68 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 68 current: chain 'E' and resid 123 through 135 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.802A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 39 through 54 removed outlier: 6.257A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU D 59 " --> pdb=" O PRO D 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.023A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AB3, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB4, first strand: chain 'F' and resid 421 through 426 removed outlier: 6.514A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 445 through 447 current: chain 'F' and resid 501 through 502 592 hydrogen bonds defined for protein. 1701 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: 1.76 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4532 1.34 - 1.46: 4052 1.46 - 1.58: 6469 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 15199 Sorted by residual: bond pdb=" CG HSM B 601 " pdb=" ND1 HSM B 601 " ideal model delta sigma weight residual 1.383 1.312 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CD2 HSM B 601 " pdb=" NE2 HSM B 601 " ideal model delta sigma weight residual 1.376 1.313 0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" N ILE C 423 " pdb=" CA ILE C 423 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 5.00e+00 bond pdb=" N TRP C 426 " pdb=" CA TRP C 426 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.21e-02 6.83e+03 4.79e+00 ... (remaining 15194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 20078 1.97 - 3.94: 431 3.94 - 5.91: 116 5.91 - 7.88: 30 7.88 - 9.85: 2 Bond angle restraints: 20657 Sorted by residual: angle pdb=" N ILE E 281 " pdb=" CA ILE E 281 " pdb=" C ILE E 281 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.38e+01 angle pdb=" N ALA C 420 " pdb=" CA ALA C 420 " pdb=" C ALA C 420 " ideal model delta sigma weight residual 112.93 107.44 5.49 1.33e+00 5.65e-01 1.70e+01 angle pdb=" C LYS F 452 " pdb=" N ASP F 453 " pdb=" CA ASP F 453 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N ALA C 421 " pdb=" CA ALA C 421 " pdb=" C ALA C 421 " ideal model delta sigma weight residual 111.75 106.95 4.80 1.28e+00 6.10e-01 1.41e+01 angle pdb=" CA ASP F 453 " pdb=" CB ASP F 453 " pdb=" CG ASP F 453 " ideal model delta sigma weight residual 112.60 116.09 -3.49 1.00e+00 1.00e+00 1.22e+01 ... (remaining 20652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.44: 8648 23.44 - 46.89: 447 46.89 - 70.33: 37 70.33 - 93.77: 29 93.77 - 117.22: 43 Dihedral angle restraints: 9204 sinusoidal: 3938 harmonic: 5266 Sorted by residual: dihedral pdb=" CB CYS D 139 " pdb=" SG CYS D 139 " pdb=" SG CYS D 153 " pdb=" CB CYS D 153 " ideal model delta sinusoidal sigma weight residual 93.00 42.28 50.72 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA CYS E 150 " pdb=" C CYS E 150 " pdb=" N THR E 151 " pdb=" CA THR E 151 " ideal model delta harmonic sigma weight residual 180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N GLU B 153 " pdb=" CA GLU B 153 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 9201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.450: 2374 0.450 - 0.901: 8 0.901 - 1.351: 1 1.351 - 1.802: 2 1.802 - 2.252: 2 Chirality restraints: 2387 Sorted by residual: 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 -0.15 -2.25 2.00e-02 2.50e+03 1.27e+04 chirality pdb=" C1 MAN H 5 " pdb=" O6 BMA H 3 " pdb=" C2 MAN H 5 " pdb=" O5 MAN H 5 " both_signs ideal model delta sigma weight residual False 2.40 0.45 1.95 2.00e-02 2.50e+03 9.47e+03 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.64 -1.76 2.00e-02 2.50e+03 7.76e+03 ... (remaining 2384 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " -0.132 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" CG ASN C 80 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.135 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " 0.513 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 