Starting phenix.real_space_refine on Fri Feb 16 02:48:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm3_20385/02_2024/6pm3_20385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm3_20385/02_2024/6pm3_20385.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/6pm3_20385/02_2024/6pm3_20385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm3_20385/02_2024/6pm3_20385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm3_20385/02_2024/6pm3_20385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm3_20385/02_2024/6pm3_20385_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= 0.000 sd= 0.003 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 105 5.16 5 C 9195 2.51 5 N 2290 2.21 5 O 2530 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: 14120 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2789 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2789 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2789 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2789 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2789 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.65, per 1000 atoms: 0.54 Number of scatterers: 14120 At special positions: 0 Unit cell: (97.114, 98.76, 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 105 16.00 O 2530 8.00 N 2290 7.00 C 9195 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=2.03 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=2.03 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=2.03 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " 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: 5.55 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: 45 helices and 25 sheets defined 35.4% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' 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: 3.628A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.767A 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 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.557A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 removed outlier: 3.566A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 325 removed outlier: 3.522A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.618A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.516A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' 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: 3.628A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.767A 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 Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.556A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 284 removed outlier: 3.565A pdb=" N LEU B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 325 removed outlier: 3.522A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG B 325 " --> pdb=" O ASN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 424 removed outlier: 3.618A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.515A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 33 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' 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: 3.628A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.767A 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 Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.557A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 284 removed outlier: 3.565A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 325 removed outlier: 3.523A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 315 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 424 removed outlier: 3.618A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.515A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 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: 3.628A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.767A 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 Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.557A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 284 removed outlier: 3.566A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 325 removed outlier: 3.522A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 315 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 424 removed outlier: 3.618A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.515A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 33 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' 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: 3.628A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.767A 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 Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.556A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 284 removed outlier: 3.566A pdb=" N LEU E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 325 removed outlier: 3.522A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 315 " --> pdb=" O PHE E 311 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG E 325 " --> pdb=" O ASN E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 424 removed outlier: 3.618A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.515A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.263A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= E, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.507A pdb=" N ASP A 210 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.264A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= J, first strand: chain 'B' and resid 209 through 213 removed outlier: 3.507A pdb=" N ASP B 210 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.263A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= M, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= O, first strand: chain 'C' and resid 209 through 213 removed outlier: 3.507A pdb=" N ASP C 210 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.263A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'D' and resid 98 through 100 Processing sheet with id= S, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'D' and resid 209 through 213 removed outlier: 3.507A pdb=" N ASP D 210 " --> pdb=" O ARG D 229 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.263A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= W, first strand: chain 'E' and resid 98 through 100 Processing sheet with id= X, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= Y, first strand: chain 'E' and resid 209 through 213 removed outlier: 3.507A pdb=" N ASP E 210 " --> pdb=" O ARG E 229 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1605 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: 4.51 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4038 1.33 - 1.46: 3654 1.46 - 1.58: 6603 1.58 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 14470 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 ... (remaining 14465 not shown) Histogram of bond angle deviations from ideal: 97.49 - 105.08: 336 105.08 - 112.67: 7380 112.67 - 120.26: 6121 120.26 - 127.85: 5641 127.85 - 135.43: 152 Bond angle restraints: 19630 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 121.54 135.43 -13.89 1.91e+00 2.74e-01 5.29e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 135.42 -13.88 1.91e+00 2.74e-01 5.28e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 135.41 -13.87 1.91e+00 2.74e-01 5.28e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 135.40 -13.86 1.91e+00 2.74e-01 5.27e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 135.39 -13.85 1.91e+00 2.74e-01 5.26e+01 ... (remaining 19625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 8415 16.78 - 33.56: 325 33.56 - 50.34: 25 50.34 - 67.12: 5 67.12 - 83.90: 10 Dihedral angle restraints: 8780 sinusoidal: 3680 harmonic: 5100 Sorted by residual: 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 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+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 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -169.90 83.90 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 8777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1870 0.079 - 0.158: 329 0.158 - 0.237: 26 0.237 - 0.317: 0 0.317 - 0.396: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CG LEU A 314 " pdb=" CB LEU A 314 " pdb=" CD1 LEU A 314 " pdb=" CD2 LEU A 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CG LEU D 314 " pdb=" CB LEU D 314 " pdb=" CD1 LEU D 314 " pdb=" CD2 LEU D 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CG LEU E 314 " pdb=" CB LEU E 314 " pdb=" CD1 LEU E 314 " pdb=" CD2 LEU E 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 2227 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 128 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C THR D 128 " -0.043 2.00e-02 2.50e+03 pdb=" O THR D 128 " 0.016 2.00e-02 2.50e+03 pdb=" N THR D 129 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C THR B 128 " 0.043 2.00e-02 2.50e+03 pdb=" O THR B 128 " -0.016 2.00e-02 2.50e+03 pdb=" N THR B 129 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 128 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C THR A 128 " 0.043 2.00e-02 2.50e+03 pdb=" O THR A 128 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 129 " -0.014 2.00e-02 2.50e+03 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4526 2.84 - 3.35: 12166 3.35 - 3.87: 23223 3.87 - 4.38: 27945 4.38 - 4.90: 47836 Nonbonded interactions: 115696 Sorted by model distance: nonbonded pdb=" NH2 ARG A 325 " pdb=" O TRP E 259 " model vdw 2.322 2.520 nonbonded pdb=" O LEU A 271 " pdb=" OG1 THR A 275 " model vdw 2.335 2.440 nonbonded pdb=" O LEU B 271 " pdb=" OG1 THR B 275 " model vdw 2.336 2.440 nonbonded pdb=" O LEU D 271 " pdb=" OG1 THR D 275 " model vdw 2.336 2.440 nonbonded pdb=" O LEU E 271 " pdb=" OG1 THR E 275 " model vdw 2.336 2.440 ... (remaining 115691 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.430 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 40.310 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.120 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.009 0.075 14470 Z= 0.586 Angle : 1.059 13.895 19630 Z= 0.547 Chirality : 0.062 0.396 2230 Planarity : 0.007 0.055 2430 Dihedral : 9.093 73.327 5440 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -4.50 (0.15), residues: 1705 helix: -4.31 (0.10), residues: 590 sheet: -1.78 (0.20), residues: 425 loop : -2.25 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP D 110 HIS 0.006 0.002 HIS A 231 PHE 0.025 0.003 PHE E 115 TYR 0.030 0.003 TYR A 144 ARG 0.009 0.001 ARG C 147 *********************** 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 443 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 1.820 Fit side-chains REVERT: A 49 LYS cc_start: 0.8605 (mttt) cc_final: 0.8380 (mtpt) REVERT: A 206 LYS cc_start: 0.8539 (mttt) cc_final: 0.8038 (mtmt) REVERT: A 400 LYS cc_start: 0.8348 (mttm) cc_final: 0.8000 (mmmt) REVERT: A 401 ARG cc_start: 0.7411 (tpt90) cc_final: 0.6974 (tpm-80) REVERT: A 402 ILE cc_start: 0.8635 (tt) cc_final: 0.8365 (mt) REVERT: B 400 LYS cc_start: 0.8285 (mttm) cc_final: 0.8057 (mmmt) REVERT: B 401 ARG cc_start: 0.7599 (tpt90) cc_final: 0.7093 (tpm-80) REVERT: B 402 ILE cc_start: 0.8627 (tt) cc_final: 0.8290 (mt) REVERT: C 49 LYS cc_start: 0.8622 (mttt) cc_final: 0.8422 (mtmt) REVERT: C 102 ASP cc_start: 0.8718 (t70) cc_final: 0.8431 (t70) REVERT: C 206 LYS cc_start: 0.8526 (mttt) cc_final: 0.7933 (mmmm) REVERT: C 279 MET cc_start: 0.9205 (tpt) cc_final: 0.8565 (tpt) REVERT: C 400 LYS cc_start: 0.8360 (mttm) cc_final: 0.8056 (mmmt) REVERT: C 401 ARG cc_start: 0.7510 (tpt90) cc_final: 0.7021 (tpm-80) REVERT: C 402 ILE cc_start: 0.8749 (tt) cc_final: 0.8444 (mt) REVERT: D 206 LYS cc_start: 0.8536 (mttt) cc_final: 0.7793 (mmmm) REVERT: D 400 LYS cc_start: 0.8247 (mttm) cc_final: 0.8001 (mmmt) REVERT: D 402 ILE cc_start: 0.8748 (tt) cc_final: 0.8417 (mt) REVERT: E 206 LYS cc_start: 0.8564 (mttt) cc_final: 0.8039 (mmmm) REVERT: E 400 LYS cc_start: 0.8359 (mttm) cc_final: 0.8071 (mmmt) REVERT: E 401 ARG cc_start: 0.7552 (tpt90) cc_final: 0.7129 (tpm-80) REVERT: E 402 ILE cc_start: 0.8760 (tt) cc_final: 0.8355 (mt) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 1.2817 time to fit residues: 619.9213 Evaluate side-chains 221 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 231 HIS A 321 ASN B 131 ASN B 321 ASN C 131 ASN C 180 ASN C 321 ASN D 131 ASN D 321 ASN E 131 ASN E 180 ASN E 321 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14470 Z= 0.251 Angle : 0.662 7.000 19630 Z= 0.344 Chirality : 0.047 0.193 2230 Planarity : 0.005 0.047 2430 Dihedral : 5.428 27.869 2095 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.10 % Allowed : 13.09 % Favored : 82.80 % 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: -2.68 (0.18), residues: 1705 helix: -2.10 (0.17), residues: 595 sheet: -1.11 (0.22), residues: 425 loop : -1.68 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 110 HIS 0.003 0.001 HIS C 217 PHE 0.013 0.002 PHE A 124 TYR 0.014 0.001 TYR A 144 ARG 0.005 0.001 ARG A 75 *********************** 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 304 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 1.745 Fit side-chains REVERT: A 400 LYS cc_start: 0.8269 (mttm) cc_final: 0.7945 (mmmt) REVERT: A 402 ILE cc_start: 0.8494 (tt) cc_final: 0.8270 (mt) REVERT: B 400 LYS cc_start: 0.8157 (mttm) cc_final: 0.7884 (mmmt) REVERT: B 402 ILE cc_start: 0.8487 (tt) cc_final: 0.8192 (mt) REVERT: C 193 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8269 (mp10) REVERT: C 279 MET cc_start: 0.9109 (tpt) cc_final: 0.8535 (tpt) REVERT: C 400 LYS cc_start: 0.8263 (mttm) cc_final: 0.7992 (mmmt) REVERT: C 401 ARG cc_start: 0.7548 (tpt90) cc_final: 0.6903 (tpm-80) REVERT: C 402 ILE cc_start: 0.8533 (tt) cc_final: 0.8265 (mt) REVERT: D 