Starting phenix.real_space_refine on Fri Feb 16 03:33:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2024/6plz_20381_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2024/6plz_20381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2024/6plz_20381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2024/6plz_20381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2024/6plz_20381_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plz_20381/02_2024/6plz_20381_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.062 sd= 2.818 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9250 2.51 5 N 2290 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14210 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.82, per 1000 atoms: 0.55 Number of scatterers: 14210 At special positions: 0 Unit cell: (108.636, 104.521, 134.149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2570 8.00 N 2290 7.00 C 9250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 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 J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 2.5 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 20 sheets defined 35.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.840A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.653A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 108 " --> pdb=" O MET A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.510A pdb=" N ILE A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.780A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.622A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.138A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 removed outlier: 3.658A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 426 removed outlier: 3.803A pdb=" N PHE A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.834A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 removed outlier: 3.878A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.636A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.512A pdb=" N ILE B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.773A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 284 removed outlier: 3.714A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 324 removed outlier: 4.113A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 426 removed outlier: 3.851A pdb=" N PHE B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.757A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 33 removed outlier: 3.895A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.615A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.506A pdb=" N ILE C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.959A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 286 removed outlier: 3.611A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 313 removed outlier: 4.139A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 323 removed outlier: 3.727A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.836A pdb=" N PHE C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.825A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.864A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.651A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.523A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.943A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.674A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 323 removed outlier: 4.092A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 315 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 426 removed outlier: 3.816A pdb=" N PHE D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.734A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 33 removed outlier: 3.867A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.670A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.516A pdb=" N ILE E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.858A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 3.642A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 324 removed outlier: 4.032A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 315 " --> pdb=" O PHE E 311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 426 removed outlier: 3.861A pdb=" N PHE E 395 " --> pdb=" O MET E 391 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.737A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.405A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.696A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= D, first strand: chain 'A' and resid 165 through 168 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.383A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.679A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= H, first strand: chain 'B' and resid 165 through 168 Processing sheet with id= I, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.395A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.697A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= L, first strand: chain 'C' and resid 165 through 168 Processing sheet with id= M, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.412A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.697A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= P, first strand: chain 'D' and resid 165 through 168 Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.367A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.655A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'E' and resid 209 through 213 443 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4315 1.34 - 1.46: 3384 1.46 - 1.58: 6691 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 14560 Sorted by residual: bond pdb=" C1 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sigma weight