Starting phenix.real_space_refine on Sat Jul 4 01:40:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql5_14064/07_2026/7ql5_14064.map" } resolution = 2.5 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= 0.004 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 84 5.16 5 C 11139 2.51 5 N 2614 2.21 5 O 3180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17028 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 390, 3165 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 370} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 390, 3165 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 370} Chain breaks: 1 bond proxies already assigned to first conformer: 3240 Chain: "B" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3239 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 376} Chain breaks: 1 Chain: "C" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3430 Classifications: {'peptide': 423} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 395} Chain breaks: 1 Chain: "D" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3010 Classifications: {'peptide': 371} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 351} Chain breaks: 1 Chain: "E" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3297 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 384} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "G" 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 chiralities: 5 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 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 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 chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 135 Unusual residues: {'NCT': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {'NCT': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {'NAG': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.33, per 1000 atoms: 0.25 Number of scatterers: 17028 At special positions: 0 Unit cell: (101.721, 103.375, 176.151, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 11 15.00 O 3180 8.00 N 2614 7.00 C 11139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.08 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 6 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN C 70 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 876.1 milliseconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 19 sheets defined 42.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.964A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.138A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.744A pdb=" N SER A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 4.546A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 324 removed outlier: 5.675A pdb=" N ILE A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Proline residue: A 321 - end of helix removed outlier: 3.701A pdb=" N MET A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 432 removed outlier: 3.624A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.682A pdb=" N THR B 6 " --> pdb=" O VAL B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.535A pdb=" N VAL B 85 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 removed outlier: 3.979A pdb=" N PHE B 180 " --> pdb=" O LYS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 180' Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 247 through 267 Processing helix chain 'B' and resid 278 through 306 Processing helix chain 'B' and resid 315 through 331 Proline residue: B 327 - end of helix Processing helix chain 'B' and resid 406 through 459 removed outlier: 3.546A pdb=" N ASP B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.034A pdb=" N ARG C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.912A pdb=" N SER C 75 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 246 removed outlier: 4.487A pdb=" N THR C 234 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.687A pdb=" N LEU C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 277 removed outlier: 3.924A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 Processing helix chain 'C' and resid 323 through 339 removed outlier: 5.510A pdb=" N LEU C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) Proline residue: C 335 - end of helix Processing helix chain 'C' and resid 420 through 478 removed outlier: 4.267A pdb=" N ASP C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 430 " --> pdb=" O THR C 426 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 431 " --> pdb=" O ASN C 427 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 68 through 73 removed outlier: 3.946A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.569A pdb=" N VAL D 85 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 235 removed outlier: 4.634A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 