83 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: D 126 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: D 400 LYS cc_start: 0.8179 (mttm) cc_final: 0.7892 (mmmt) REVERT: D 401 ARG cc_start: 0.7291 (tpt-90) cc_final: 0.6651 (tpm-80) REVERT: D 402 ILE cc_start: 0.8469 (tt) cc_final: 0.8228 (mt) REVERT: E 156 MET cc_start: 0.8857 (mtp) cc_final: 0.8639 (mtp) REVERT: E 193 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: E 282 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: E 398 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7279 (mtt-85) REVERT: E 400 LYS cc_start: 0.8206 (mttm) cc_final: 0.7945 (mmmt) REVERT: E 401 ARG cc_start: 0.7675 (tpt90) cc_final: 0.7197 (tpm-80) REVERT: E 402 ILE cc_start: 0.8504 (tt) cc_final: 0.8271 (mt) outliers start: 63 outliers final: 9 residues processed: 276 average time/residue: 1.2591 time to fit residues: 380.6648 Evaluate side-chains 212 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 398 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 0.0570 chunk 153 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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: 0.8608 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14470 Z= 0.143 Angle : 0.552 6.129 19630 Z= 0.288 Chirality : 0.044 0.219 2230 Planarity : 0.004 0.045 2430 Dihedral : 4.814 22.392 2095 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.04 % Allowed : 15.50 % Favored : 80.46 % 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: -1.39 (0.19), residues: 1705 helix: -0.49 (0.21), residues: 580 sheet: -0.68 (0.23), residues: 425 loop : -1.30 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.002 0.001 HIS C 217 PHE 0.012 0.001 PHE D 417 TYR 0.012 0.001 TYR C 317 ARG 0.003 0.000 ARG B 401 *********************** 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 297 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 1.530 Fit side-chains REVERT: A 193 GLN cc_start: 0.8653 (mt0) cc_final: 0.8435 (mt0) REVERT: A 287 ARG cc_start: 0.7801 (ptp-170) cc_final: 0.7409 (mtm180) REVERT: A 400 LYS cc_start: 0.8253 (mttm) cc_final: 0.7895 (mmmt) REVERT: A 401 ARG cc_start: 0.7342 (tpt-90) cc_final: 0.6752 (tpm-80) REVERT: A 402 ILE cc_start: 0.8368 (tt) cc_final: 0.8137 (mt) REVERT: B 243 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8486 (mtm) REVERT: B 287 ARG cc_start: 0.7820 (ptp-170) cc_final: 0.7414 (mtm180) REVERT: B 400 LYS cc_start: 0.8145 (mttm) cc_final: 0.7851 (mmmt) REVERT: B 401 ARG cc_start: 0.7229 (tpt-90) cc_final: 0.6601 (tpm-80) REVERT: B 402 ILE cc_start: 0.8356 (tt) cc_final: 0.8119 (mt) REVERT: B 403 ASP cc_start: 0.8336 (t0) cc_final: 0.8103 (t0) REVERT: C 279 MET cc_start: 0.9028 (tpt) cc_final: 0.8603 (tpt) REVERT: C 400 LYS cc_start: 0.8307 (mttm) cc_final: 0.8007 (mmmt) REVERT: C 401 ARG cc_start: 0.7687 (tpt90) cc_final: 0.6970 (tpm-80) REVERT: C 402 ILE cc_start: 0.8467 (tt) cc_final: 0.8214 (mt) REVERT: D 109 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8161 (tt) REVERT: D 130 ASP cc_start: 0.7396 (m-30) cc_final: 0.7119 (t0) REVERT: D 287 ARG cc_start: 0.7804 (ptp-170) cc_final: 0.7435 (mtm180) REVERT: D 400 LYS cc_start: 0.8134 (mttm) cc_final: 0.7893 (mmmt) REVERT: D 401 ARG cc_start: 0.7307 (tpt-90) cc_final: 0.6660 (tpm-80) REVERT: D 402 ILE cc_start: 0.8449 (tt) cc_final: 0.8184 (mt) REVERT: E 156 MET cc_start: 0.8883 (mtp) cc_final: 0.8677 (mtp) REVERT: E 398 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7362 (mtt-85) REVERT: E 400 LYS cc_start: 0.8251 (mttm) cc_final: 0.7963 (mmmt) REVERT: E 401 ARG cc_start: 0.7605 (tpt90) cc_final: 0.7009 (tpm-80) REVERT: E 402 ILE cc_start: 0.8429 (tt) cc_final: 0.8169 (mt) outliers start: 62 outliers final: 22 residues processed: 272 average time/residue: 1.2086 time to fit residues: 361.0791 Evaluate side-chains 215 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 190 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 398 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.0050 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 0.0470 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 202 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14470 Z= 0.155 Angle : 0.546 6.850 19630 Z= 0.282 Chirality : 0.044 0.281 2230 Planarity : 0.004 0.038 2430 Dihedral : 4.540 20.363 2095 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.45 % Allowed : 16.68 % Favored : 79.87 % 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: -0.80 (0.20), residues: 1705 helix: 0.18 (0.22), residues: 580 sheet: -0.35 (0.24), residues: 425 loop : -1.15 