80 " 0.238 2.00e-02 2.50e+03 2.46e-01 7.58e+02 pdb=" CG ASN E 80 " -0.116 2.00e-02 2.50e+03 pdb=" OD1 ASN E 80 " -0.067 2.00e-02 2.50e+03 pdb=" ND2 ASN E 80 " -0.365 2.00e-02 2.50e+03 pdb=" C1 NAG E 501 " 0.309 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 149 " 0.137 2.00e-02 2.50e+03 1.44e-01 2.58e+02 pdb=" CG ASN C 149 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN C 149 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN C 149 " -0.218 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.179 2.00e-02 2.50e+03 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 173 2.63 - 3.20: 13593 3.20 - 3.76: 22774 3.76 - 4.33: 32017 4.33 - 4.90: 53293 Nonbonded interactions: 121850 Sorted by model distance: nonbonded pdb=" OE2 GLU B 179 " pdb=" OG SER F 446 " model vdw 2.062 3.040 nonbonded pdb=" OH TYR B 97 " pdb=" OE2 GLU B 155 " model vdw 2.090 3.040 nonbonded pdb=" O TYR B 304 " pdb=" OG SER B 308 " model vdw 2.179 3.040 nonbonded pdb=" ND2 ASN D 88 " pdb=" O PRO D 115 " model vdw 2.203 3.120 nonbonded pdb=" OE2 GLU B 153 " pdb=" NE ARG B 207 " model vdw 2.206 3.120 ... (remaining 121845 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' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 8 through 308 or resid 419 through 447)) selection = chain 'C' selection = (chain 'E' and (resid 8 through 308 or resid 419 through 447)) } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.950 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 0.101 15227 Z= 0.220 Angle : 1.236 44.493 20735 Z= 0.500 Chirality : 0.101 2.252 2387 Planarity : 0.004 0.052 2536 Dihedral : 16.572 117.217 5802 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1764 helix: 1.63 (0.22), residues: 595 sheet: -0.66 (0.24), residues: 461 loop : -0.61 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 255 TYR 0.013 0.001 TYR E 157 PHE 0.023 0.002 PHE A 626 TRP 0.017 0.001 TRP B 237 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00459 (15199) covalent geometry : angle 0.75843 (20657) SS BOND : bond 0.00491 ( 6) SS BOND : angle 1.60742 ( 12) hydrogen bonds : bond 0.11413 ( 592) hydrogen bonds : angle 5.21017 ( 1701) link_ALPHA1-3 : bond 0.00852 ( 3) link_ALPHA1-3 : angle 12.24884 ( 9) link_ALPHA1-6 : bond 0.00748 ( 3) link_ALPHA1-6 : angle 23.58160 ( 9) link_BETA1-4 : bond 0.01220 ( 8) link_BETA1-4 : angle 13.08238 ( 24) link_NAG-ASN : bond 0.05484 ( 8) link_NAG-ASN : angle 19.68379 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 597 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 227 MET cc_start: 0.7754 (ppp) cc_final: 0.7422 (ppp) REVERT: C 49 MET cc_start: 0.8388 (ppp) cc_final: 0.7889 (ppp) REVERT: C 90 GLN cc_start: 0.8881 (mp10) cc_final: 0.8574 (mp10) REVERT: E 49 MET cc_start: 0.8276 (mmm) cc_final: 0.7839 (tmm) REVERT: E 282 ASP cc_start: 0.8718 (m-30) cc_final: 0.8505 (t70) REVERT: E 283 MET cc_start: 0.8339 (ttt) cc_final: 0.8114 (ttm) REVERT: D 228 ILE cc_start: 0.9177 (tt) cc_final: 0.8814 (tt) REVERT: F 3 GLN cc_start: 0.8089 (mp10) cc_final: 0.7597 (mp10) REVERT: F 5 GLN cc_start: 0.8079 (mp-120) cc_final: 0.7829 (mm-40) REVERT: F 6 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6684 (tm-30) REVERT: F 405 LEU cc_start: 0.6888 (tt) cc_final: 0.6553 (tp) REVERT: F 412 SER cc_start: 0.8232 (p) cc_final: 0.7515 (p) REVERT: F 414 HIS cc_start: 0.8172 (m90) cc_final: 0.7690 (m90) REVERT: F 456 THR cc_start: 0.9067 (m) cc_final: 0.8406 (p) REVERT: F 470 MET cc_start: 0.8381 (mpp) cc_final: 0.7838 (mpp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0962 time to fit residues: 26.6862 Evaluate side-chains 135 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 ASN D 216 HIS F 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054652 restraints weight = 48022.422| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.60 r_work: 0.2860 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15227 Z= 0.149 Angle : 0.667 11.670 20735 Z= 