3.637A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 319 Processing helix chain 'D' and resid 379 through 425 Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.939A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 174 through 178 removed outlier: 4.171A pdb=" N PHE E 178 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 237 Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.563A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 273 Processing helix chain 'E' and resid 281 through 310 removed outlier: 3.574A pdb=" N ARG E 310 " --> pdb=" O ASN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 Proline residue: E 330 - end of helix Processing helix chain 'E' and resid 420 through 472 removed outlier: 3.682A pdb=" N GLN E 430 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN E 431 " --> pdb=" O THR E 427 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU E 436 " --> pdb=" O ASP E 432 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP E 453 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.105A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.105A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.077A pdb=" N TYR A 198 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TRP A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS A 204 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.987A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 127 removed outlier: 6.254A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N VAL B 174 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 35 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.469A pdb=" N SER B 148 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU B 205 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN B 214 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE B 188 " --> pdb=" O GLN B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.469A pdb=" N SER B 148 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLU B 205 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 82 removed outlier: 4.712A pdb=" N GLY C 116 " --> pdb=" O ASP C 64 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 removed outlier: 4.712A pdb=" N GLY C 116 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR C 51 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 45 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 53 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP C 57 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU C 39 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASP C 59 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU C 37 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA C 61 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 35 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N TYR C 63 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE C 33 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 11.654A pdb=" N HIS C 65 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 13.919A pdb=" N VAL C 31 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.969A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 220 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.969A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 167 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.207A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.207A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 92 removed outlier: 6.143A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.907A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.907A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ALA E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU E 43 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU E 37 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU E 35 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN E 59 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU E 33 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ASN E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL E 31 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N TYR E 63 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 13.726A pdb=" N ILE E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.237A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 216 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE E 186 " --> pdb=" O GLN E 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.237A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) 877 hydrogen bonds defined for protein. 