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 84 HIS 0.002 0.001 HIS C 125 PHE 0.012 0.001 PHE E 417 TYR 0.011 0.001 TYR C 317 ARG 0.006 0.000 ARG E 75 *********************** 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 251 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 198 time to evaluate : 1.693 Fit side-chains REVERT: A 287 ARG cc_start: 0.7820 (ptp-170) cc_final: 0.7421 (mtm180) REVERT: A 400 LYS cc_start: 0.8297 (mttm) cc_final: 0.7934 (mmmt) REVERT: A 401 ARG cc_start: 0.7373 (tpt-90) cc_final: 0.6627 (tpm-80) REVERT: A 402 ILE cc_start: 0.8406 (tt) cc_final: 0.8079 (mt) REVERT: B 287 ARG cc_start: 0.7762 (ptp-170) cc_final: 0.7388 (mtm180) REVERT: B 400 LYS cc_start: 0.8168 (mttm) cc_final: 0.7862 (mmmt) REVERT: B 401 ARG cc_start: 0.7248 (tpt-90) cc_final: 0.6580 (tpm-80) REVERT: B 402 ILE cc_start: 0.8323 (tt) cc_final: 0.8026 (mt) REVERT: B 403 ASP cc_start: 0.8307 (t0) cc_final: 0.8073 (t0) REVERT: C 279 MET cc_start: 0.9022 (tpt) cc_final: 0.8707 (tpt) REVERT: C 400 LYS cc_start: 0.8277 (mttm) cc_final: 0.7979 (mmmt) REVERT: C 401 ARG cc_start: 0.7695 (tpt90) cc_final: 0.7065 (tpm-80) REVERT: C 402 ILE cc_start: 0.8503 (tt) cc_final: 0.8220 (mt) REVERT: D 83 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8519 (mt0) REVERT: D 109 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8124 (tt) REVERT: D 287 ARG cc_start: 0.7833 (ptp-170) cc_final: 0.7431 (mtm180) REVERT: D 400 LYS cc_start: 0.8154 (mttm) cc_final: 0.7886 (mmmt) REVERT: D 401 ARG cc_start: 0.7279 (tpt-90) cc_final: 0.6668 (tpm-80) REVERT: D 402 ILE cc_start: 0.8431 (tt) cc_final: 0.8086 (mt) REVERT: E 72 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8574 (mmm) REVERT: E 227 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: E 282 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: E 400 LYS cc_start: 0.8223 (mttm) cc_final: 0.7928 (mmmt) REVERT: E 401 ARG cc_start: 0.7588 (tpt90) cc_final: 0.6934 (tpm-80) REVERT: E 402 ILE cc_start: 0.8419 (tt) cc_final: 0.8139 (mt) outliers start: 53 outliers final: 30 residues processed: 233 average time/residue: 1.3442 time to fit residues: 341.9778 Evaluate side-chains 218 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 82 GLN D 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14470 Z= 0.200 Angle : 0.555 8.358 19630 Z= 0.286 Chirality : 0.045 0.236 2230 Planarity : 0.004 0.038 2430 Dihedral : 4.513 22.000 2095 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.91 % Allowed : 17.52 % Favored : 78.57 % 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: -0.30 (0.20), residues: 1705 helix: 0.63 (0.22), residues: 575 sheet: 0.24 (0.25), residues: 395 loop : -1.07 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 84 HIS 0.002 0.001 HIS A 125 PHE 0.011 0.001 PHE D 417 TYR 0.011 0.001 TYR C 317 ARG 0.004 0.000 ARG C 212 *********************** 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 241 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 181 time to evaluate : 1.706 Fit side-chains REVERT: A 287 ARG cc_start: 0.7852 (ptp-170) cc_final: 0.7432 (mtm180) REVERT: A 400 LYS cc_start: 0.8210 (mttm) cc_final: 0.7850 (mmmt) REVERT: A 402 ILE cc_start: 0.8454 (tt) cc_final: 0.8055 (mt) REVERT: B 243 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8527 (mtm) REVERT: B 287 ARG cc_start: 0.7818 (ptp-170) cc_final: 0.7302 (mtm180) REVERT: B 400 LYS cc_start: 0.8152 (mttm) cc_final: 0.7861 (mmmt) REVERT: B 401 ARG cc_start: 0.7287 (tpt-90) cc_final: 0.6653 (tpm-80) REVERT: B 402 ILE cc_start: 0.8335 (tt) cc_final: 0.8048 (mt) REVERT: B 403 ASP cc_start: 0.8291 (t0) cc_final: 0.8049 (t0) REVERT: C 72 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: C 276 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9030 (m) REVERT: C 279 MET cc_start: 0.9066 (tpt) cc_final: 0.8736 (tpt) REVERT: C 400 LYS cc_start: 0.8294 (mttm) cc_final: 0.7977 (mmmt) REVERT: C 401 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7006 (tpm-80) REVERT: C 402 ILE cc_start: 0.8493 (tt) cc_final: 0.8179 (mt) REVERT: D 83 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: D 109 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8170 (tt) REVERT: D 287 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7464 (mtm180) REVERT: D 400 LYS cc_start: 0.8172 (mttm) cc_final: 0.7900 (mmmt) REVERT: D 401 ARG cc_start: 0.7290 (tpt-90) cc_final: 0.6680 (tpm-80) REVERT: D 402 ILE cc_start: 0.8499 (tt) cc_final: 0.8088 (mt) REVERT: E 72 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8622 (mmm) REVERT: E 83 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: E 126 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: E 282 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: E 400 LYS cc_start: 0.8219 (mttm) cc_final: 0.7913 (mmmt) REVERT: E 401 ARG cc_start: 0.7606 (tpt90) cc_final: 0.6861 (tpm-80) REVERT: E 402 ILE cc_start: 0.8406 (tt) cc_final: 0.8090 (mt) outliers start: 60 outliers final: 37 residues processed: 219 average time/residue: 1.3384 time to fit residues: 320.0672 Evaluate side-chains 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 56 THR 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 276 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 0.0070 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 82 GLN D 82 GLN E 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14470 Z= 0.148 Angle : 0.517 6.065 19630 Z= 0.267 Chirality : 0.044 0.266 2230 Planarity : 0.003 0.032 2430 Dihedral : 4.337 21.021 2095 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.80 % Allowed : 18.50 % Favored : 78.70 % 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: -0.05 (0.20), residues: 1705 helix: 0.95 (0.22), residues: 575 sheet: 0.36 (0.26), residues: 395 loop : -1.01 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 84 HIS 0.002 0.001 HIS D 327 PHE 0.011 0.001 PHE D 417 TYR 0.011 0.001 TYR E 317 ARG 0.004 0.000 ARG A 401 *********************** 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 224 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 1.699 Fit side-chains REVERT: A 287 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7435 (mtm180) REVERT: A 391 MET cc_start: 0.4993 (tpp) cc_final: 0.4672 (tpt) REVERT: A 400 LYS cc_start: 0.8251 (mttm) cc_final: 0.7896 (mmmt) REVERT: A 402 ILE cc_start: 0.8413 (tt) cc_final: 0.7994 (mt) REVERT: A 403 ASP cc_start: 0.8265 (t0) cc_final: 0.7933 (t0) REVERT: B 243 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8328 (mtm) REVERT: B 287 ARG cc_start: 0.7780 (ptp-170) cc_final: 0.7273 (mtm180) REVERT: B 400 LYS cc_start: 0.8171 (mttm) cc_final: 0.7854 (mmmt) REVERT: B 401 ARG cc_start: 0.7278 (tpt-90) cc_final: 0.6636 (tpm-80) REVERT: B 402 ILE cc_start: 0.8292 (tt) cc_final: 0.7986 (mt) REVERT: B 403 ASP cc_start: 0.8268 (t0) cc_final: 0.8030 (t0) REVERT: C 72 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: C 279 MET cc_start: 0.9034 (tpt) cc_final: 0.8785 (tpt) REVERT: C 400 LYS cc_start: 0.8241 (mttm) cc_final: 0.7964 (mmmt) REVERT: C 401 ARG cc_start: 0.7646 (tpt90) cc_final: 0.6947 (tpm-80) REVERT: C 402 ILE cc_start: 0.8500 (tt) cc_final: 0.8143 (mt) REVERT: D 83 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: D 109 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8179 (tt) REVERT: D 287 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7466 (mtm180) REVERT: D 400 LYS cc_start: 0.8188 (mttm) cc_final: 0.7901 (mmmt) REVERT: D 401 ARG cc_start: 0.7357 (tpt-90) cc_final: 0.6618 (tpm-80) REVERT: D 402 ILE cc_start: 0.8480 (tt) cc_final: 0.8021 (mt) REVERT: E 72 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8636 (mmm) REVERT: E 83 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8621 (mt0) REVERT: E 126 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: E 243 MET cc_start: 0.8899 (mtm) cc_final: 0.8668 (mtt) REVERT: E 400 LYS cc_start: 0.8226 (mttm) cc_final: 0.7906 (mmmt) REVERT: E 401 ARG cc_start: 0.7543 (tpt90) cc_final: 0.6889 (tpm-80) REVERT: E 402 ILE cc_start: 0.8389 (tt) cc_final: 0.8021 (mt) outliers start: 43 outliers final: 26 residues processed: 211 average time/residue: 1.3934 time to fit residues: 320.2686 Evaluate side-chains 199 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 412 LEU 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 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 0.0670 chunk 101 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN D 82 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14470 Z= 0.145 Angle : 0.516 6.702 19630 Z= 0.265 Chirality : 0.044 0.318 2230 Planarity : 0.003 0.032 2430 Dihedral : 4.212 20.978 2095 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.32 % Allowed : 18.31 % Favored : 78.37 % 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: 0.20 (0.21), residues: 1705 helix: 1.24 (0.22), residues: 575 sheet: 0.50 (0.26), residues: 395 loop : -0.96 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 422 HIS 0.002 0.001 HIS B 327 PHE 0.011 0.001 PHE D 417 TYR 0.011 0.001 TYR B 317 ARG 0.004 0.000 ARG A 401 *********************** 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 223 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 