residual 1.410 1.456 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.562 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.44e+00 ... (remaining 14555 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.62: 368 105.62 - 112.71: 7491 112.71 - 119.80: 4920 119.80 - 126.89: 6742 126.89 - 133.99: 219 Bond angle restraints: 19740 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.27e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 132.40 -10.86 1.91e+00 2.74e-01 3.23e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.38 -10.84 1.91e+00 2.74e-01 3.22e+01 ... (remaining 19735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 8583 21.43 - 42.86: 157 42.86 - 64.28: 60 64.28 - 85.71: 70 85.71 - 107.14: 35 Dihedral angle restraints: 8905 sinusoidal: 3805 harmonic: 5100 Sorted by residual: dihedral pdb=" CB CYS A 214 " pdb=" SG CYS A 214 " pdb=" SG CYS A 225 " pdb=" CB CYS A 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.49 90.49 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.31 90.31 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 214 " pdb=" SG CYS B 214 " pdb=" SG CYS B 225 " pdb=" CB CYS B 225 " ideal model delta sinusoidal sigma weight residual -86.00 -176.23 90.23 1 1.00e+01 1.00e-02 9.64e+01 ... (remaining 8902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1822 0.066 - 0.132: 347 0.132 - 0.198: 61 0.198 - 0.264: 10 0.264 - 0.330: 15 Chirality restraints: 2255 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN E 54 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 54 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 54 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2252 not shown) Planarity restraints: 2450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 151 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C VAL C 151 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL C 151 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU C 152 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " -0.040 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 411 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " 0.039 5.00e-02 4.00e+02 5.90e-02 5.56e+00 pdb=" N PRO D 411 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " 0.033 5.00e-02 4.00e+02 ... (remaining 2447 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4611 2.85 - 3.36: 12514 3.36 - 3.88: 22554 3.88 - 4.39: 26593 4.39 - 4.90: 46400 Nonbonded interactions: 112672 Sorted by model distance: nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.338 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.359 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.365 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.369 2.440 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.377 2.440 ... (remaining 112667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 7.430 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.410 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.006 0.055 14560 Z= 0.369 Angle : 0.968 10.963 19740 Z= 0.508 Chirality : 0.061 0.330 2255 Planarity : 0.007 0.060 2445 Dihedral : 14.941 107.141 5565 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.15), residues: 1705 helix: -4.61 (0.08), residues: 580 sheet: -2.73 (0.20), residues: 425 loop : -2.66 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 110 HIS 0.004 0.002 HIS A 327 PHE 0.019 0.003 PHE D 115 TYR 0.015 0.002 TYR E 144 ARG 0.010 0.001 ARG D 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8824 (ptm) cc_final: 0.8384 (ptp) REVERT: A 28 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 102 ASP cc_start: 0.8208 (t70) cc_final: 0.7601 (t70) REVERT: A 129 THR cc_start: 0.8518 (m) cc_final: 0.8247 (p) REVERT: A 130 ASP cc_start: 0.8180 (m-30) cc_final: 0.7959 (m-30) REVERT: A 210 ASP cc_start: 0.8104 (m-30) cc_final: 0.7680 (m-30) REVERT: A 261 ASN cc_start: 0.8383 (t0) cc_final: 0.8006 (t0) REVERT: A 391 MET cc_start: 0.8341 (tpt) cc_final: 0.7987 (tpp) REVERT: B 24 MET cc_start: 0.8875 (ptm) cc_final: 0.7957 (ptp) REVERT: B 28 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 36 LYS cc_start: 0.9145 (mttt) cc_final: 0.8907 (mppt) REVERT: B 43 ARG cc_start: 0.9079 (mtm-85) cc_final: 0.8448 (mtm180) REVERT: B 102 ASP cc_start: 0.8241 (t70) cc_final: 0.7674 (t70) REVERT: B 129 THR cc_start: 0.8514 (m) cc_final: 0.8206 (p) REVERT: B 179 MET cc_start: 0.8665 (tpt) cc_final: 0.8392 (mmt) REVERT: B 181 ASP cc_start: 0.8407 (m-30) cc_final: 0.8161 (m-30) REVERT: B 210 ASP cc_start: 0.8000 (m-30) cc_final: 0.7644 (m-30) REVERT: B 391 MET cc_start: 0.8299 (tpt) cc_final: 0.7861 (tpp) REVERT: B 397 SER cc_start: 0.8717 (t) cc_final: 0.8404 (p) REVERT: C 24 MET cc_start: 0.8770 (ptm) cc_final: 0.7717 (ptp) REVERT: C 28 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 36 LYS cc_start: 0.9206 (mttt) cc_final: 0.8928 (mppt) REVERT: C 43 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8625 (mtm-85) REVERT: C 102 ASP cc_start: 0.8235 (t70) cc_final: 0.7761 (t70) REVERT: C 163 MET cc_start: 0.8149 (mpp) cc_final: 0.6896 (mpp) REVERT: C 164 ASP cc_start: 0.8082 (p0) cc_final: 0.7799 (p0) REVERT: C 208 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7869 (mt-10) REVERT: C 210 ASP cc_start: 0.8129 (m-30) cc_final: 0.7783 (m-30) REVERT: C 233 GLU cc_start: 0.7512 (tt0) cc_final: 0.7296 (tt0) REVERT: C 261 ASN cc_start: 0.8425 (t0) cc_final: 0.7975 (t0) REVERT: C 391 MET cc_start: 0.8264 (tpt) cc_final: 0.8011 (tpp) REVERT: C 397 SER cc_start: 0.8683 (t) cc_final: 0.8391 (p) REVERT: C 403 ASP cc_start: 0.8397 (t0) cc_final: 0.8027 (t0) REVERT: D 24 MET cc_start: 0.8763 (ptm) cc_final: 0.8321 (ptp) REVERT: D 28 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8152 (mt-10) REVERT: D 36 LYS