2543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 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: 1.19 - 1.32: 2615 1.32 - 1.45: 4883 1.45 - 1.58: 9793 1.58 - 1.71: 26 1.71 - 1.84: 137 Bond restraints: 17454 Sorted by residual: bond pdb=" C9 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.651 -0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C9 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.647 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C8 NCT A 601 " pdb=" C9 NCT A 601 " ideal model delta sigma weight residual 1.532 1.352 0.180 2.00e-02 2.50e+03 8.08e+01 bond pdb=" C8 NCT D 601 " pdb=" C9 NCT D 601 " ideal model delta sigma weight residual 1.532 1.353 0.179 2.00e-02 2.50e+03 8.02e+01 bond pdb=" C6 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.331 0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 17449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 23247 2.78 - 5.57: 386 5.57 - 8.35: 86 8.35 - 11.13: 29 11.13 - 13.91: 19 Bond angle restraints: 23767 Sorted by residual: angle pdb=" O VAL D 405 " pdb=" C VAL D 405 " pdb=" N ILE D 406 " ideal model delta sigma weight residual 121.87 113.22 8.65 9.70e-01 1.06e+00 7.96e+01 angle pdb=" CA VAL D 405 " pdb=" C VAL D 405 " pdb=" N ILE D 406 " ideal model delta sigma weight residual 117.15 125.84 -8.69 1.14e+00 7.69e-01 5.81e+01 angle pdb=" C TYR B 134 " pdb=" CA TYR B 134 " pdb=" CB TYR B 134 " ideal model delta sigma weight residual 109.83 116.04 -6.21 9.90e-01 1.02e+00 3.94e+01 angle pdb=" O SER E 294 " pdb=" C SER E 294 " pdb=" N MET E 295 " ideal model delta sigma weight residual 122.12 127.48 -5.36 1.06e+00 8.90e-01 2.55e+01 angle pdb=" C CYS A 142 " pdb=" CA CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sigma weight residual 109.48 117.96 -8.48 1.68e+00 3.54e-01 2.55e+01 ... (remaining 23762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 9814 35.22 - 70.43: 238 70.43 - 105.65: 20 105.65 - 140.86: 6 140.86 - 176.08: 2 Dihedral angle restraints: 10080 sinusoidal: 4177 harmonic: 5903 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual -86.00 -44.76 -41.24 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" C27 POV C 602 " pdb=" C28 POV C 602 " pdb=" C29 POV C 602 " pdb="C210 POV C 602 " ideal model delta sinusoidal sigma weight residual 127.48 -56.44 -176.08 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C CYS A 142 " pdb=" N CYS A 142 " pdb=" CA CYS A 142 " pdb=" CB CYS A 142 " ideal model delta harmonic sigma weight residual -122.60 -133.82 11.22 0 2.50e+00 1.60e-01 2.02e+01 ... (remaining 10077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2497 0.075 - 0.151: 298 0.151 - 0.226: 19 0.226 - 0.302: 7 0.302 - 0.377: 3 Chirality restraints: 2824 Sorted by residual: chirality pdb=" CA CYS A 142 " pdb=" N CYS A 142 " pdb=" C CYS A 142 " pdb=" CB CYS A 142 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA PHE D 233 " pdb=" N PHE D 233 " pdb=" C PHE D 233 " pdb=" CB PHE D 233 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2821 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 137 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C PHE A 137 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE A 137 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 138 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 417 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ILE D 417 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE D 417 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS D 418 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 228 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C LEU D 228 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU D 228 " -0.013 2.00e-02 2.50e+03 pdb=" N THR D 229 " -0.012 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1198 2.74 - 3.28: 16851 3.28 - 3.82: 29137 3.82 - 4.36: 35783 4.36 - 4.90: 60378 Nonbonded interactions: 143347 Sorted by model distance: nonbonded pdb=" OG SER D 302 " pdb=" OG1 THR D 305 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 89 " pdb=" OG1 THR A 150 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 152 " pdb=" OG1 THR A 154 " model vdw 2.201 3.040 nonbonded pdb=" O ILE A 420 " pdb=" OG SER A 424 " model vdw 2.210 3.040 nonbonded pdb=" O LEU B 92 " pdb=" ND2 ASN B 95 " model vdw 2.210 3.120 ... (remaining 143342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 226 or resid 228 through 323 or resid 378 throug \ h 425 or (resid 603 through 604 and (name N or name C1 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C2 \ 3 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or nam \ e C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or \ name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )))) selection = (chain 'D' and (resid 1 through 226 or resid 228 through 425 or resid 602 throug \ h 603)) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'K' and (resid 1 or resid 4 through 6)) selection = (chain 'L' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.600 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 