Starting phenix.real_space_refine on Thu Mar 5 00:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ql5_14064/03_2026/7ql5_14064.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ql5_14064/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ql5_14064/03_2026/7ql5_14064.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ql5_14064/03_2026/7ql5_14064.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ql5_14064/03_2026/7ql5_14064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ql5_14064/03_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-5986/lib/python3.9/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 dihedrals: 21 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 dihedrals: 15 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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 dihedrals: 18 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: 67 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: 4.42, per 1000 atoms: 0.26 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: 1.76 Conformation dependent library (CDL) restraints added in 687.2 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: 0.53 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: 2.91 Time building geometry restraints manager: 2.23 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: 10475 35.22 - 70.43: 307 70.43 - 105.65: 93 105.65 - 140.86: 22 140.86 - 176.08: 2 Dihedral angle restraints: 10899 sinusoidal: 4996 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 10896 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.940 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 18.219 176.076 7038 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 covalent geometry : bond 0.00771 (17454) covalent geometry : angle 0.94696 (23767) SS BOND : bond 0.01915 ( 7) SS BOND : angle 3.78267 ( 14) hydrogen bonds : bond 0.15391 ( 799) hydrogen bonds : angle 5.78584 ( 2543) link_ALPHA1-3 : bond 0.00455 ( 7) link_ALPHA1-3 : angle 1.74124 ( 21) link_ALPHA1-6 : bond 0.00505 ( 9) link_ALPHA1-6 : angle 1.65160 ( 27) link_BETA1-4 : bond 0.00885 ( 13) link_BETA1-4 : angle 2.58644 ( 39) link_NAG-ASN : bond 0.01229 ( 8) link_NAG-ASN : angle 2.15231 ( 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 : 0.511 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: 0.4796 time to fit residues: 103.8808 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 : 0.644 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 310 ASN C 98 ASN C 103 HIS D 297 ASN D 306 HIS E 300 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088615 restraints weight = 25946.126| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.96 r_work: 0.3048 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17498 Z= 0.185 Angle : 0.635 10.021 23892 Z= 0.314 Chirality : 0.047 0.237 2824 Planarity : 0.004 0.043 2854 Dihedral : 18.241 176.376 3201 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.63 % Allowed : 8.71 % Favored : 89.65 % 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: 2.19 (0.19), residues: 747 sheet: 0.15 (0.24), residues: 422 loop : -0.40 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 485 TYR 0.016 0.001 TYR D 151 PHE 0.018 0.002 PHE C 294 TRP 0.012 0.001 TRP E 453 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00420 (17454) covalent geometry : angle 0.61104 (23767) SS BOND : bond 0.00928 ( 7) SS BOND : angle 3.23292 ( 14) hydrogen bonds : bond 0.05393 ( 799) hydrogen bonds : angle 4.77597 ( 2543) link_ALPHA1-3 : bond 0.00967 ( 7) link_ALPHA1-3 : angle 2.42051 ( 21) link_ALPHA1-6 : bond 0.00687 ( 9) link_ALPHA1-6 : angle 1.89400 ( 27) link_BETA1-4 : bond 0.00700 ( 13) link_BETA1-4 : angle 2.73508 ( 39) link_NAG-ASN : bond 0.00388 ( 8) link_NAG-ASN : angle 2.01145 ( 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 : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9049 (mmt) cc_final: 0.8805 (tpp) REVERT: A 207 MET cc_start: 0.9129 (mtm) cc_final: 0.8899 (mtp) REVERT: A 262 GLU cc_start: 0.7861 (tt0) cc_final: 0.7439 (tp30) REVERT: A 273 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7485 (mp) REVERT: A 306 HIS cc_start: 0.7579 (m90) cc_final: 0.7332 (m-70) REVERT: C 454 ASP cc_start: 0.6971 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: D 397 GLU cc_start: 0.6145 (tp30) cc_final: 0.5718 (tm-30) REVERT: E 299 MET cc_start: 0.8305 (ttt) cc_final: 0.7795 (ttp) outliers start: 30 outliers final: 10 residues processed: 161 average time/residue: 0.5134 time to fit residues: 94.4489 Evaluate side-chains 152 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 253 ILE Chi-restraints excluded: chain B residue 273 THR 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 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: 2.