1.636 Fit side-chains REVERT: A 179 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8589 (tpt) REVERT: A 206 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8452 (mmmm) REVERT: A 287 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7430 (mtm180) REVERT: A 400 LYS cc_start: 0.8251 (mttm) cc_final: 0.7892 (mmmt) REVERT: A 402 ILE cc_start: 0.8384 (tt) cc_final: 0.7935 (mt) REVERT: A 403 ASP cc_start: 0.8230 (t0) cc_final: 0.7921 (t0) REVERT: B 243 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: B 287 ARG cc_start: 0.7797 (ptp-170) cc_final: 0.7236 (mtm180) REVERT: B 400 LYS cc_start: 0.8185 (mttm) cc_final: 0.7852 (mmmt) REVERT: B 401 ARG cc_start: 0.7228 (tpt-90) cc_final: 0.6613 (tpm-80) REVERT: B 402 ILE cc_start: 0.8273 (tt) cc_final: 0.7959 (mt) REVERT: B 403 ASP cc_start: 0.8243 (t0) cc_final: 0.8020 (t0) REVERT: C 72 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8004 (mtp) REVERT: C 276 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.9033 (m) REVERT: C 400 LYS cc_start: 0.8238 (mttm) cc_final: 0.7939 (mmmt) REVERT: C 402 ILE cc_start: 0.8484 (tt) cc_final: 0.8101 (mt) REVERT: D 83 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8566 (mt0) REVERT: D 109 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8178 (tt) REVERT: D 126 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7392 (tp30) REVERT: D 287 ARG cc_start: 0.7834 (ptp-170) cc_final: 0.7426 (mtm180) REVERT: D 400 LYS cc_start: 0.8195 (mttm) cc_final: 0.7904 (mmmt) REVERT: D 401 ARG cc_start: 0.7361 (tpt-90) cc_final: 0.6629 (tpm-80) REVERT: D 402 ILE cc_start: 0.8482 (tt) cc_final: 0.7994 (mt) REVERT: E 72 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8648 (mmm) REVERT: E 83 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: E 243 MET cc_start: 0.8896 (mtm) cc_final: 0.8668 (mtt) REVERT: E 400 LYS cc_start: 0.8148 (mttm) cc_final: 0.7908 (mmmt) REVERT: E 401 ARG cc_start: 0.7532 (tpt90) cc_final: 0.6785 (tpm-80) REVERT: E 402 ILE cc_start: 0.8369 (tt) cc_final: 0.7966 (mt) outliers start: 51 outliers final: 31 residues processed: 209 average time/residue: 1.3724 time to fit residues: 312.8791 Evaluate side-chains 210 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 56 THR 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 179 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN D 82 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14470 Z= 0.178 Angle : 0.546 10.921 19630 Z= 0.278 Chirality : 0.045 0.305 2230 Planarity : 0.003 0.031 2430 Dihedral : 4.257 21.362 2095 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.06 % Allowed : 18.76 % Favored : 78.18 % 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: 0.34 (0.21), residues: 1705 helix: 1.36 (0.22), residues: 580 sheet: 0.58 (0.26), residues: 395 loop : -0.89 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 84 HIS 0.002 0.001 HIS B 327 PHE 0.010 0.001 PHE D 115 TYR 0.012 0.001 TYR B 317 ARG 0.004 0.000 ARG C 401 *********************** 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 220 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 173 time to evaluate : 1.680 Fit side-chains REVERT: A 179 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (tpt) REVERT: A 206 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8449 (mmmm) REVERT: A 287 ARG cc_start: 0.7836 (ptp-170) cc_final: 0.7384 (mtm180) REVERT: A 400 LYS cc_start: 0.8258 (mttm) cc_final: 0.7890 (mmmt) REVERT: A 402 ILE cc_start: 0.8388 (tt) cc_final: 0.7912 (mt) REVERT: A 403 ASP cc_start: 0.8252 (t0) cc_final: 0.7932 (t0) REVERT: B 243 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8369 (mtm) REVERT: B 287 ARG cc_start: 0.7730 (ptp-170) cc_final: 0.7224 (mtm180) REVERT: B 400 LYS cc_start: 0.8176 (mttm) cc_final: 0.7842 (mmmt) REVERT: B 401 ARG cc_start: 0.7228 (tpt-90) cc_final: 0.6661 (tpm170) REVERT: B 402 ILE cc_start: 0.8277 (tt) cc_final: 0.7947 (mt) REVERT: B 403 ASP cc_start: 0.8252 (t0) cc_final: 0.8023 (t0) REVERT: C 72 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: C 276 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.9037 (m) REVERT: C 400 LYS cc_start: 0.8231 (mttm) cc_final: 0.7949 (mmmt) REVERT: C 402 ILE cc_start: 0.8487 (tt) cc_final: 0.8091 (mt) REVERT: D 83 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: D 109 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8243 (tt) REVERT: D 243 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8507 (mtt) REVERT: D 287 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.7343 (mtm180) REVERT: D 400 LYS cc_start: 