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 : 0.008 0.199 17498 Z= 0.395 Angle : 0.960 13.913 23892 Z= 0.435 Chirality : 0.050 0.377 2824 Planarity : 0.004 0.040 2854 Dihedral : 14.836 176.076 6219 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.03 % Allowed : 5.66 % Favored : 93.30 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.63 % 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 (0.19), residues: 1970 helix: 1.97 (0.19), residues: 732 sheet: 0.32 (0.25), residues: 407 loop : -0.38 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.015 0.001 TYR D 234 PHE 0.013 0.001 PHE B 137 TRP 0.007 0.001 TRP E 453 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.39 (17454) covalent geometry : angle 0.94696 / 0.43 (23767) SS BOND : bond 0.01915 / 1.01 ( 7) SS BOND : angle 3.78267 / 2.11 ( 14) hydrogen bonds : bond 0.15391 / 10.49 ( 799) hydrogen bonds : angle 5.78584 / 4.11 ( 2543) link_ALPHA1-3 : bond 0.00455 / 0.29 ( 7) link_ALPHA1-3 : angle 1.74124 / 1.10 ( 21) link_ALPHA1-6 : bond 0.00505 / 0.35 ( 9) link_ALPHA1-6 : angle 1.65160 / 1.13 ( 27) link_BETA1-4 : bond 0.00885 / 0.64 ( 13) link_BETA1-4 : angle 2.58644 / 1.73 ( 39) link_NAG-ASN : bond 0.01229 / 0.65 ( 8) link_NAG-ASN : angle 2.15231 / 1.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8826 (mmt) cc_final: 0.8608 (tpp) REVERT: A 262 GLU cc_start: 0.7211 (tt0) cc_final: 0.6916 (tp30) REVERT: A 306 HIS cc_start: 0.7498 (m90) cc_final: 0.7226 (m-70) REVERT: B 310 ASN cc_start: 0.7947 (t0) cc_final: 0.7623 (t0) REVERT: D 397 GLU cc_start: 0.5954 (tp30) cc_final: 0.5546 (tm-30) REVERT: E 472 PHE cc_start: 0.7923 (m-80) cc_final: 0.7633 (m-10) outliers start: 19 outliers final: 6 residues processed: 189 average time/residue: 0.4725 time to fit residues: 102.9387 Evaluate side-chains 146 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 98 ASN C 103 HIS D 297 ASN D 306 HIS E 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086721 restraints weight = 24706.245| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.02 r_work: 0.3008 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (10 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17498 Z= 0.185 Angle : 0.609 9.970 23892 Z= 0.308 Chirality : 0.046 0.302 2824 Planarity : 0.004 0.044 2854 Dihedral : 14.583 177.076 2382 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.63 % Allowed : 8.66 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.05 (0.19), residues: 1970 helix: 2.20 (0.19), residues: 747 sheet: 0.20 (0.24), residues: 414 loop : -0.43 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 485 TYR 0.015 0.001 TYR D 151 PHE 0.017 0.002 PHE C 294 TRP 0.011 0.001 TRP E 453 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (17454) covalent geometry : angle 0.59084 / 0.30 (23767) SS BOND : bond 0.00861 / 0.45 ( 7) SS BOND : angle 3.17247 / 1.84 ( 14) hydrogen bonds : bond 0.05549 / 3.72 ( 799) hydrogen bonds : angle 4.80727 / 3.41 ( 2543) link_ALPHA1-3 : bond 0.00540 / 0.36 ( 7) link_ALPHA1-3 : angle 1.65818 / 1.07 ( 21) link_ALPHA1-6 : bond 0.00592 / 0.42 ( 9) link_ALPHA1-6 : angle 1.57695 / 1.16 ( 27) link_BETA1-4 : bond 0.00747 / 0.55 ( 13) link_BETA1-4 : angle 2.31649 / 1.63 ( 39) link_NAG-ASN : bond 0.00363 / 0.20 ( 8) link_NAG-ASN : angle 1.95371 / 1.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9052 (mmt) cc_final: 0.8831 (tpp) REVERT: A 262 GLU cc_start: 0.7864 (tt0) cc_final: 0.7407 (tp30) REVERT: A 306 HIS cc_start: 0.7500 (m90) cc_final: 0.7244 (m-70) REVERT: B 314 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7525 (ttp) REVERT: C 454 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: D 397 GLU cc_start: 0.6081 (tp30) cc_final: 0.5655 (tm-30) REVERT: E 299 MET cc_start: 0.8331 (ttt) cc_final: 0.7808 (ttp) outliers start: 30 outliers final: 13 residues processed: 159 average time/residue: 0.4896 time to fit residues: 89.1599 Evaluate side-chains 154 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 50 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084322 restraints weight = 27147.030| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.06 r_work: 0.2963 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (17 function evaluations) r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 17498 Z= 0.243 Angle : 0.652 7.102 23892 Z= 0.332 Chirality : 0.048 0.253 2824 Planarity : 0.005 0.044 2854 Dihedral : 13.746 165.125 2378 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.34 % Allowed : 9.91 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.93 (0.19), residues: 1970 helix: 2.11 (0.19), residues: 749 sheet: 0.17 (0.24), residues: 419 loop : -0.55 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 125 TYR 0.016 0.002 TYR D 151 PHE 0.021 0.002 PHE C 294 TRP 0.011 0.002 TRP E 453 HIS 0.007 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.24 (17454) covalent geometry : angle 0.63482 / 0.33 (23767) SS BOND : bond 0.00901 / 0.49 ( 7) SS BOND : angle 2.87854 / 1.70 ( 14) hydrogen bonds : bond 0.05608 / 3.76 ( 799) hydrogen bonds : angle 4.82237 / 3.42 ( 2543) link_ALPHA1-3 : bond 0.00557 / 0.38 ( 7) link_ALPHA1-3 : angle 1.65455 / 1.06 ( 21) link_ALPHA1-6 : bond 0.00570 / 0.42 ( 9) link_ALPHA1-6 : angle 1.53701 / 1.15 ( 27) link_BETA1-4 : bond 0.00775 / 0.56 ( 13) link_BETA1-4 : angle 2.56296 / 1.82 ( 39) link_NAG-ASN : bond 0.00422 / 0.25 ( 8) link_NAG-ASN : angle 2.04419 / 1.23 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.9166 (mtm) cc_final: 0.8834 (mtp) REVERT: A 262 GLU cc_start: 0.7829 (tt0) cc_final: 0.7372 (tp30) REVERT: A 273 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 306 HIS cc_start: 0.7524 (m90) cc_final: 0.7295 (m-70) REVERT: B 272 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.6830 (tm-30) REVERT: B 324 GLU cc_start: 0.6987 (mp0) cc_final: 0.6783 (mp0) REVERT: C 331 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5780 (mm) REVERT: D 397 GLU cc_start: 0.6107 (tp30) cc_final: 0.5695 (tm-30) outliers start: 43 outliers final: 22 residues processed: 165 average time/residue: 0.4716 time to fit residues: 88.9023 Evaluate side-chains 156 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 160 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 137 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 0.2980 chunk 129 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088050 restraints weight = 26473.728| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.11 r_work: 0.3031 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17498 Z= 0.121 Angle : 0.534 6.952 23892 Z= 0.269 Chirality : 0.043 0.201 2824 Planarity : 0.004 0.046 2854 Dihedral : 12.570 123.245 2378 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.34 % Allowed : 10.35 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.15 (0.19), residues: 1970 helix: 2.37 (0.19), residues: 755 sheet: 0.11 (0.24), residues: 424 loop : -0.42 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.016 0.001 TYR D 151 PHE 0.017 0.001 PHE C 294 TRP 0.009 0.001 TRP E 60 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (17454) covalent geometry : angle 0.51877 / 0.27 (23767) SS BOND : bond 0.00777 / 0.40 ( 7) SS BOND : angle 1.80452 / 1.00 ( 14) hydrogen bonds : bond 0.04328 / 2.88 ( 799) hydrogen bonds : angle 4.38436 / 3.11 ( 2543) link_ALPHA1-3 : bond 0.00565 / 0.36 ( 7) link_ALPHA1-3 : angle 1.51439 / 0.99 ( 21) link_ALPHA1-6 : bond 0.00570 / 0.41 ( 9) link_ALPHA1-6 : angle 1.51714 / 1.08 ( 27) link_BETA1-4 : bond 0.00755 / 0.56 ( 13) link_BETA1-4 : angle 2.20150 / 1.59 ( 39) link_NAG-ASN : bond 0.00180 / 0.10 ( 8) link_NAG-ASN : angle 1.71651 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7766 (tt0) cc_final: 0.7301 (tp30) REVERT: A 273 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7333 (mp) REVERT: A 306 HIS cc_start: 0.7441 (m90) cc_final: 0.7222 (m-70) REVERT: B 332 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7625 (mt) REVERT: D 245 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7747 (pp) REVERT: D 397 GLU cc_start: 0.6089 (tp30) cc_final: 0.5661 (tm-30) REVERT: E 299 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7738 (ttp) outliers start: 43 outliers final: 17 residues processed: 166 average time/residue: 0.4788 time to fit residues: 91.3646 Evaluate side-chains 154 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 132 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 196 optimal weight: 0.3980 chunk 131 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 297 ASN D 306 HIS E 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086499 restraints weight = 33067.987| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.36 r_work: 0.2998 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17498 Z= 0.136 Angle : 0.544 8.036 23892 Z= 0.273 Chirality : 0.043 0.201 2824 Planarity : 0.004 0.045 2854 Dihedral : 12.077 121.641 2378 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.45 % Allowed : 11.11 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.21 (0.19), residues: 1970 helix: 2.45 (0.19), residues: 750 sheet: 0.21 (0.24), residues: 417 loop : -0.44 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.013 0.001 TYR D 151 PHE 0.017 0.001 PHE C 294 TRP 0.007 0.001 TRP E 60 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (17454) covalent geometry : angle 0.52898 / 0.27 (23767) SS BOND : bond 0.00781 / 0.41 ( 7) SS BOND : angle 1.93018 / 1.09 ( 14) hydrogen bonds : bond 0.04383 / 2.93 ( 799) hydrogen bonds : angle 4.37260 / 3.11 ( 2543) link_ALPHA1-3 : bond 0.00536 / 0.35 ( 7) link_ALPHA1-3 : angle 1.54469 / 1.00 ( 21) link_ALPHA1-6 : bond 0.00562 / 0.41 ( 9) link_ALPHA1-6 : angle 1.51023 / 1.10 ( 27) link_BETA1-4 : bond 0.00729 / 0.54 ( 13) link_BETA1-4 : angle 2.23150 / 1.60 ( 39) link_NAG-ASN : bond 0.00151 / 0.09 ( 8) link_NAG-ASN : angle 1.70576 / 1.