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 GLN D 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089402 restraints weight = 28930.090| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.09 r_work: 0.3059 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17498 Z= 0.139 Angle : 0.564 7.961 23892 Z= 0.280 Chirality : 0.045 0.243 2824 Planarity : 0.004 0.046 2854 Dihedral : 16.390 152.724 3197 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.91 % Allowed : 10.02 % Favored : 88.07 % 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: 1.17 (0.19), residues: 1970 helix: 2.35 (0.19), residues: 755 sheet: 0.15 (0.24), residues: 428 loop : -0.38 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 485 TYR 0.015 0.001 TYR D 151 PHE 0.018 0.001 PHE C 294 TRP 0.008 0.001 TRP E 60 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00308 (17454) covalent geometry : angle 0.54360 (23767) SS BOND : bond 0.00788 ( 7) SS BOND : angle 2.24702 ( 14) hydrogen bonds : bond 0.04711 ( 799) hydrogen bonds : angle 4.50289 ( 2543) link_ALPHA1-3 : bond 0.01112 ( 7) link_ALPHA1-3 : angle 2.04643 ( 21) link_ALPHA1-6 : bond 0.00729 ( 9) link_ALPHA1-6 : angle 1.92117 ( 27) link_BETA1-4 : bond 0.00758 ( 13) link_BETA1-4 : angle 2.54215 ( 39) link_NAG-ASN : bond 0.00207 ( 8) link_NAG-ASN : angle 1.76116 ( 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 180 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7836 (tt0) cc_final: 0.7399 (tp30) REVERT: A 273 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7350 (mp) REVERT: A 306 HIS cc_start: 0.7531 (m90) cc_final: 0.7306 (m-70) REVERT: D 245 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7650 (pt) REVERT: D 397 GLU cc_start: 0.6108 (tp30) cc_final: 0.5681 (tm-30) REVERT: E 299 MET cc_start: 0.8363 (ttt) cc_final: 0.7833 (ttp) REVERT: E 335 MET cc_start: 0.5190 (mmp) cc_final: 0.4514 (mmp) outliers start: 35 outliers final: 16 residues processed: 166 average time/residue: 0.4983 time to fit residues: 94.5199 Evaluate side-chains 152 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 B residue 168 ARG Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 273 LEU 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 238 VAL Chi-restraints excluded: chain E residue 333 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 160 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 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 = 0.3563 r_free = 0.3563 target = 0.116488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088238 restraints weight = 27972.313| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.03 r_work: 0.3043 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 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 = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17498 Z= 0.167 Angle : 0.588 7.886 23892 Z= 0.291 Chirality : 0.046 0.223 2824 Planarity : 0.004 0.044 2854 Dihedral : 15.374 123.725 3197 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 10.02 % Favored : 87.25 % 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: 1.17 (0.19), residues: 1970 helix: 2.40 (0.19), residues: 749 sheet: 0.16 (0.24), residues: 423 loop : -0.43 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.014 0.001 TYR D 151 PHE 0.014 0.001 PHE E 467 TRP 0.008 0.001 TRP E 453 HIS 0.005 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00383 (17454) covalent geometry : angle 0.56797 (23767) SS BOND : bond 0.00814 ( 7) SS BOND : angle 2.18917 ( 14) hydrogen bonds : bond 0.04705 ( 799) hydrogen bonds : angle 4.50312 ( 2543) link_ALPHA1-3 : bond 0.01107 ( 7) link_ALPHA1-3 : angle 1.89768 ( 21) link_ALPHA1-6 : bond 0.00726 ( 9) link_ALPHA1-6 : angle 1.92660 ( 27) link_BETA1-4 : bond 0.00719 ( 13) link_BETA1-4 : angle 2.61366 ( 39) link_NAG-ASN : bond 0.00254 ( 8) link_NAG-ASN : angle 1.83178 ( 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: 50 poor density : 133 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.9151 (mtm) cc_final: 0.8876 (mtp) REVERT: A 262 GLU cc_start: 0.7856 (tt0) cc_final: 0.7416 (tp30) REVERT: A 273 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7348 (mp) REVERT: B 425 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7164 (mtpt) REVERT: D 