cc_start: 0.9184 (mttt) cc_final: 0.8872 (mppt) REVERT: D 43 ARG cc_start: 0.9068 (mtm-85) cc_final: 0.8359 (mtm180) REVERT: D 130 ASP cc_start: 0.8194 (m-30) cc_final: 0.7988 (m-30) REVERT: D 210 ASP cc_start: 0.8128 (m-30) cc_final: 0.7785 (m-30) REVERT: D 212 ARG cc_start: 0.7591 (ptp-170) cc_final: 0.7328 (ptp-110) REVERT: D 227 GLU cc_start: 0.8072 (pt0) cc_final: 0.7847 (pt0) REVERT: D 261 ASN cc_start: 0.8332 (t0) cc_final: 0.7936 (t0) REVERT: D 391 MET cc_start: 0.8231 (tpt) cc_final: 0.7745 (tpp) REVERT: E 24 MET cc_start: 0.8900 (ptm) cc_final: 0.8318 (ptp) REVERT: E 28 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8165 (mt-10) REVERT: E 31 ASP cc_start: 0.8747 (m-30) cc_final: 0.8540 (m-30) REVERT: E 36 LYS cc_start: 0.9130 (mttt) cc_final: 0.8858 (mppt) REVERT: E 43 ARG cc_start: 0.9017 (mtm-85) cc_final: 0.8596 (mtm-85) REVERT: E 129 THR cc_start: 0.8479 (m) cc_final: 0.8173 (p) REVERT: E 164 ASP cc_start: 0.8302 (p0) cc_final: 0.7993 (p0) REVERT: E 210 ASP cc_start: 0.8143 (m-30) cc_final: 0.7845 (m-30) REVERT: E 227 GLU cc_start: 0.8139 (pt0) cc_final: 0.7852 (pt0) REVERT: E 261 ASN cc_start: 0.8389 (t0) cc_final: 0.7952 (t0) REVERT: E 391 MET cc_start: 0.8250 (tpt) cc_final: 0.7830 (tpp) outliers start: 0 outliers final: 4 residues processed: 451 average time/residue: 1.3222 time to fit residues: 650.7347 Evaluate side-chains 286 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain D residue 241 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 141 ASN B 171 GLN B 180 ASN C 171 GLN D 141 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14560 Z= 0.267 Angle : 0.720 10.931 19740 Z= 0.362 Chirality : 0.050 0.292 2255 Planarity : 0.005 0.039 2445 Dihedral : 15.727 73.853 2203 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.69 % Allowed : 13.66 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.17), residues: 1705 helix: -3.18 (0.14), residues: 590 sheet: -1.96 (0.23), residues: 420 loop : -2.08 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.003 0.001 HIS E 327 PHE 0.015 0.001 PHE E 48 TYR 0.013 0.001 TYR C 144 ARG 0.005 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 290 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.6662 (mtp180) REVERT: A 94 TYR cc_start: 0.7591 (t80) cc_final: 0.7254 (t80) REVERT: A 102 ASP cc_start: 0.8064 (t70) cc_final: 0.7612 (t70) REVERT: A 208 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7719 (tp30) REVERT: A 261 ASN cc_start: 0.8448 (t0) cc_final: 0.7985 (t0) REVERT: A 391 MET cc_start: 0.8381 (tpt) cc_final: 0.7988 (tpp) REVERT: A 393 LYS cc_start: 0.6842 (mmtt) cc_final: 0.6176 (mptp) REVERT: B 36 LYS cc_start: 0.9168 (mttt) cc_final: 0.8959 (mppt) REVERT: B 43 ARG cc_start: 0.9111 (mtm-85) cc_final: 0.8425 (mtm180) REVERT: B 102 ASP cc_start: 0.8057 (t70) cc_final: 0.7672 (t70) REVERT: B 179 MET cc_start: 0.8739 (tpt) cc_final: 0.8477 (tpp) REVERT: B 303 MET cc_start: 0.8065 (mtm) cc_final: 0.7863 (mmt) REVERT: B 391 MET cc_start: 0.8304 (tpt) cc_final: 0.7807 (tpp) REVERT: B 397 SER cc_start: 0.8510 (t) cc_final: 0.8265 (p) REVERT: C 36 LYS cc_start: 0.9162 (mttt) cc_final: 0.8942 (mppt) REVERT: C 43 ARG cc_start: 0.8973 (mtm-85) cc_final: 0.8382 (mtm180) REVERT: C 261 ASN cc_start: 0.8444 (t0) cc_final: 0.8001 (t0) REVERT: C 279 MET cc_start: 0.8864 (tpt) cc_final: 0.8658 (tpt) REVERT: C 325 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.7092 (mtp-110) REVERT: C 391 MET cc_start: 0.8231 (tpt) cc_final: 0.7940 (tpp) REVERT: C 393 LYS cc_start: 0.6817 (mmtt) cc_final: 0.6030 (mptp) REVERT: C 397 SER cc_start: 0.8574 (t) cc_final: 0.8340 (p) REVERT: C 403 ASP cc_start: 0.8395 (t0) cc_final: 0.8050 (t0) REVERT: D 36 LYS cc_start: 0.9183 (mttt) cc_final: 0.8896 (mppt) REVERT: D 102 ASP cc_start: 0.8058 (t70) cc_final: 0.7797 (t0) REVERT: D 212 ARG cc_start: 0.7462 (ptp-170) cc_final: 0.7182 (ptp-110) REVERT: D 261 ASN cc_start: 0.8361 (t0) cc_final: 0.7915 (t0) REVERT: D 391 MET cc_start: 0.8219 (tpt) cc_final: 0.7767 (tpp) REVERT: D 397 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8144 (p) REVERT: E 36 LYS cc_start: 0.9155 (mttt) cc_final: 0.8898 (mppt) REVERT: E 179 MET cc_start: 0.8537 (tpt) cc_final: 0.8275 (tpt) REVERT: E 208 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: E 227 GLU cc_start: 0.8007 (pt0) cc_final: 0.7718 (pt0) REVERT: E 261 ASN cc_start: 0.8431 (t0) cc_final: 0.8003 (t0) REVERT: E 391 MET cc_start: 0.8266 (tpt) cc_final: 0.7744 (tpp) REVERT: E 397 SER cc_start: 0.8558 (OUTLIER) cc_final: 0.8353 (p) outliers start: 57 outliers final: 19 residues processed: 328 average time/residue: 1.1787 time to fit residues: 425.3684 Evaluate side-chains 264 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 240 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 153 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 77 ASN B 82 GLN C 77 ASN C 82 GLN D 77 ASN D 82 GLN E 77 ASN E 82 GLN E 141 ASN E 231 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14560 Z= 0.186 Angle : 0.665 9.793 19740 Z= 0.327 Chirality : 0.048 0.258 2255 Planarity : 0.004 0.029 2445 Dihedral : 12.642 62.680 2195 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.30 % Allowed : 17.22 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.19), residues: 1705 helix: -2.09 (0.17), residues: 590 sheet: -1.45 (0.24), residues: 440 loop : -1.63 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 84 HIS 0.003 0.001 HIS C 217 PHE 0.009 0.001 PHE E 48 TYR 0.012 0.001 TYR A 144 ARG 0.005 0.000 ARG E 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 257 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6703 (mtp180) REVERT: A 102 ASP cc_start: 0.8065 (t70) cc_final: 0.7740 (t70) REVERT: A 208 