0.315 Chirality : 0.046 0.344 2387 Planarity : 0.004 0.040 2536 Dihedral : 11.672 126.439 2453 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.63 % Allowed : 6.19 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1764 helix: 1.90 (0.21), residues: 593 sheet: -0.56 (0.24), residues: 449 loop : -0.43 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.016 0.001 TYR B 299 PHE 0.017 0.001 PHE E 186 TRP 0.018 0.001 TRP E 241 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00330 (15199) covalent geometry : angle 0.62264 (20657) SS BOND : bond 0.00442 ( 6) SS BOND : angle 1.26005 ( 12) hydrogen bonds : bond 0.03960 ( 592) hydrogen bonds : angle 4.32834 ( 1701) link_ALPHA1-3 : bond 0.00796 ( 3) link_ALPHA1-3 : angle 3.44693 ( 9) link_ALPHA1-6 : bond 0.01305 ( 3) link_ALPHA1-6 : angle 2.64088 ( 9) link_BETA1-4 : bond 0.00776 ( 8) link_BETA1-4 : angle 2.65634 ( 24) link_NAG-ASN : bond 0.01157 ( 8) link_NAG-ASN : angle 5.96337 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 597 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8096 (tm-30) REVERT: C 49 MET cc_start: 0.8613 (ppp) cc_final: 0.8132 (ppp) REVERT: C 155 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8091 (mm-30) REVERT: E 55 MET cc_start: 0.9026 (mmm) cc_final: 0.8664 (mmm) REVERT: E 278 VAL cc_start: 0.8626 (p) cc_final: 0.7899 (m) REVERT: E 283 MET cc_start: 0.8700 (ttt) cc_final: 0.8457 (ttm) REVERT: F 414 HIS cc_start: 0.8476 (m90) cc_final: 0.7978 (m90) REVERT: F 456 THR cc_start: 0.8954 (m) cc_final: 0.8723 (p) REVERT: F 470 MET cc_start: 0.8251 (mpp) cc_final: 0.7920 (mpp) REVERT: F 504 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8628 (mm-40) outliers start: 10 outliers final: 4 residues processed: 153 average time/residue: 0.0952 time to fit residues: 23.6916 Evaluate side-chains 136 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain F residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 HIS D 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.067524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053117 restraints weight = 48939.581| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.59 r_work: 0.2824 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15227 Z= 0.187 Angle : 0.614 9.902 20735 Z= 0.298 Chirality : 0.044 0.341 2387 Planarity : 0.003 0.035 2536 Dihedral : 9.419 115.386 2453 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.01 % Allowed : 8.53 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1764 helix: 2.12 (0.21), residues: 589 sheet: -0.58 (0.23), residues: 461 loop : -0.41 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 406 TYR 0.017 0.001 TYR B 299 PHE 0.017 0.001 PHE C 293 TRP 0.013 0.001 TRP E 241 HIS 0.004 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00423 (15199) covalent geometry : angle 0.58001 (20657) SS BOND : bond 0.00432 ( 6) SS BOND : angle 1.36771 ( 12) hydrogen bonds : bond 0.03848 ( 592) hydrogen bonds : angle 4.26857 ( 1701) link_ALPHA1-3 : bond 0.00883 ( 3) link_ALPHA1-3 : angle 3.27744 ( 9) link_ALPHA1-6 : bond 0.00820 ( 3) link_ALPHA1-6 : angle 1.70102 ( 9) link_BETA1-4 : bond 0.00531 ( 8) link_BETA1-4 : angle 2.13714 ( 24) link_NAG-ASN : bond 0.00908 ( 8) link_NAG-ASN : angle 5.08885 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.610 Fit side-chains REVERT: A 56 HIS cc_start: 0.9068 (t-90) cc_final: 0.8840 (m-70) REVERT: A 597 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 49 MET cc_start: 0.8663 (ppp) cc_final: 0.8171 (ppp) REVERT: C 95 ASP cc_start: 0.8780 (p0) cc_final: 0.8330 (p0) REVERT: C 155 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8066 (mm-30) REVERT: E 185 GLN cc_start: 0.9111 (pm20) cc_final: 0.8555 (pm20) REVERT: E 283 MET cc_start: 0.8790 (ttt) cc_final: 0.8419 (tpp) REVERT: E 426 TRP cc_start: 0.8618 (t60) cc_final: 0.8361 (t-100) REVERT: D 229 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8571 (tp-100) REVERT: D 258 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: F 5 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8480 (mm-40) REVERT: F 414 HIS cc_start: 0.8584 (m90) cc_final: 0.8137 (m90) outliers start: 16 outliers final: 9 residues processed: 144 average time/residue: 0.0961 time to fit residues: 22.4715 Evaluate side-chains 140 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.067046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052693 restraints weight = 48913.883| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.56 r_work: 0.2808 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15227 Z= 0.189 Angle : 0.597 9.551 20735 Z= 0.291 Chirality : 0.044 0.351 2387 Planarity : 0.003 0.040 2536 Dihedral : 8.805 117.158 2453 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.64 % Allowed : 9.54 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1764 helix: 2.19 (0.21), residues: 585 sheet: -0.53 (0.24), residues: 455 loop : -0.40 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 406 TYR 0.017 0.001 TYR B 299 PHE 0.015 0.001 PHE D 304 TRP 0.012 0.001 TRP B 237 HIS 0.004 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00428 (15199) covalent geometry : angle 0.56436 (20657) SS BOND : bond 0.00397 ( 6) SS BOND : angle 1.12432 ( 12) hydrogen bonds : bond 0.03740 ( 592) hydrogen bonds : angle 4.21340 ( 1701) link_ALPHA1-3 : bond 0.00965 ( 3) link_ALPHA1-3 : angle 3.50997 ( 9) link_ALPHA1-6 : bond 0.00892 ( 3) link_ALPHA1-6 : angle 1.83702 ( 9) link_BETA1-4 : bond 0.00377 ( 8) link_BETA1-4 : angle 2.06066 ( 24) link_NAG-ASN : bond 0.00894 ( 8) link_NAG-ASN : angle 4.74874 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.583 Fit side-chains REVERT: A 56 HIS cc_start: 0.9061 (t-90) cc_final: 0.8790 (m-70) REVERT: A 597 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 55 MET cc_start: 0.9230 (mmp) cc_final: 0.8921 (mmp) REVERT: C 49 MET cc_start: 0.8683 (ppp) cc_final: 0.8260 (ppp) REVERT: C 95 ASP cc_start: 0.8806 (p0) cc_final: 0.8204 (p0) REVERT: E 49 MET cc_start: 0.9069 (mtm) cc_final: 0.8213 (tmm) REVERT: E 185 GLN cc_start: 0.9056 (pm20) cc_final: 0.8551 (pm20) REVERT: D 258 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: F 414 HIS cc_start: 0.8574 (m90) cc_final: 0.8160 (m90) REVERT: F 452 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8591 (tppt) REVERT: F 456 THR cc_start: 0.9363 (m) cc_final: 0.8936 (p) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 0.0902 time to fit residues: 21.0574 Evaluate side-chains 139 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 145 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.052274 restraints weight = 48963.091| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.50 r_work: 0.2806 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15227 Z= 0.188 Angle : 0.594 9.577 20735 Z= 0.290 Chirality : 0.044 0.364 2387 Planarity : 0.003 0.041 2536 Dihedral : 8.398 114.567 2453 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.71 % Allowed : 10.87 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1764 helix: 2.23 (0.21), residues: 584 sheet: -0.50 (0.24), residues: 455 loop : -0.38 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 31 TYR 0.018 0.001 TYR B 299 PHE 0.012 0.001 PHE A 672 TRP 0.014 0.001 TRP B 237 HIS 0.004 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00426 (15199) covalent geometry : angle 0.56124 (20657) SS BOND : bond 0.00456 ( 6) SS BOND : angle 1.21995 ( 12) hydrogen bonds : bond 0.03694 ( 592) hydrogen bonds : angle 4.16174 ( 1701) link_ALPHA1-3 : bond 0.01011 ( 3) link_ALPHA1-3 : angle 3.62432 ( 9) link_ALPHA1-6 : bond 0.00787 ( 3) link_ALPHA1-6 : angle 2.18540 ( 9) link_BETA1-4 : bond 0.00320 ( 8) link_BETA1-4 : angle 2.02175 ( 24) link_NAG-ASN : bond 0.00868 ( 8) link_NAG-ASN : angle 4.65831 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 56 HIS cc_start: 0.9078 (t-90) cc_final: 0.8679 (t70) REVERT: A 597 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8084 (tm-30) REVERT: B 55 MET cc_start: 0.9311 (mmp) cc_final: 0.8605 (mmp) REVERT: B 138 MET cc_start: 0.8833 (ptp) cc_final: 0.8262 (ptt) REVERT: C 49 MET cc_start: 0.8703 (ppp) cc_final: 0.8275 (ppp) REVERT: C 95 ASP cc_start: 0.8833 (p0) cc_final: 0.8250 (p0) REVERT: C 284 TYR cc_start: 0.8659 (t80) cc_final: 0.8385 (t80) REVERT: E 49 MET cc_start: 0.9045 (mtm) cc_final: 0.8197 (tmm) REVERT: E 185 GLN cc_start: 0.9114 (pm20) cc_final: 0.8696 (pm20) REVERT: D 229 GLN cc_start: 0.9031 (tp40) cc_final: 0.8738 (tp40) REVERT: F 414 HIS cc_start: 0.8555 (m90) cc_final: 0.8146 (m90) REVERT: F 456 THR cc_start: 0.9405 (m) cc_final: 0.9015 (p) outliers start: 27 outliers final: 17 residues processed: 144 average time/residue: 0.0947 time to fit residues: 22.3708 Evaluate side-chains 145 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 164 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.067637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053298 restraints weight = 48024.377| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.52 r_work: 0.2840 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15227 Z= 0.116 Angle : 0.572 9.677 20735 Z= 0.278 Chirality : 0.043 0.373 2387 Planarity : 0.003 0.041 2536 Dihedral : 7.829 110.621 2453 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.39 % Allowed : 11.43 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1764 helix: 2.37 (0.22), residues: 584 sheet: -0.40 (0.24), residues: 447 loop : -0.38 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 250 TYR 0.017 0.001 TYR B 299 PHE 0.011 0.001 PHE D 157 TRP 0.011 0.001 TRP B 237 HIS 0.004 0.000 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00256 (15199) covalent geometry : angle 0.54054 (20657) SS BOND : bond 0.00320 ( 6) SS BOND : angle 0.87695 ( 12) hydrogen bonds : bond 0.03395 ( 592) hydrogen bonds : angle 4.03422 ( 1701) link_ALPHA1-3 : bond 0.01050 ( 3) link_ALPHA1-3 : angle 3.74013 ( 9) link_ALPHA1-6 : bond 0.00801 ( 3) link_ALPHA1-6 : angle 2.07378 ( 9) link_BETA1-4 : bond 0.00384 ( 8) link_BETA1-4 : angle 1.94059 ( 24) link_NAG-ASN : bond 0.00950 ( 8) link_NAG-ASN : angle 4.46091 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.587 Fit side-chains REVERT: A 56 HIS cc_start: 0.9055 (t-90) cc_final: 0.8670 (t70) REVERT: A 597 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 662 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7987 (t80) REVERT: B 55 MET cc_start: 0.9287 (mmp) cc_final: 0.8693 (mmp) REVERT: B 138 MET cc_start: 0.8623 (ptp) cc_final: 0.8245 (ptt) REVERT: C 49 MET cc_start: 0.8687 (ppp) cc_final: 0.8273 (ppp) REVERT: C 95 ASP cc_start: 0.8797 (p0) cc_final: 0.8220 (p0) REVERT: C 284 TYR cc_start: 0.8660 (t80) cc_final: 0.8370 (t80) REVERT: E 49 MET cc_start: 0.9037 (mtm) cc_final: 0.8210 (tmm) REVERT: E 185 GLN cc_start: 0.9091 (pm20) cc_final: 0.8728 (pm20) REVERT: E 190 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: D 148 MET cc_start: 0.8810 (mpp) cc_final: 0.8338 (mpp) REVERT: F 456 THR cc_start: 0.9387 (m) cc_final: 0.8996 (p) outliers start: 22 outliers final: 16 residues processed: 145 average time/residue: 0.0971 time to fit residues: 22.8779 Evaluate side-chains 146 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 412 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051924 restraints weight = 48330.444| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.58 r_work: 0.2803 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15227 Z= 0.192 Angle : 0.602 9.704 20735 Z= 0.294 Chirality : 0.044 0.370 2387 Planarity : 0.003 0.040 2536 Dihedral : 7.475 109.029 2453 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.83 % Allowed : 11.50 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1764 helix: 2.32 (0.21), residues: 586 sheet: -0.46 (0.24), residues: 460 loop : -0.30 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 31 TYR 0.018 0.001 TYR B 299 PHE 0.013 0.001 PHE D 304 TRP 0.016 0.001 TRP B 237 HIS 0.003 0.001 