245 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7797 (pt) REVERT: D 397 GLU cc_start: 0.6118 (tp30) cc_final: 0.5663 (tm-30) REVERT: E 299 MET cc_start: 0.8331 (ttt) cc_final: 0.7821 (ttp) outliers start: 50 outliers final: 22 residues processed: 164 average time/residue: 0.4973 time to fit residues: 93.3452 Evaluate side-chains 155 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 B residue 42 ILE Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 273 THR 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 112 VAL Chi-restraints excluded: chain C residue 230 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 132 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN D 297 ASN E 300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.086895 restraints weight = 27950.272| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.04 r_work: 0.3019 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 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 = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17498 Z= 0.202 Angle : 0.622 8.479 23892 Z= 0.309 Chirality : 0.047 0.216 2824 Planarity : 0.004 0.045 2854 Dihedral : 14.893 123.987 3197 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.78 % Allowed : 10.40 % Favored : 86.82 % 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: 1.08 (0.19), residues: 1970 helix: 2.33 (0.19), residues: 750 sheet: 0.21 (0.24), residues: 414 loop : -0.54 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.014 0.002 TYR D 151 PHE 0.016 0.002 PHE E 467 TRP 0.008 0.001 TRP E 453 HIS 0.006 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00472 (17454) covalent geometry : angle 0.60168 (23767) SS BOND : bond 0.00849 ( 7) SS BOND : angle 2.36276 ( 14) hydrogen bonds : bond 0.04949 ( 799) hydrogen bonds : angle 4.58785 ( 2543) link_ALPHA1-3 : bond 0.01039 ( 7) link_ALPHA1-3 : angle 1.84588 ( 21) link_ALPHA1-6 : bond 0.00757 ( 9) link_ALPHA1-6 : angle 1.91213 ( 27) link_BETA1-4 : bond 0.00740 ( 13) link_BETA1-4 : angle 2.76128 ( 39) link_NAG-ASN : bond 0.00321 ( 8) link_NAG-ASN : angle 1.95015 ( 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: 51 poor density : 131 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.9176 (mtm) cc_final: 0.8912 (mtp) REVERT: A 262 GLU cc_start: 0.7877 (tt0) cc_final: 0.7447 (tp30) REVERT: A 273 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 306 HIS cc_start: 0.7595 (m90) cc_final: 0.7322 (m-70) REVERT: B 272 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: B 425 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7217 (mtpt) REVERT: D 245 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7917 (pt) REVERT: D 262 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: D 397 GLU cc_start: 0.6122 (tp30) cc_final: 0.5675 (tm-30) REVERT: E 299 MET cc_start: 0.8366 (ttt) cc_final: 0.7885 (ttp) outliers start: 51 outliers final: 26 residues processed: 165 average time/residue: 0.4929 time to fit residues: 92.8298 Evaluate side-chains 158 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 110 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 111 ASP 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 307 THR Chi-restraints excluded: chain D residue 312 VAL 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 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: 30.0000 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 159 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087076 restraints weight = 31140.957| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.15 r_work: 0.3023 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- 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: 8 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17498 Z= 0.181 Angle : 0.602 7.685 23892 Z= 0.298 Chirality : 0.046 0.214 2824 Planarity : 0.004 0.046 2854 Dihedral : 14.321 122.925 3197 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.83 % Allowed : 10.84 % Favored : 86.33 % 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: 1.10 (0.19), residues: 1970 helix: 2.38 (0.19), residues: 750 sheet: 0.17 (0.24), residues: 419 loop : -0.53 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 79 TYR 0.014 0.001 TYR D 151 PHE 0.015 0.001 PHE C 294 TRP 0.008 0.001 TRP E 453 HIS 0.005 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00418 (17454) covalent geometry : angle 0.58163 (23767) SS BOND : bond 0.00841 ( 7) SS BOND : angle 2.24742 ( 14) hydrogen bonds : bond 0.04694 ( 799) hydrogen bonds : angle 4.51781 ( 2543) link_ALPHA1-3 : bond 0.01010 ( 7) link_ALPHA1-3 : angle 1.84396 ( 21) link_ALPHA1-6 : bond 0.00798 ( 9) link_ALPHA1-6 : angle 1.86922 ( 27) link_BETA1-4 : bond 0.00748 ( 13) link_BETA1-4 : angle 2.73308 ( 39) link_NAG-ASN : bond 0.00278 ( 8) link_NAG-ASN : angle 1.93626 ( 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 182 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 207 MET cc_start: 0.9175 (mtm) cc_final: 0.8915 (mtp) REVERT: A 262 GLU cc_start: 0.7865 (tt0) cc_final: 0.7432 (tp30) REVERT: A 273 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7382 (mp) REVERT: A 306 HIS cc_start: 0.7577 (m90) cc_final: 0.7303 (m-70) REVERT: B 272 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: B 425 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7205 (mtpt) REVERT: D 108 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.8717 (pp) REVERT: D 142 CYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6289 (m) REVERT: D 245 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7900 (pt) REVERT: D 397 GLU cc_start: 0.6124 (tp30) cc_final: 0.5692 (tm-30) REVERT: E 299 MET cc_start: 0.8376 (ttt) cc_final: 0.7896 (ttp) REVERT: E 335 MET cc_start: 0.5119 (OUTLIER) cc_final: 0.4487 (mmp) outliers start: 52 outliers final: 25 residues processed: 164 average time/residue: 0.4968 time to fit residues: 93.4065 Evaluate side-chains 162 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 229 THR 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 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 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 110 VAL Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 108 LEU 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 287 LEU Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 73 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 130 optimal weight: 0.1980 chunk 110 optimal weight: 9.9990 chunk 2 optimal weight: 0.0030 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 297 ASN D 306 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091800 restraints weight = 30827.816| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.15 r_work: 0.3091 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1631 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 : 0.539 9.163 23892 Z= 0.263 Chirality : 0.044 0.237 2824 Planarity : 0.004 0.047 2854 Dihedral : 13.290 119.180 3197 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.74 % Allowed : 11.87 % Favored : 86.38 % 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: 1.27 (0.20), residues: 1970 helix: 2.48 (0.19), residues: 762 sheet: 0.19 (0.24), residues: 424 loop : -0.39 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.016 0.001 TYR D 151 PHE 0.015 0.001 PHE C 294 TRP 0.012 0.001 TRP E 60 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00237 (17454) covalent geometry : angle 0.52095 (23767) SS BOND : bond 0.00754 ( 7) SS BOND : angle 1.63318 ( 14) hydrogen bonds : bond 0.03819 ( 799) hydrogen bonds : angle 4.17252 ( 2543) link_ALPHA1-3 : bond 0.01102 ( 7) link_ALPHA1-3 : angle 1.80705 ( 21) link_ALPHA1-6 : bond 0.00947 ( 9) link_ALPHA1-6 : angle 1.84788 ( 27) link_BETA1-4 : bond 0.00800 ( 13) link_BETA1-4 : angle 2.40368 ( 39) link_NAG-ASN : bond 0.00221 ( 8) link_NAG-ASN : angle 1.62143 ( 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 174 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7838 (tt0) cc_final: 0.7380 (tp30) REVERT: B 425 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7040 (mtpt) REVERT: D 127 TYR cc_start: 0.8760 (t80) cc_final: 0.8412 (t80) REVERT: D 142 CYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5653 (m) REVERT: D 245 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7791 (pt) REVERT: D 262 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: D 397 GLU cc_start: 0.6094 (tp30) cc_final: 0.5660 (tm-30) REVERT: E 299 MET cc_start: 0.8325 (ttt) cc_final: 0.7807 (ttp) outliers start: 32 outliers final: 12 residues processed: 161 average time/residue: 0.5149 time to fit residues: 94.5731 Evaluate side-chains 150 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL 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 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 333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 57 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN D 297 ASN D 306 HIS E 196 ASN E 198 GLN E 471 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088203 restraints