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 137 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7860 (tt0) cc_final: 0.7385 (tp30) REVERT: A 273 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7320 (mp) REVERT: B 425 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7063 (mtpt) REVERT: B 456 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8052 (tp) REVERT: D 142 CYS cc_start: 0.6505 (OUTLIER) cc_final: 0.5990 (m) REVERT: D 245 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7668 (pp) REVERT: D 397 GLU cc_start: 0.6044 (tp30) cc_final: 0.5592 (tm-30) REVERT: E 299 MET cc_start: 0.8358 (ttt) cc_final: 0.7804 (ttp) outliers start: 45 outliers final: 22 residues processed: 168 average time/residue: 0.4302 time to fit residues: 83.0073 Evaluate side-chains 159 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 0.0170 chunk 91 optimal weight: 0.0980 chunk 136 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 267 GLN D 297 ASN D 306 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.118134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087803 restraints weight = 35100.459| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.43 r_work: 0.3021 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17498 Z= 0.115 Angle : 0.524 8.000 23892 Z= 0.262 Chirality : 0.043 0.195 2824 Planarity : 0.004 0.047 2854 Dihedral : 11.514 119.008 2378 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.40 % Allowed : 11.33 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.21 (0.19), residues: 1970 helix: 2.41 (0.19), residues: 763 sheet: 0.24 (0.24), residues: 420 loop : -0.46 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 168 TYR 0.014 0.001 TYR D 151 PHE 0.016 0.001 PHE C 294 TRP 0.009 0.001 TRP E 60 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17454) covalent geometry : angle 0.50950 / 0.26 (23767) SS BOND : bond 0.00763 / 0.39 ( 7) SS BOND : angle 1.78809 / 1.00 ( 14) hydrogen bonds : bond 0.04038 / 2.69 ( 799) hydrogen bonds : angle 4.24715 / 3.02 ( 2543) link_ALPHA1-3 : bond 0.00547 / 0.35 ( 7) link_ALPHA1-3 : angle 1.51033 / 0.97 ( 21) link_ALPHA1-6 : bond 0.00552 / 0.39 ( 9) link_ALPHA1-6 : angle 1.48563 / 1.06 ( 27) link_BETA1-4 : bond 0.00747 / 0.55 ( 13) link_BETA1-4 : angle 2.12404 / 1.53 ( 39) link_NAG-ASN : bond 0.00153 / 0.09 ( 8) link_NAG-ASN : angle 1.61195 / 0.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7837 (tt0) cc_final: 0.7348 (tp30) REVERT: A 306 HIS cc_start: 0.7431 (m90) cc_final: 0.7149 (m-70) REVERT: B 318 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8014 (tt) REVERT: B 425 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7076 (mtpt) REVERT: B 456 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8142 (tp) REVERT: C 154 ASP cc_start: 0.8691 (p0) cc_final: 0.8466 (p0) REVERT: D 142 CYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5795 (m) REVERT: D 245 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7610 (pt) REVERT: D 262 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: D 397 GLU cc_start: 0.6059 (tp30) cc_final: 0.5596 (tm-30) REVERT: E 299 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7782 (ttp) REVERT: E 471 HIS cc_start: 0.8112 (t-90) cc_final: 0.7909 (t-90) outliers start: 44 outliers final: 15 residues processed: 169 average time/residue: 0.4996 time to fit residues: 96.8959 Evaluate side-chains 158 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 130 optimal weight: 0.1980 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 0.0070 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 ASN D 297 ASN D 306 HIS E 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090293 restraints weight = 29335.393| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.23 r_work: 0.3063 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17498 Z= 0.102 Angle : 0.505 7.333 23892 Z= 0.252 Chirality : 0.042 0.189 2824 Planarity : 0.004 0.047 2854 Dihedral : 10.863 116.285 2377 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.69 % Allowed : 12.31 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.32 (0.20), residues: 1970 helix: 2.53 (0.19), residues: 762 sheet: 0.29 (0.24), residues: 420 loop : -0.43 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 168 TYR 0.012 0.001 TYR D 151 PHE 0.011 0.001 PHE C 294 TRP 0.010 0.001 TRP E 60 HIS 0.003 0.001 HIS A 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (17454) covalent geometry : angle 0.49176 / 0.25 (23767) SS BOND : bond 0.00740 / 0.37 ( 7) SS BOND : angle 1.59063 / 0.86 ( 14) hydrogen bonds : bond 0.03705 / 2.47 ( 799) hydrogen bonds : angle 4.09195 / 2.91 ( 2543) link_ALPHA1-3 : bond 0.00548 / 0.34 ( 7) link_ALPHA1-3 : angle 1.48523 / 0.95 ( 21) link_ALPHA1-6 : bond 0.00542 / 0.38 ( 9) link_ALPHA1-6 : angle 1.46481 / 1.02 ( 27) link_BETA1-4 : bond 0.00739 / 0.54 ( 13) link_BETA1-4 : angle 2.00969 / 1.45 ( 39) link_NAG-ASN : bond 0.00163 / 0.09 ( 8) link_NAG-ASN : angle 1.46113 / 0.