HIS E 107 Details of bonding type rmsd covalent geometry : bond 0.00437 (15199) covalent geometry : angle 0.57195 (20657) SS BOND : bond 0.00390 ( 6) SS BOND : angle 1.13075 ( 12) hydrogen bonds : bond 0.03596 ( 592) hydrogen bonds : angle 4.12120 ( 1701) link_ALPHA1-3 : bond 0.00927 ( 3) link_ALPHA1-3 : angle 3.76872 ( 9) link_ALPHA1-6 : bond 0.00775 ( 3) link_ALPHA1-6 : angle 2.35844 ( 9) link_BETA1-4 : bond 0.00286 ( 8) link_BETA1-4 : angle 2.00267 ( 24) link_NAG-ASN : bond 0.00880 ( 8) link_NAG-ASN : angle 4.40210 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.511 Fit side-chains REVERT: A 56 HIS cc_start: 0.9090 (t-90) cc_final: 0.8704 (t70) REVERT: A 597 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 662 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7967 (t80) REVERT: B 55 MET cc_start: 0.9318 (mmp) cc_final: 0.8876 (mmp) REVERT: B 138 MET cc_start: 0.8822 (ptp) cc_final: 0.8561 (ptp) REVERT: C 49 MET cc_start: 0.8711 (ppp) cc_final: 0.8264 (ppp) REVERT: C 95 ASP cc_start: 0.8818 (p0) cc_final: 0.8208 (p0) REVERT: E 9 MET cc_start: 0.8912 (tpp) cc_final: 0.8642 (tpp) REVERT: E 49 MET cc_start: 0.9046 (mtm) cc_final: 0.8208 (tmm) REVERT: E 185 GLN cc_start: 0.9107 (pm20) cc_final: 0.8734 (pm20) REVERT: E 190 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: D 148 MET cc_start: 0.8820 (mpp) cc_final: 0.8374 (mpp) REVERT: F 456 THR cc_start: 0.9440 (m) cc_final: 0.9053 (p) outliers start: 29 outliers final: 24 residues processed: 144 average time/residue: 0.1012 time to fit residues: 23.2893 Evaluate side-chains 154 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 412 SER Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 36 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 160 optimal weight: 0.0980 chunk 140 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.052849 restraints weight = 48187.115| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.51 r_work: 0.2831 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15227 Z= 0.127 Angle : 0.579 10.412 20735 Z= 0.282 Chirality : 0.043 0.358 2387 Planarity : 0.003 0.042 2536 Dihedral : 7.072 104.874 2453 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 2.08 % Allowed : 11.62 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1764 helix: 2.40 (0.22), residues: 585 sheet: -0.44 (0.24), residues: 455 loop : -0.27 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 250 TYR 0.017 0.001 TYR B 299 PHE 0.010 0.001 PHE C 293 TRP 0.014 0.001 TRP B 237 HIS 0.003 0.001 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00286 (15199) covalent geometry : angle 0.54982 (20657) SS BOND : bond 0.00446 ( 6) SS BOND : angle 0.89711 ( 12) hydrogen bonds : bond 0.03373 ( 592) hydrogen bonds : angle 4.02905 ( 1701) link_ALPHA1-3 : bond 0.00933 ( 3) link_ALPHA1-3 : angle 3.81587 ( 9) link_ALPHA1-6 : bond 0.00830 ( 3) link_ALPHA1-6 : angle 2.27482 ( 9) link_BETA1-4 : bond 0.00319 ( 8) link_BETA1-4 : angle 1.85244 ( 24) link_NAG-ASN : bond 0.00915 ( 8) link_NAG-ASN : angle 4.28826 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.518 Fit side-chains REVERT: A 56 HIS cc_start: 0.9072 (t-90) cc_final: 0.8703 (t70) REVERT: A 597 GLN cc_start: 0.8771 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 634 MET cc_start: 0.9011 (mmm) cc_final: 0.8783 (mmm) REVERT: A 662 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7777 (t80) REVERT: B 55 MET cc_start: 0.9333 (mmp) cc_final: 0.9013 (mmp) REVERT: C 49 MET cc_start: 0.8730 (ppp) cc_final: 0.8309 (ppp) REVERT: C 95 ASP cc_start: 0.8795 (p0) cc_final: 0.8230 (p0) REVERT: C 155 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8033 (mm-30) REVERT: C 284 TYR cc_start: 0.8682 (t80) cc_final: 0.8365 (t80) REVERT: E 9 MET cc_start: 0.8911 (tpp) cc_final: 0.8627 (tpp) REVERT: E 49 MET cc_start: 0.9018 (mtm) cc_final: 0.8206 (tmm) REVERT: E 185 GLN cc_start: 0.9096 (pm20) cc_final: 0.8765 (pm20) REVERT: E 190 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: D 148 MET cc_start: 0.8743 (mpp) cc_final: 0.8425 (mpp) REVERT: F 456 THR cc_start: 0.9453 (m) cc_final: 0.9080 (p) outliers start: 33 outliers final: 24 residues processed: 146 average time/residue: 0.0918 time to fit residues: 21.6854 Evaluate side-chains 156 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 155 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 298 GLU Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 412 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 118 optimal weight: 0.7980 chunk 145 optimal weight: 0.0270 chunk 10 optimal weight: 4.9990 chunk 172 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN D 110 HIS D 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.068722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054663 restraints weight = 48089.862| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.48 r_work: 0.2871 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15227 Z= 0.102 Angle : 0.572 12.463 20735 Z= 0.276 Chirality : 0.043 0.354 2387 Planarity : 0.003 0.042 2536 Dihedral : 6.555 98.474 2453 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.71 % Allowed : 11.75 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1764 helix: 2.52 (0.22), residues: 583 sheet: -0.33 (0.24), residues: 445 loop : -0.19 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 250 TYR 0.014 0.001 TYR B 299 PHE 0.010 0.001 PHE D 157 TRP 0.011 0.001 TRP B 237 HIS 0.003 0.000 HIS D 110 Details of bonding type rmsd covalent geometry : bond 0.00223 (15199) covalent geometry : angle 0.54399 (20657) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.76397 ( 12) hydrogen bonds : bond 0.03081 ( 592) hydrogen bonds : angle 3.92922 ( 1701) link_ALPHA1-3 : bond 0.00980 ( 3) link_ALPHA1-3 : angle 3.87672 ( 9) link_ALPHA1-6 : bond 0.00822 ( 3) link_ALPHA1-6 : angle 2.21636 ( 9) link_BETA1-4 : bond 0.00360 ( 8) link_BETA1-4 : angle 1.71959 ( 24) link_NAG-ASN : bond 0.00952 ( 8) link_NAG-ASN : angle 4.18208 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.523 Fit side-chains REVERT: A 56 HIS cc_start: 0.9028 (t-90) cc_final: 0.8673 (t70) REVERT: A 581 MET cc_start: 0.8906 (mmm) cc_final: 0.8463 (mmm) REVERT: A 597 GLN cc_start: 0.8720 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 662 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 666 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: B 55 MET cc_start: 0.9302 (mmp) cc_final: 0.8919 (mmp) REVERT: B 224 GLN cc_start: 0.8975 (tp40) cc_final: 0.8775 (tp40) REVERT: B 227 MET cc_start: 0.8409 (ppp) cc_final: 0.7950 (ppp) REVERT: B 237 TRP cc_start: 0.8990 (m-10) cc_final: 0.8595 (m-10) REVERT: C 49 MET cc_start: 0.8737 (ppp) cc_final: 0.8306 (ppp) REVERT: C 95 ASP cc_start: 0.8757 (p0) cc_final: 0.8215 (p0) REVERT: E 9 MET cc_start: 0.8925 (tpp) cc_final: 0.8637 (tpp) REVERT: E 49 MET cc_start: 0.8977 (mtm) cc_final: 0.8237 (tmm) REVERT: E 95 ASP cc_start: 0.8559 (p0) cc_final: 0.8207 (p0) REVERT: E 185 GLN cc_start: 0.9064 (pm20) cc_final: 0.8769 (pm20) REVERT: E 190 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: D 148 MET cc_start: 0.8727 (mpp) cc_final: 0.8451 (mpp) REVERT: F 1 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7524 (tm-30) REVERT: F 446 SER cc_start: 0.8966 (t) cc_final: 0.8568 (t) REVERT: F 456 THR cc_start: 0.9466 (m) cc_final: 0.9060 (p) outliers start: 27 outliers final: 19 residues processed: 153 average time/residue: 0.0938 time to fit residues: 23.2692 Evaluate side-chains 149 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 63 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 46 optimal weight: 0.0010 chunk 161 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.053504 restraints weight = 48327.141| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.50 r_work: 0.2842 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15227 Z= 0.145 Angle : 0.595 14.902 20735 Z= 0.287 Chirality : 0.043 0.363 2387 Planarity : 0.003 