weight = 38863.907| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.42 r_work: 0.3026 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- 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: 8 | |-----------------------------------------------------------------------------| |-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: 8 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17498 Z= 0.152 Angle : 0.579 8.125 23892 Z= 0.284 Chirality : 0.045 0.228 2824 Planarity : 0.004 0.045 2854 Dihedral : 13.218 120.478 3196 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.69 % Allowed : 12.47 % Favored : 85.84 % 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: 1.24 (0.19), residues: 1970 helix: 2.45 (0.19), residues: 757 sheet: 0.21 (0.24), residues: 418 loop : -0.42 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.012 0.001 TYR D 151 PHE 0.013 0.001 PHE C 294 TRP 0.010 0.001 TRP D 311 HIS 0.011 0.001 HIS E 471 Details of bonding type rmsd covalent geometry : bond 0.00349 (17454) covalent geometry : angle 0.55984 (23767) SS BOND : bond 0.00801 ( 7) SS BOND : angle 2.02275 ( 14) hydrogen bonds : bond 0.04288 ( 799) hydrogen bonds : angle 4.32518 ( 2543) link_ALPHA1-3 : bond 0.00977 ( 7) link_ALPHA1-3 : angle 1.82367 ( 21) link_ALPHA1-6 : bond 0.00898 ( 9) link_ALPHA1-6 : angle 1.87306 ( 27) link_BETA1-4 : bond 0.00744 ( 13) link_BETA1-4 : angle 2.52127 ( 39) link_NAG-ASN : bond 0.00232 ( 8) link_NAG-ASN : angle 1.80257 ( 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 164 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7897 (tt0) cc_final: 0.7424 (tp30) REVERT: B 425 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7105 (mtpt) REVERT: D 142 CYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6054 (m) REVERT: D 245 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7878 (pt) REVERT: D 397 GLU cc_start: 0.6132 (tp30) cc_final: 0.5707 (tm-30) REVERT: E 299 MET cc_start: 0.8402 (ttt) cc_final: 0.7886 (ttp) outliers start: 31 outliers final: 17 residues processed: 154 average time/residue: 0.5455 time to fit residues: 95.9120 Evaluate side-chains 152 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL 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 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 38 THR 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 333 LEU Chi-restraints excluded: chain E residue 461 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 22 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 156 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN D 297 ASN D 306 HIS E 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090619 restraints weight = 31579.580| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.18 r_work: 0.3074 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1696 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= 0.119 Angle : 0.551 7.972 23892 Z= 0.270 Chirality : 0.044 0.231 2824 Planarity : 0.004 0.046 2854 Dihedral : 12.838 119.636 3196 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.69 % Allowed : 12.69 % Favored : 85.62 % 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: 1.27 (0.20), residues: 1970 helix: 2.46 (0.19), residues: 762 sheet: 0.25 (0.24), residues: 421 loop : -0.42 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 168 TYR 0.013 0.001 TYR D 151 PHE 0.014 0.001 PHE C 294 TRP 0.010 0.001 TRP E 60 HIS 0.012 0.001 HIS E 471 Details of bonding type rmsd covalent geometry : bond 0.00259 (17454) covalent geometry : angle 0.53370 (23767) SS BOND : bond 0.00759 ( 7) SS BOND : angle 1.75104 ( 14) hydrogen bonds : bond 0.03940 ( 799) hydrogen bonds : angle 4.21097 ( 2543) link_ALPHA1-3 : bond 0.01004 ( 7) link_ALPHA1-3 : angle 1.77779 ( 21) link_ALPHA1-6 : bond 0.00974 ( 9) link_ALPHA1-6 : angle 1.80758 ( 27) link_BETA1-4 : bond 0.00787 ( 13) link_BETA1-4 : angle 2.39019 ( 39) link_NAG-ASN : bond 0.00198 ( 8) link_NAG-ASN : angle 1.67423 ( 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 161 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.7823 (tt0) cc_final: 0.7365 (tp30) REVERT: B 318 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8014 (tt) REVERT: B 425 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7037 (mtpt) REVERT: D 142 CYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5791 (m) REVERT: D 245 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7809 (pt) REVERT: D 397 GLU cc_start: 0.6083 (tp30) cc_final: 0.5659 (tm-30) REVERT: E 299 MET cc_start: 