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8593 (p0) cc_final: 0.8273 (p0) REVERT: A 262 GLU cc_start: 0.7807 (tt0) cc_final: 0.7291 (tp30) REVERT: C 154 ASP cc_start: 0.8756 (p0) cc_final: 0.8401 (p0) REVERT: D 142 CYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5605 (m) REVERT: E 299 MET cc_start: 0.8314 (ttt) cc_final: 0.7787 (ttp) outliers start: 31 outliers final: 16 residues processed: 171 average time/residue: 0.4643 time to fit residues: 91.2563 Evaluate side-chains 156 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 57 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 188 optimal weight: 0.0050 chunk 18 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 ASN D 217 ASN D 297 ASN D 306 HIS E 471 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.119155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088403 restraints weight = 40160.003| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.61 r_work: 0.3022 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17498 Z= 0.111 Angle : 0.522 10.765 23892 Z= 0.259 Chirality : 0.042 0.193 2824 Planarity : 0.004 0.046 2854 Dihedral : 10.664 116.507 2376 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.53 % Allowed : 12.91 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.32 (0.20), residues: 1970 helix: 2.54 (0.19), residues: 762 sheet: 0.27 (0.24), residues: 422 loop : -0.42 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 168 TYR 0.012 0.001 TYR A 151 PHE 0.010 0.001 PHE C 294 TRP 0.011 0.001 TRP D 311 HIS 0.011 0.001 HIS E 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (17454) covalent geometry : angle 0.50828 / 0.26 (23767) SS BOND : bond 0.00754 / 0.39 ( 7) SS BOND : angle 1.70002 / 0.93 ( 14) hydrogen bonds : bond 0.03812 / 2.53 ( 799) hydrogen bonds : angle 4.11942 / 2.93 ( 2543) link_ALPHA1-3 : bond 0.00524 / 0.33 ( 7) link_ALPHA1-3 : angle 1.49930 / 0.96 ( 21) link_ALPHA1-6 : bond 0.00536 / 0.38 ( 9) link_ALPHA1-6 : angle 1.45903 / 1.02 ( 27) link_BETA1-4 : bond 0.00721 / 0.53 ( 13) link_BETA1-4 : angle 2.03186 / 1.46 ( 39) link_NAG-ASN : bond 0.00131 / 0.08 ( 8) link_NAG-ASN : angle 1.50208 / 0.87 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8646 (p0) cc_final: 0.8253 (p0) REVERT: A 262 GLU cc_start: 0.7850 (tt0) cc_final: 0.7325 (tp30) REVERT: B 318 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7868 (tt) REVERT: C 154 ASP cc_start: 0.8772 (p0) cc_final: 0.8424 (p0) REVERT: D 142 CYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5753 (m) REVERT: D 398 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: E 299 MET cc_start: 0.8362 (ttt) cc_final: 0.7773 (ttp) REVERT: E 472 PHE cc_start: 0.8239 (m-80) cc_final: 0.7806 (m-10) outliers start: 28 outliers final: 16 residues processed: 160 average time/residue: 0.5216 time to fit residues: 95.2685 Evaluate side-chains 154 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 22 optimal weight: 0.1980 chunk 130 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 166 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 267 GLN C 445 ASN D 297 ASN D 306 HIS E 471 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.120212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090345 restraints weight = 33170.179| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.32 r_work: 0.3062 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17498 Z= 0.103 Angle : 0.514 10.392 23892 Z= 0.254 Chirality : 0.042 0.191 2824 Planarity : 0.004 0.047 2854 Dihedral : 10.287 115.203 2376 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.47 % Allowed : 13.29 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.36 (0.20), residues: 1970 helix: 2.64 (0.19), residues: 751 sheet: 0.30 (0.24), residues: 422 loop : -0.45 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 168 TYR 0.012 0.001 TYR D 151 PHE 0.010 0.001 PHE C 294 TRP 0.009 0.001 TRP D 311 HIS 0.008 0.001 HIS E 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17454) covalent geometry : angle 0.50108 / 0.25 (23767) SS BOND : bond 0.00734 / 0.37 ( 7) SS BOND : angle 1.58734 / 0.86 ( 14) hydrogen bonds : bond 0.03630 / 2.41 ( 799) hydrogen bonds : angle 4.04696 / 2.88 ( 2543) link_ALPHA1-3 : bond 0.00529 / 0.33 ( 7) link_ALPHA1-3 : angle 1.48654 / 0.95 ( 21) link_ALPHA1-6 : bond 0.00529 / 0.37 ( 9) link_ALPHA1-6 : angle 1.44833 / 1.01 ( 27) link_BETA1-4 : bond 0.00724 / 0.53 ( 13) link_BETA1-4 : angle 1.96632 / 1.42 ( 39) link_NAG-ASN : bond 0.00150 / 0.09 ( 8) link_NAG-ASN : angle 1.42968 / 0.