0.043 2536 Dihedral : 6.392 95.795 2453 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 12.32 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1764 helix: 2.49 (0.22), residues: 584 sheet: -0.32 (0.24), residues: 455 loop : -0.21 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 207 TYR 0.017 0.001 TYR B 299 PHE 0.011 0.001 PHE D 304 TRP 0.017 0.001 TRP E 241 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00329 (15199) covalent geometry : angle 0.56775 (20657) SS BOND : bond 0.00326 ( 6) SS BOND : angle 0.95610 ( 12) hydrogen bonds : bond 0.03254 ( 592) hydrogen bonds : angle 4.00033 ( 1701) link_ALPHA1-3 : bond 0.00996 ( 3) link_ALPHA1-3 : angle 3.88478 ( 9) link_ALPHA1-6 : bond 0.00770 ( 3) link_ALPHA1-6 : angle 2.34132 ( 9) link_BETA1-4 : bond 0.00304 ( 8) link_BETA1-4 : angle 1.71402 ( 24) link_NAG-ASN : bond 0.00864 ( 8) link_NAG-ASN : angle 4.17562 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.572 Fit side-chains REVERT: A 56 HIS cc_start: 0.9048 (t-90) cc_final: 0.8701 (t70) REVERT: A 581 MET cc_start: 0.8939 (mmm) cc_final: 0.8363 (mmm) REVERT: A 597 GLN cc_start: 0.8754 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 634 MET cc_start: 0.9210 (mmm) cc_final: 0.8995 (mmm) REVERT: A 662 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.7955 (t80) REVERT: B 55 MET cc_start: 0.9411 (mmp) cc_final: 0.8965 (mmp) REVERT: B 227 MET cc_start: 0.8401 (ppp) cc_final: 0.7762 (ppp) REVERT: C 49 MET cc_start: 0.8765 (ppp) cc_final: 0.8316 (ppp) REVERT: C 95 ASP cc_start: 0.8768 (p0) cc_final: 0.8319 (p0) REVERT: E 9 MET cc_start: 0.8937 (tpp) cc_final: 0.8655 (tpp) REVERT: E 49 MET cc_start: 0.8989 (mtm) cc_final: 0.8249 (tmm) REVERT: E 95 ASP cc_start: 0.8612 (p0) cc_final: 0.8264 (p0) REVERT: E 185 GLN cc_start: 0.9074 (pm20) cc_final: 0.8777 (pm20) REVERT: E 190 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: F 1 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7641 (tm-30) REVERT: F 446 SER cc_start: 0.9006 (t) cc_final: 0.8595 (t) REVERT: F 456 THR cc_start: 0.9475 (m) cc_final: 0.9114 (p) outliers start: 25 outliers final: 21 residues processed: 141 average time/residue: 0.0971 time to fit residues: 22.2476 Evaluate side-chains 150 residues out of total 1583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 662 TYR Chi-restraints excluded: chain A residue 666 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 267 HIS Chi-restraints excluded: chain E residue 415 TYR Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 275 ASN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 412 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.053567 restraints weight = 48274.605| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.54 r_work: 0.2842 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15227 Z= 0.134 Angle : 0.587 10.333 20735 Z= 0.284 Chirality : 0.043 0.358 2387 Planarity : 0.003 0.043 2536 Dihedral : 6.183 90.949 2453 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 1.71 % Allowed : 12.26 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1764 helix: 2.46 (0.22), residues: 584 sheet: -0.28 (0.24), residues: 455 loop : -0.20 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 250 TYR 0.017 0.001 TYR B 299 PHE 0.010 0.001 PHE D 304 TRP 0.014 0.001 TRP B 237 HIS 0.002 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00304 (15199) covalent geometry : angle 0.56008 (20657) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.92247 ( 12) hydrogen bonds : bond 0.03265 ( 592) hydrogen bonds : angle 3.98020 ( 1701) link_ALPHA1-3 : bond 0.01085 ( 3) link_ALPHA1-3 : angle 3.66478 ( 9) link_ALPHA1-6 : bond 0.00845 ( 3) link_ALPHA1-6 : angle 2.34524 ( 9) link_BETA1-4 : bond 0.00298 ( 8) link_BETA1-4 : angle 1.64451 ( 24) link_NAG-ASN : bond 0.00851 ( 8) link_NAG-ASN : angle 4.12940 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2886.90 seconds wall clock time: 50 minutes 19.47 seconds (3019.47 seconds total)