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: A 391 MET cc_start: 0.8366 (tpt) cc_final: 0.7961 (tpp) REVERT: A 393 LYS cc_start: 0.6874 (mmtt) cc_final: 0.6203 (mptp) REVERT: B 43 ARG cc_start: 0.9137 (mtm-85) cc_final: 0.8488 (mtm180) REVERT: B 102 ASP cc_start: 0.8117 (t70) cc_final: 0.7743 (t70) REVERT: B 163 MET cc_start: 0.8609 (mtm) cc_final: 0.7881 (mpp) REVERT: B 391 MET cc_start: 0.8281 (tpt) cc_final: 0.7843 (tpp) REVERT: B 397 SER cc_start: 0.8402 (t) cc_final: 0.8177 (p) REVERT: C 36 LYS cc_start: 0.9166 (mttt) cc_final: 0.8963 (mppt) REVERT: C 43 ARG cc_start: 0.9050 (mtm-85) cc_final: 0.8463 (mtm180) REVERT: C 72 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8410 (mtt) REVERT: C 102 ASP cc_start: 0.8200 (t70) cc_final: 0.7759 (t0) REVERT: C 170 MET cc_start: 0.8394 (ttm) cc_final: 0.8187 (ttm) REVERT: C 189 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7790 (ptpp) REVERT: C 391 MET cc_start: 0.8217 (tpt) cc_final: 0.7853 (tpp) REVERT: C 393 LYS cc_start: 0.6712 (mmtt) cc_final: 0.5939 (mptp) REVERT: D 36 LYS cc_start: 0.9190 (mttt) cc_final: 0.8905 (mppt) REVERT: D 212 ARG cc_start: 0.7353 (ptp-170) cc_final: 0.7077 (ptp-110) REVERT: D 391 MET cc_start: 0.8192 (tpt) cc_final: 0.7718 (tpp) REVERT: D 393 LYS cc_start: 0.6628 (mmtt) cc_final: 0.5852 (mptp) REVERT: D 397 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8084 (p) REVERT: E 36 LYS cc_start: 0.9163 (mttt) cc_final: 0.8918 (mppt) REVERT: E 43 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8508 (mtm180) REVERT: E 229 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8283 (mtp85) REVERT: E 391 MET cc_start: 0.8212 (tpt) cc_final: 0.7645 (tpp) REVERT: E 393 LYS cc_start: 0.6775 (mmtt) cc_final: 0.6078 (mptp) outliers start: 51 outliers final: 12 residues processed: 291 average time/residue: 1.2850 time to fit residues: 408.7599 Evaluate side-chains 248 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN C 62 ASN C 141 ASN D 62 ASN E 62 ASN E 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14560 Z= 0.178 Angle : 0.634 9.781 19740 Z= 0.310 Chirality : 0.046 0.243 2255 Planarity : 0.003 0.026 2445 Dihedral : 9.902 56.884 2195 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.01 % Allowed : 18.45 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.20), residues: 1705 helix: -1.09 (0.20), residues: 595 sheet: -1.20 (0.24), residues: 440 loop : -1.39 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 84 HIS 0.002 0.001 HIS B 327 PHE 0.009 0.001 PHE E 48 TYR 0.015 0.001 TYR D 144 ARG 0.005 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 246 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6701 (mtp180) REVERT: A 102 ASP cc_start: 0.8058 (t70) cc_final: 0.7789 (t0) REVERT: A 391 MET cc_start: 0.8358 (tpt) cc_final: 0.7966 (tpp) REVERT: A 393 LYS cc_start: 0.6781 (mmtt) cc_final: 0.6124 (mptp) REVERT: B 43 ARG cc_start: 0.9153 (mtm-85) cc_final: 0.8490 (mtm180) REVERT: B 71 THR cc_start: 0.9376 (OUTLIER) cc_final: 0.9009 (t) REVERT: B 102 ASP cc_start: 0.8120 (t70) cc_final: 0.7759 (t70) REVERT: B 156 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8491 (mtt) REVERT: B 179 MET cc_start: 0.8676 (tpt) cc_final: 0.8471 (mmt) REVERT: B 202 GLN cc_start: 0.8460 (mt0) cc_final: 0.8192 (mt0) REVERT: B 229 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8159 (mtp85) REVERT: B 303 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7616 (mmt) REVERT: B 391 MET cc_start: 0.8291 (tpt) cc_final: 0.7813 (tpp) REVERT: B 393 LYS cc_start: 0.6738 (mmtt) cc_final: 0.5897 (mptp) REVERT: C 43 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.8434 (mtm180) REVERT: C 72 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8465 (mmm) REVERT: C 391 MET cc_start: 0.8201 (tpt) cc_final: 0.7791 (tpp) REVERT: C 393 LYS cc_start: 0.6657 (mmtt) cc_final: 0.5868 (mptp) REVERT: D 36 LYS cc_start: 0.9183 (mttt) cc_final: 0.8896 (mppt) REVERT: D 71 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9102 (p) REVERT: D 156 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8774 (mtt) REVERT: D 303 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7674 (mmm) REVERT: D 391 MET cc_start: 0.8188 (tpt) cc_final: 0.7709 (tpp) REVERT: D 393 LYS cc_start: 0.6645 (mmtt) cc_final: 0.6076 (ptpt) REVERT: D 397 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7986 (p) REVERT: E 36 LYS cc_start: 0.9145 (mttt) cc_final: 0.8892 (mppt) REVERT: E 43 ARG cc_start: 0.8833 (mtm-85) cc_final: 0.8435 (mtm180) REVERT: E 71 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.8929 (t) REVERT: E 229 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8254 (mtp85) REVERT: E 391 MET cc_start: 0.8193 (tpt) cc_final: 0.7584 (tpp) REVERT: E 393 LYS cc_start: 0.6745 (mmtt) cc_final: 0.6073 (mptp) outliers start: 62 outliers final: 16 residues processed: 285 average time/residue: 1.2591 time to fit residues: 392.4172 Evaluate side-chains 242 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 241 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14560 Z= 0.377 Angle : 0.698 10.101 19740 Z= 0.349 Chirality : 0.049 0.217 2255 Planarity : 0.004 0.033 2445 Dihedral : 8.895 56.547 2195 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.85 % Allowed : 18.90 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1705 helix: -0.86 (0.21), residues: 600 sheet: -1.20 (0.25), residues: 425 loop : -1.35 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 259 HIS 0.004 0.001 HIS B 217 PHE 0.012 0.002 PHE B 116 TYR 0.019 0.002 TYR A 425 ARG 0.011 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 248 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9032 (mtm-85) cc_final: 0.8214 (mtm180) REVERT: A 71 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.8878 (t) REVERT: A 81 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.6699 (mtp180) REVERT: A 189 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7587 (ptpt) REVERT: A 208 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: A 292 LYS cc_start: 0.8245 (mttt) cc_final: 0.8003 (mmpt) REVERT: A 391 MET cc_start: 0.8371 (tpt) cc_final: 0.7972 (tpp) REVERT: A 393 LYS cc_start: 0.6839 (mmtt) cc_final: 0.6152 (mptp) REVERT: B 36 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8919 (mppt) REVERT: B 102 ASP cc_start: 0.8199 (t70) cc_final: 0.7930 (t70) REVERT: B 156 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8398 (mtt) REVERT: B 202 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: B 303 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7656 (mmt) REVERT: B 391 MET cc_start: 0.8301 (tpt) cc_final: 0.7824 (tpp) REVERT: B 393 LYS cc_start: 0.6734 (mmtt) cc_final: 0.5881 (mptp) REVERT: C 43 ARG cc_start: 0.9127 (mtm-85) cc_final: 0.8374 (mtm180) REVERT: C 71 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.8832 (t) REVERT: C 102 ASP cc_start: 0.8325 (t70) cc_final: 0.7895 (t0) REVERT: C 391 MET cc_start: 0.8157 (tpt) cc_final: 0.7797 (tpp) REVERT: C 393 LYS cc_start: 0.6676 (mmtt) cc_final: 0.5880 (mptp) REVERT: D 28 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8067 (mt-10) REVERT: D 36 LYS cc_start: 0.9220 (mttt) cc_final: 0.8944 (mppt) REVERT: D 156 MET cc_start: 0.9128 (mtt) cc_final: 0.8756 (mtt) REVERT: D 216 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8195 (mtpp) REVERT: D 261 ASN cc_start: 0.8343 (t0) cc_final: 0.7867 (t0) REVERT: D 292 LYS cc_start: 0.8179 (mttt) cc_final: 0.7853 (mmpt) REVERT: D 303 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7751 (mmm) REVERT: D 391 MET cc_start: 0.8159 (tpt) cc_final: 0.7697 (tpp) REVERT: D 393 LYS cc_start: 0.6645 (mmtt) cc_final: 0.6063 (ptpt) REVERT: D 397 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7937 (p) REVERT: E 24 MET cc_start: 0.8218 (ptp) cc_final: 0.7947 (ptp) REVERT: E 36 LYS cc_start: 0.9156 (mttt) cc_final: 0.8900 (mppt) REVERT: E 43 ARG cc_start: 0.8971 (mtm-85) cc_final: 0.8463 (mtm180) REVERT: E 71 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9076 (p) REVERT: E 94 TYR cc_start: 0.7705 (t80) cc_final: 0.7358 (t80) REVERT: E 261 ASN cc_start: 0.8389 (t0) cc_final: 0.7867 (t0) REVERT: E 391 MET cc_start: 0.8212 (tpt) cc_final: 0.7583 (tpp) REVERT: E 393 LYS cc_start: 0.6787 (mmtt) cc_final: 0.6114 (mptp) outliers start: 75 outliers final: 43 residues processed: 297 average time/residue: 1.2503 time to fit residues: 406.1353 Evaluate side-chains 283 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 229 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 397 SER Chi-restraints excluded: chain E residue 416 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN D 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14560 Z= 0.172 Angle : 0.600 7.369 19740 Z= 0.298 Chirality : 0.045 0.175 2255 Planarity : 0.003 0.026 2445 Dihedral : 8.213 56.303 2195 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.75 % Allowed : 21.55 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1705 helix: -0.39 (0.21), residues: 595 sheet: -1.05 (0.25), residues: 425 loop : -1.24 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 259 HIS 0.002 0.001 HIS E 217 PHE 0.008 0.001 PHE B 395 TYR 0.013 0.001 TYR E 317 ARG 0.005 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 237 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: A 71 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.8901 (t) REVERT: A 81 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6624 (mtp180) REVERT: A 156 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8413 (mtt) REVERT: A 189 LYS cc_start: 0.7519 (ptpt) cc_final: 0.7303 (ptpt) REVERT: A 261 ASN cc_start: 0.8294 (t0) cc_final: 0.7684 (t0) REVERT: A 391 MET cc_start: 0.8378 (tpt) cc_final: 0.7959 (tpp) REVERT: A 393 LYS cc_start: 0.6822 (mmtt) cc_final: 0.6148 (mptp) REVERT: B 36 LYS cc_start: 0.9236 (mmtp) cc_final: 0.8926 (mppt) REVERT: B 43 ARG cc_start: 0.9156 (mtm-85) cc_final: 0.8604 (mtm180) REVERT: B 71 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.8764 (t) REVERT: B 102 ASP cc_start: 0.8188 (t70) cc_final: 0.7877 (t70) REVERT: B 156 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: B 229 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8169 (mtp85) REVERT: B 303 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7597 (mmt) REVERT: B 391 MET cc_start: 0.8255 (tpt) cc_final: 0.7758 (tpp) REVERT: B 393 LYS cc_start: 0.6674 (mmtt) cc_final: 0.5856 (mptp) REVERT: C 36 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8957 (mppt) REVERT: C 43 ARG cc_start: 0.9076 (mtm-85) cc_final: 0.8424 (mtm180) REVERT: C 71 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.8861 (t) REVERT: C 102 ASP cc_start: 0.8305 (t70) cc_final: 0.7922 (t0) REVERT: C 261 ASN cc_start: 0.8337 (t0) cc_final: 0.7626 (t0) REVERT: C 325 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.6913 (ttp80) REVERT: C 391 MET cc_start: 0.8150 (tpt) cc_final: 0.7756 (tpp) REVERT: C 393 LYS cc_start: 0.6678 (mmtt) cc_final: 0.5926 (mptp) REVERT: D 36 LYS cc_start: 0.9202 (mttt) cc_final: 0.8934 (mppt) REVERT: D 43 ARG cc_start: 0.9095 (mtm-85) cc_final: 0.8879 (mtm-85) REVERT: D 71 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9113 (p) REVERT: D 156 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8693 (mtt) REVERT: D 216 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8224 (mtpp) REVERT: D 243 MET cc_start: 0.8319 (mtt) cc_final: 0.8103 (mtt) REVERT: D 261 ASN cc_start: 0.8292 (t0) cc_final: 0.7802 (t0) REVERT: D 303 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7739 (mmm) REVERT: D 391 MET cc_start: 0.8153 (tpt) cc_final: 0.7646 (tpp) REVERT: D 393 LYS cc_start: 0.6605 (mmtt) cc_final: 0.6251 (ptpt) REVERT: D 397 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7882 (p) REVERT: E 36 LYS cc_start: 0.9145 (mttt) cc_final: 0.8897 (mppt) REVERT: E 43 ARG cc_start: 0.8917 (mtm-85) cc_final: 0.8408 (mtm180) REVERT: E 71 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9048 (p) REVERT: E 156 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8799 (mtt) REVERT: E 229 ARG cc_start: 0.8556 (mtp85) cc_final: 0.8257 (mtp85) REVERT: E 391 MET cc_start: 0.8189 (tpt) cc_final: 0.7416 (tpp) REVERT: E 393 LYS cc_start: 0.6730 (mmtt) cc_final: 0.6067 (mptp) outliers start: 58 outliers final: 21 residues processed: 276 average time/residue: 1.2669 time to fit residues: 382.5173 Evaluate side-chains 258 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 224 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 427 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14560 Z= 0.181 Angle : 0.581 7.485 19740 Z= 0.290 Chirality : 0.044 0.171 2255 Planarity : 0.003 0.027 2445 Dihedral : 7.695 56.294 2195 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.30 % Allowed : 22.14 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1705 helix: -0.20 (0.21), residues: 600 sheet: -1.04 (0.25), residues: 415 loop : -1.19 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 259 HIS 0.002 0.001 HIS E 327 PHE 0.008 0.001 PHE C 115 TYR 0.013 0.001 TYR E 317 ARG 0.007 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 1.767 Fit side-chains REVERT: A 71 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.8909 (t) REVERT: A 81 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6657 (mtp180) REVERT: A 163 MET cc_start: 0.9008 (mtm) cc_final: 0.8739 (mpp) REVERT: A 189 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7197 (pttt) REVERT: A 229 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8121 (mtp85) REVERT: A 261 ASN cc_start: 0.8306 (t0) cc_final: 0.7689 (t0) REVERT: A 325 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6683 (ttp-110) REVERT: A 391 MET cc_start: 0.8356 (tpt) cc_final: 0.7925 (tpp) REVERT: A 393 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6165 (mptp) REVERT: B 36 LYS cc_start: 0.9229 (mmtp) cc_final: 0.8911 (mppt) REVERT: B 43 ARG cc_start: 0.9176 (mtm-85) cc_final: 0.8542 (mtm180) REVERT: B 71 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.8844 (t) REVERT: B 102 ASP cc_start: 0.8201 (t70) cc_final: 0.7885 (t70) REVERT: B 156 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: B 202 GLN cc_start: 0.8493 (mt0) cc_final: 0.8182 (mt0) REVERT: B 229 ARG cc_start: 0.8491 (mtp85) cc_final: 0.8137 (mtp85) REVERT: B 303 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7595 (mmt) REVERT: B 391 MET cc_start: 0.8243 (tpt) cc_final: 0.7723 (tpp) REVERT: B 393 LYS cc_start: 0.6697 (mmtt) cc_final: 0.5880 (mptp) REVERT: C 36 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8971 (mppt) REVERT: C 43 ARG cc_start: 0.9097 (mtm-85) cc_final: 0.8426 (mtm180) REVERT: C 71 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.8868 (t) REVERT: C 102 ASP cc_start: 0.8336 (t70) cc_final: 0.7935 (t0) REVERT: C 261 ASN cc_start: 0.8311 (t0) cc_final: 0.7636 (t0) REVERT: C 325 ARG cc_start: 0.7298 (ttp-110) cc_final: 0.6938 (ttp80) REVERT: C 391 MET cc_start: 0.8165 (tpt) cc_final: 0.7748 (tpp) REVERT: C 393 LYS cc_start: 0.6694 (mmtt) cc_final: 0.5926 (mptp) REVERT: D 36 LYS cc_start: 0.9197 (mttt) cc_final: 0.8930 (mppt) REVERT: D 156 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8711 (mtt) REVERT: D 163 MET cc_start: 0.8821 (mtm) cc_final: 0.8561 (mpp) REVERT: D 189 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7431 (ptpt) REVERT: D 216 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8263 (mtpp) REVERT: D 261 ASN cc_start: 0.8296 (t0) cc_final: 0.7794 (t0) REVERT: D 303 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (mmm) REVERT: D 391 MET cc_start: 0.8142 (tpt) cc_final: 0.7620 (tpp) REVERT: D 393 LYS cc_start: 0.6623 (mmtt) cc_final: 0.6278 (ptpt) REVERT: D 397 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7891 (p) REVERT: E 36 LYS cc_start: 0.9130 (mttt) cc_final: 0.8894 (mppt) REVERT: E 43 ARG cc_start: 0.8942 (mtm-85) cc_final: 0.8431 (mtm180) REVERT: E 71 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9036 (p) REVERT: E 156 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8748 (mtt) REVERT: E 229 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8222 (mtp85) REVERT: E 261 ASN cc_start: 0.8321 (t0) cc_final: 0.7767 (t0) REVERT: E 391 MET cc_start: 0.8200 (tpt) cc_final: 0.7408 (tpp) REVERT: E 393 LYS cc_start: 0.6754 (mmtt) cc_final: 0.6065 (mptp) outliers start: 51 outliers final: 20 residues processed: 270 average time/residue: 1.2337 time to fit residues: 364.9933 Evaluate side-chains 258 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 224 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14560 Z= 0.205 Angle : 0.575 6.860 19740 Z= 0.289 Chirality : 0.044 0.172 2255 Planarity : 0.003 0.037 2445 Dihedral : 7.420 56.013 2195 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.69 % Allowed : 22.39 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1705 helix: -0.05 (0.21), residues: 600 sheet: -0.92 (0.25), residues: 415 loop : -1.13 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 259 HIS 0.003 0.001 HIS D 327 PHE 0.008 0.001 PHE C 115 TYR 0.014 0.001 TYR E 317 ARG 0.008 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 229 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.8502 (mtm180) REVERT: A 71 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.8912 (t) REVERT: A 81 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6671 (mtp180) REVERT: A 189 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7500 (ptpt) REVERT: A 229 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8075 (mtp85) REVERT: A 261 ASN cc_start: 0.8311 (t0) cc_final: 0.7697 (t0) REVERT: A 391 MET cc_start: 0.8323 (tpt) cc_final: 0.7874 (tpp) REVERT: A 393 LYS cc_start: 0.6834 (mmtt) cc_final: 0.6164 (mptp) REVERT: B 36 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8922 (mppt) REVERT: B 43 ARG cc_start: 0.9196 (mtm-85) cc_final: 0.8519 (mtm180) REVERT: B 71 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.8809 (t) REVERT: B 102 ASP cc_start: 0.8216 (t70) cc_final: 0.7921 (t70) REVERT: B 156 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8361 (mtt) REVERT: B 202 GLN cc_start: 0.8480 (mt0) cc_final: 0.8182 (mt0) REVERT: B 229 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8121 (mtp85) REVERT: B 303 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7588 (mmt) REVERT: B 391 MET cc_start: 0.8255 (tpt) cc_final: 0.7720 (tpp) REVERT: B 393 LYS cc_start: 0.6698 (mmtt) cc_final: 0.5888 (mptp) REVERT: C 36 LYS cc_start: 0.9267 (mmtp) cc_final: 0.8987 (mppt) REVERT: C 43 ARG cc_start: 0.9100 (mtm-85) cc_final: 0.8426 (mtm180) REVERT: C 71 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.8846 (t) REVERT: C 102 ASP cc_start: 0.8344 (t70) cc_final: 0.7923 (t0) REVERT: C 236 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7613 (tmm) REVERT: C 261 ASN cc_start: 0.8317 (t0) cc_final: 0.7646 (t0) REVERT: C 325 ARG cc_start: 0.7314 (ttp-110) cc_final: 0.6955 (ttp80) REVERT: C 391 MET cc_start: 0.8157 (tpt) cc_final: 0.7737 (tpp) REVERT: C 393 LYS cc_start: 0.6704 (mmtt) cc_final: 0.6383 (tppt) REVERT: D 36 LYS cc_start: 0.9200 (mttt) cc_final: 0.8932 (mppt) REVERT: D 156 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8719 (mtt) REVERT: D 189 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7404 (ptpt) REVERT: D 261 ASN cc_start: 0.8311 (t0) cc_final: 0.7788 (t0) REVERT: D 303 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7730 (mmm) REVERT: D 391 MET cc_start: 0.8130 (tpt) cc_final: 0.7578 (tpp) REVERT: D 393 LYS cc_start: 0.6633 (mmtt) cc_final: 0.6291 (ptpt) REVERT: D 397 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7888 (p) REVERT: E 36 LYS cc_start: 0.9133 (mttt) cc_final: 0.8892 (mppt) REVERT: E 43 ARG cc_start: 0.8940 (mtm-85) cc_final: 0.8491 (mtm180) REVERT: E 71 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.8998 (p) REVERT: E 156 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8804 (mtt) REVERT: E 229 ARG cc_start: 0.8546 (mtp85) cc_final: 0.8207 (mtp85) REVERT: E 261 ASN cc_start: 0.8276 (t0) cc_final: 0.7688 (t0) REVERT: E 391 MET cc_start: 0.8189 (tpt) cc_final: 0.7385 (tpp) REVERT: E 393 LYS cc_start: 0.6758 (mmtt) cc_final: 0.6028 (mptp) outliers start: 57 outliers final: 28 residues processed: 268 average time/residue: 1.2173 time to fit residues: 358.2162 Evaluate side-chains 263 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 289 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 161 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14560 Z= 0.201 Angle : 0.567 6.626 19740 Z= 0.286 Chirality : 0.044 0.172 2255 Planarity : 0.003 0.032 2445 Dihedral : 7.266 55.738 2195 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.69 % Allowed : 22.39 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.20), residues: 1705 helix: 0.11 (0.21), residues: 600 sheet: -0.80 (0.25), residues: 415 loop : -1.09 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 259 HIS 0.006 0.001 HIS C 217 PHE 0.010 0.001 PHE C 115 TYR 0.014 0.001 TYR E 317 ARG 0.007 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 227 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9044 (mtm-85) cc_final: 0.8477 (mtm180) REVERT: A 71 THR cc_start: 0.9412 (OUTLIER) cc_final: 0.8907 (t) REVERT: A 81 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6661 (mtp180) REVERT: A 189 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7420 (pttt) REVERT: A 229 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8074 (mtp85) REVERT: A 261 ASN cc_start: 0.8315 (t0) cc_final: 0.7706 (t0) REVERT: A 325 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6737 (ttp-110) REVERT: A 391 MET cc_start: 0.8323 (tpt) cc_final: 0.7872 (tpp) REVERT: A 393 LYS cc_start: 0.6819 (mmtt) cc_final: 0.6152 (mptp) REVERT: B 36 LYS cc_start: 0.9236 (mmtp) cc_final: 0.8912 (mppt) REVERT: B 43 ARG cc_start: 0.9195 (mtm-85) cc_final: 0.8521 (mtm180) REVERT: B 102 ASP cc_start: 0.8221 (t70) cc_final: 0.7946 (t70) REVERT: B 156 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8356 (mtt) REVERT: B 202 GLN cc_start: 0.8472 (mt0) cc_final: 0.8176 (mt0) REVERT: B 229 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8117 (mtp85) REVERT: B 303 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7586 (mmt) REVERT: B 391 MET cc_start: 0.8264 (tpt) cc_final: 0.7719 (tpp) REVERT: B 393 LYS cc_start: 0.6707 (mmtt) cc_final: 0.5899 (mptp) REVERT: C 36 LYS cc_start: 0.9275 (mmtp) cc_final: 0.9004 (mppt) REVERT: C 43 ARG cc_start: 0.9101 (mtm-85) cc_final: 0.8428 (mtm180) REVERT: C 71 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.8824 (t) REVERT: C 102 ASP cc_start: 0.8352 (t70) cc_final: 0.7919 (t0) REVERT: C 236 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7666 (tmm) REVERT: C 261 ASN cc_start: 0.8310 (t0) cc_final: 0.7652 (t0) REVERT: C 325 ARG cc_start: 0.7371 (ttp-110) cc_final: 0.7019 (ttp80) REVERT: C 391 MET cc_start: 0.8187 (tpt) cc_final: 0.7807 (tpp) REVERT: C 393 LYS cc_start: 0.6701 (mmtt) cc_final: 0.6381 (tppt) REVERT: D 36 LYS cc_start: 0.9199 (mttt) cc_final: 