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8565 (p0) cc_final: 0.8190 (p0) REVERT: A 262 GLU cc_start: 0.7821 (tt0) cc_final: 0.7330 (tp30) REVERT: B 318 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7867 (tt) REVERT: B 425 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7028 (mtpt) REVERT: C 154 ASP cc_start: 0.8761 (p0) cc_final: 0.8443 (p0) REVERT: D 127 TYR cc_start: 0.8736 (t80) cc_final: 0.8413 (t80) REVERT: D 142 CYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5637 (m) REVERT: E 299 MET cc_start: 0.8370 (ttt) cc_final: 0.7858 (ttp) outliers start: 27 outliers final: 16 residues processed: 165 average time/residue: 0.5172 time to fit residues: 97.5091 Evaluate side-chains 155 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 7 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 169 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 267 GLN C 445 ASN D 297 ASN D 306 HIS E 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090459 restraints weight = 28902.130| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.17 r_work: 0.3068 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17498 Z= 0.108 Angle : 0.520 11.254 23892 Z= 0.256 Chirality : 0.042 0.193 2824 Planarity : 0.004 0.046 2854 Dihedral : 10.173 114.693 2376 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.31 % Allowed : 13.62 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.34 (0.20), residues: 1970 helix: 2.63 (0.19), residues: 751 sheet: 0.29 (0.25), residues: 422 loop : -0.45 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 168 TYR 0.012 0.001 TYR A 151 PHE 0.015 0.001 PHE C 241 TRP 0.009 0.001 TRP D 311 HIS 0.003 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (17454) covalent geometry : angle 0.50744 / 0.25 (23767) SS BOND : bond 0.00737 / 0.38 ( 7) SS BOND : angle 1.63718 / 0.89 ( 14) hydrogen bonds : bond 0.03679 / 2.44 ( 799) hydrogen bonds : angle 4.06599 / 2.89 ( 2543) link_ALPHA1-3 : bond 0.00519 / 0.33 ( 7) link_ALPHA1-3 : angle 1.49146 / 0.95 ( 21) link_ALPHA1-6 : bond 0.00527 / 0.37 ( 9) link_ALPHA1-6 : angle 1.44737 / 1.01 ( 27) link_BETA1-4 : bond 0.00712 / 0.52 ( 13) link_BETA1-4 : angle 1.97877 / 1.42 ( 39) link_NAG-ASN : bond 0.00128 / 0.08 ( 8) link_NAG-ASN : angle 1.44123 / 0.83 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8554 (p0) cc_final: 0.8184 (p0) REVERT: A 262 GLU cc_start: 0.7817 (tt0) cc_final: 0.7327 (tp30) REVERT: B 318 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7843 (tt) REVERT: B 425 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7026 (mtpt) REVERT: C 154 ASP cc_start: 0.8704 (p0) cc_final: 0.8415 (p0) REVERT: D 127 TYR cc_start: 0.8743 (t80) cc_final: 0.8431 (t80) REVERT: D 142 CYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5617 (m) REVERT: E 299 MET cc_start: 0.8343 (ttt) cc_final: 0.7828 (ttp) outliers start: 24 outliers final: 17 residues processed: 152 average time/residue: 0.4814 time to fit residues: 83.9056 Evaluate side-chains 157 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 0.0470 chunk 153 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 181 optimal weight: 0.0010 overall best weight: 1.1286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 ASN D 297 ASN D 306 HIS E 196 ASN E 198 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.118010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.088658 restraints weight = 26373.180| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.07 r_work: 0.3039 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17498 Z= 0.131 Angle : 0.551 11.514 23892 Z= 0.272 Chirality : 0.043 0.200 2824 Planarity : 0.004 0.045 2854 Dihedral : 10.216 114.910 2376 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.25 % Allowed : 13.78 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.30 (0.20), residues: 1970 helix: 2.54 (0.19), residues: 757 sheet: 0.25 (0.24), residues: 422 loop : -0.44 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 168 TYR 0.013 0.001 TYR A 151 PHE 0.017 0.001 PHE C 241 TRP 0.023 0.001 TRP D 311 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (17454) covalent geometry : angle 0.53743 / 0.27 (23767) SS BOND : bond 0.00755 / 0.39 ( 7) SS BOND : angle 1.86229 / 1.04 ( 14) hydrogen bonds : bond 0.03994 / 2.66 ( 799) hydrogen bonds : angle 4.20022 / 2.98 ( 2543) link_ALPHA1-3 : bond 0.00495 / 0.32 ( 7) link_ALPHA1-3 : angle 1.52667 / 0.97 ( 21) link_ALPHA1-6 : bond 0.00522 / 0.37 ( 9) link_ALPHA1-6 : angle 1.46037 / 1.04 ( 27) link_BETA1-4 : bond 0.00683 / 0.50 ( 13) link_BETA1-4 : angle 2.07643 / 1.48 ( 39) link_NAG-ASN : bond 0.00146 / 0.09 ( 8) link_NAG-ASN : angle 1.59932 / 0.93 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6831.19 seconds wall clock time: 117 minutes 4.17 seconds (7024.17 seconds total)