0.8350 (ttt) cc_final: 0.7827 (ttp) REVERT: E 472 PHE cc_start: 0.8177 (m-80) cc_final: 0.7783 (m-10) outliers start: 31 outliers final: 16 residues processed: 149 average time/residue: 0.5471 time to fit residues: 92.5065 Evaluate side-chains 150 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL 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 312 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 7 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN D 297 ASN D 306 HIS E 198 GLN E 471 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.090768 restraints weight = 30291.956| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.14 r_work: 0.3076 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17498 Z= 0.122 Angle : 0.559 10.732 23892 Z= 0.272 Chirality : 0.044 0.234 2824 Planarity : 0.004 0.046 2854 Dihedral : 12.519 119.100 3196 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.36 % Allowed : 13.02 % Favored : 85.62 % 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: 1.29 (0.20), residues: 1970 helix: 2.48 (0.19), residues: 762 sheet: 0.25 (0.24), residues: 421 loop : -0.40 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 331 TYR 0.013 0.001 TYR D 151 PHE 0.013 0.001 PHE C 294 TRP 0.008 0.001 TRP D 311 HIS 0.007 0.001 HIS E 471 Details of bonding type rmsd covalent geometry : bond 0.00269 (17454) covalent geometry : angle 0.54244 (23767) SS BOND : bond 0.00760 ( 7) SS BOND : angle 1.77223 ( 14) hydrogen bonds : bond 0.03951 ( 799) hydrogen bonds : angle 4.19253 ( 2543) link_ALPHA1-3 : bond 0.00966 ( 7) link_ALPHA1-3 : angle 1.76844 ( 21) link_ALPHA1-6 : bond 0.01004 ( 9) link_ALPHA1-6 : angle 1.77349 ( 27) link_BETA1-4 : bond 0.00770 ( 13) link_BETA1-4 : angle 2.35803 ( 39) link_NAG-ASN : bond 0.00193 ( 8) link_NAG-ASN : angle 1.67684 ( 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 160 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8651 (p0) cc_final: 0.8342 (p0) REVERT: A 262 GLU cc_start: 0.7840 (tt0) cc_final: 0.7375 (tp30) REVERT: B 318 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7987 (tt) REVERT: B 425 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7056 (mtpt) REVERT: D 142 CYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5754 (m) REVERT: D 245 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7789 (pt) REVERT: E 299 MET cc_start: 0.8323 (ttt) cc_final: 0.7807 (ttp) outliers start: 25 outliers final: 15 residues processed: 151 average time/residue: 0.5170 time to fit residues: 88.8404 Evaluate side-chains 150 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 318 ILE Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 110 VAL 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 423 VAL Chi-restraints excluded: chain E residue 38 THR 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 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 102 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3565 r_free = 0.3565 target = 0.116498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088316 restraints weight = 26400.830| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.99 r_work: 0.3039 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 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 = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17498 Z= 0.183 Angle : 0.618 11.536 23892 Z= 0.304 Chirality : 0.046 0.230 2824 Planarity : 0.004 0.045 2854 Dihedral : 12.705 120.665 3196 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.47 % Allowed : 13.40 % Favored : 85.13 % 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: 1.18 (0.19), residues: 1970 helix: 2.42 (0.19), residues: 757 sheet: 0.17 (0.24), residues: 418 loop : -0.46 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 168 TYR 0.015 0.001 TYR C 202 PHE 0.014 0.002 PHE E 467 TRP 0.021 0.001 TRP D 311 HIS 0.005 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00426 (17454) covalent geometry : angle 0.59988 (23767) SS BOND : bond 0.00823 ( 7) SS BOND : angle 2.24656 ( 14) hydrogen bonds : bond 0.04570 ( 799) hydrogen bonds : angle 4.42413 ( 2543) link_ALPHA1-3 : bond 0.00895 ( 7) link_ALPHA1-3 : angle 1.78753 ( 21) link_ALPHA1-6 : bond 0.00958 ( 9) link_ALPHA1-6 : angle 1.81938 ( 27) link_BETA1-4 : bond 0.00749 ( 13) link_BETA1-4 : angle 2.57013 ( 39) link_NAG-ASN : bond 0.00318 ( 8) link_NAG-ASN : angle 1.91098 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7163.37 seconds wall clock time: 122 minutes 26.21 seconds (7346.21 seconds total)