0.8932 (mppt) REVERT: D 156 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8701 (mtt) REVERT: D 261 ASN cc_start: 0.8309 (t0) cc_final: 0.7788 (t0) REVERT: D 391 MET cc_start: 0.8136 (tpt) cc_final: 0.7571 (tpp) REVERT: D 393 LYS cc_start: 0.6648 (mmtt) cc_final: 0.6295 (ptpt) REVERT: D 397 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7857 (p) REVERT: E 36 LYS cc_start: 0.9130 (mttt) cc_final: 0.8892 (mppt) REVERT: E 43 ARG cc_start: 0.8959 (mtm-85) cc_final: 0.8372 (mtm180) REVERT: E 71 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.8991 (p) REVERT: E 156 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8827 (mtt) REVERT: E 229 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8212 (mtp85) REVERT: E 236 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7615 (tmm) REVERT: E 261 ASN cc_start: 0.8332 (t0) cc_final: 0.7718 (t0) REVERT: E 391 MET cc_start: 0.8176 (tpt) cc_final: 0.7377 (tpp) REVERT: E 393 LYS cc_start: 0.6772 (mmtt) cc_final: 0.6033 (mptp) outliers start: 57 outliers final: 30 residues processed: 263 average time/residue: 1.2568 time to fit residues: 361.8106 Evaluate side-chains 266 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14560 Z= 0.236 Angle : 0.579 6.754 19740 Z= 0.293 Chirality : 0.045 0.171 2255 Planarity : 0.003 0.033 2445 Dihedral : 7.210 55.540 2195 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.91 % Allowed : 23.17 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1705 helix: 0.22 (0.21), residues: 600 sheet: -0.68 (0.25), residues: 425 loop : -1.12 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 259 HIS 0.003 0.001 HIS C 217 PHE 0.009 0.001 PHE C 115 TYR 0.016 0.001 TYR D 425 ARG 0.007 0.000 ARG A 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9056 (mtm-85) cc_final: 0.8471 (mtm180) REVERT: A 71 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.8897 (t) REVERT: A 81 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6675 (mtp180) REVERT: A 189 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7507 (pttt) REVERT: A 229 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8025 (mtp85) REVERT: A 261 ASN cc_start: 0.8307 (t0) cc_final: 0.7696 (t0) REVERT: A 325 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6839 (ttp-110) REVERT: A 391 MET cc_start: 0.8324 (tpt) cc_final: 0.7867 (tpp) REVERT: A 393 LYS cc_start: 0.6831 (mmtt) cc_final: 0.6161 (mptp) REVERT: B 36 LYS cc_start: 0.9234 (mmtp) cc_final: 0.8922 (mppt) REVERT: B 43 ARG cc_start: 0.9209 (mtm-85) cc_final: 0.8540 (mtm180) REVERT: B 229 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8126 (mtp85) REVERT: B 303 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7532 (mmt) REVERT: B 391 MET cc_start: 0.8271 (tpt) cc_final: 0.7756 (tpp) REVERT: B 393 LYS cc_start: 0.6724 (mmtt) cc_final: 0.5912 (mptp) REVERT: C 36 LYS cc_start: 0.9287 (mmtp) cc_final: 0.9018 (mppt) REVERT: C 43 ARG cc_start: 0.9101 (mtm-85) cc_final: 0.8363 (mtm180) REVERT: C 71 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.8919 (t) REVERT: C 236 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7726 (tmm) REVERT: C 261 ASN cc_start: 0.8316 (t0) cc_final: 0.7666 (t0) REVERT: C 325 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7042 (ttp80) REVERT: C 391 MET cc_start: 0.8204 (tpt) cc_final: 0.7810 (tpp) REVERT: C 393 LYS cc_start: 0.6717 (mmtt) cc_final: 0.6396 (tppt) REVERT: D 36 LYS cc_start: 0.9209 (mttt) cc_final: 0.8934 (mppt) REVERT: D 156 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8736 (mtt) REVERT: D 261 ASN cc_start: 0.8313 (t0) cc_final: 0.7789 (t0) REVERT: D 391 MET cc_start: 0.8125 (tpt) cc_final: 0.7536 (tpp) REVERT: D 393 LYS cc_start: 0.6654 (mmtt) cc_final: 0.6306 (ptpt) REVERT: D 397 SER cc_start: 0.8089 (OUTLIER) cc_final: 0.7882 (p) REVERT: E 36 LYS cc_start: 0.9128 (mttt) cc_final: 0.8883 (mppt) REVERT: E 43 ARG cc_start: 0.8969 (mtm-85) cc_final: 0.8332 (mtm180) REVERT: E 71 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8975 (p) REVERT: E 156 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8877 (mtt) REVERT: E 229 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8215 (mtp85) REVERT: E 236 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7656 (tmm) REVERT: E 261 ASN cc_start: 0.8317 (t0) cc_final: 0.7713 (t0) REVERT: E 391 MET cc_start: 0.8197 (tpt) cc_final: 0.7384 (tpp) REVERT: E 393 LYS cc_start: 0.6759 (mmtt) cc_final: 0.6004 (mptp) outliers start: 45 outliers final: 30 residues processed: 261 average time/residue: 1.2639 time to fit residues: 361.4551 Evaluate side-chains 265 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 223 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 ARG Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 397 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 397 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 138 optimal weight: 0.0060 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096252 restraints weight = 18762.659| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.22 r_work: 0.2928 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14560 Z= 0.128 Angle : 0.543 5.723 19740 Z= 0.273 Chirality : 0.043 0.176 2255 Planarity : 0.003 0.027 2445 Dihedral : 6.961 55.254 2195 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.88 % Allowed : 24.66 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1705 helix: 0.62 (0.22), residues: 590 sheet: -0.37 (0.26), residues: 380 loop : -0.98 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 259 HIS 0.002 0.001 HIS E 327 PHE 0.009 0.001 PHE C 115 TYR 0.011 0.001 TYR A 144 ARG 0.006 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6239.05 seconds wall clock time: 111 minutes 4.81 seconds (6664.81 seconds total)