0.8207 (mttm) cc_final: 0.7909 (mmmt) REVERT: D 401 ARG cc_start: 0.7361 (tpt-90) cc_final: 0.6625 (tpm-80) REVERT: D 402 ILE cc_start: 0.8511 (tt) cc_final: 0.8000 (mt) REVERT: E 72 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8687 (mmm) REVERT: E 83 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8639 (mt0) REVERT: E 126 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: E 243 MET cc_start: 0.8885 (mtm) cc_final: 0.8650 (mtt) REVERT: E 400 LYS cc_start: 0.8135 (mttm) cc_final: 0.7909 (mmmt) REVERT: E 401 ARG cc_start: 0.7461 (tpt90) cc_final: 0.6732 (tpm-80) REVERT: E 402 ILE cc_start: 0.8343 (tt) cc_final: 0.7920 (mt) outliers start: 47 outliers final: 32 residues processed: 209 average time/residue: 1.3826 time to fit residues: 314.7181 Evaluate side-chains 212 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 56 THR 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 179 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 83 GLN Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 152 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 119 optimal weight: 0.0170 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 131 ASN C 131 ASN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14470 Z= 0.143 Angle : 0.510 6.274 19630 Z= 0.262 Chirality : 0.044 0.288 2230 Planarity : 0.003 0.030 2430 Dihedral : 4.157 21.079 2095 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.87 % Allowed : 18.89 % Favored : 78.24 % 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: 0.50 (0.21), residues: 1705 helix: 1.54 (0.22), residues: 580 sheet: 0.65 (0.27), residues: 395 loop : -0.82 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 84 HIS 0.002 0.001 HIS B 327 PHE 0.010 0.001 PHE D 417 TYR 0.011 0.001 TYR C 317 ARG 0.004 0.000 ARG C 401 *********************** 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 218 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 1.753 Fit side-chains REVERT: A 179 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8724 (tpt) REVERT: A 206 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8452 (mmmm) REVERT: A 287 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7402 (mtm180) REVERT: A 400 LYS cc_start: 0.8229 (mttm) cc_final: 0.7855 (mmmt) REVERT: A 402 ILE cc_start: 0.8355 (tt) cc_final: 0.7866 (mt) REVERT: A 403 ASP cc_start: 0.8268 (t0) cc_final: 0.7946 (t0) REVERT: B 243 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8374 (mtm) REVERT: B 287 ARG cc_start: 0.7770 (ptp-170) cc_final: 0.7290 (mtm180) REVERT: B 400 LYS cc_start: 0.8170 (mttm) cc_final: 0.7843 (mmmt) REVERT: B 401 ARG cc_start: 0.7316 (tpt-90) cc_final: 0.6698 (tpm170) REVERT: B 402 ILE cc_start: 0.8232 (tt) cc_final: 0.7882 (mt) REVERT: B 403 ASP cc_start: 0.8224 (t0) cc_final: 0.8011 (t0) REVERT: C 72 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.7869 (mtp) REVERT: C 400 LYS cc_start: 0.8268 (mttm) cc_final: 0.7983 (mmmt) REVERT: C 402 ILE cc_start: 0.8468 (tt) cc_final: 0.8063 (mt) REVERT: D 83 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: D 109 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8206 (tt) REVERT: D 243 MET cc_start: 0.8850 (mmm) cc_final: 0.8484 (mtt) REVERT: D 287 ARG cc_start: 0.7817 (ptp-170) cc_final: 0.7381 (mtm180) REVERT: D 400 LYS cc_start: 0.8224 (mttm) cc_final: 0.7929 (mmmt) REVERT: D 401 ARG cc_start: 0.7358 (tpt-90) cc_final: 0.6618 (tpm-80) REVERT: D 402 ILE cc_start: 0.8440 (tt) cc_final: 0.7897 (mt) REVERT: E 126 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: E 243 MET cc_start: 0.8873 (mtm) cc_final: 0.8638 (mtt) REVERT: E 400 LYS cc_start: 0.8156 (mttm) cc_final: 0.7939 (mmmt) REVERT: E 401 ARG cc_start: 0.7474 (tpt90) cc_final: 0.6722 (tpm-80) REVERT: E 402 ILE cc_start: 0.8346 (tt) cc_final: 0.7897 (mt) outliers start: 44 outliers final: 26 residues processed: 209 average time/residue: 1.3927 time to fit residues: 316.8392 Evaluate side-chains 206 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU 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 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0010 chunk 76 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN C 82 GLN D 82 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14470 Z= 0.266 Angle : 0.596 11.489 19630 Z= 0.304 Chirality : 0.046 0.285 2230 Planarity : 0.004 0.032 2430 Dihedral : 4.464 24.398 2095 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.67 % Allowed : 19.15 % Favored : 78.18 % 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: 0.52 (0.21), residues: 1705 helix: 1.49 (0.22), residues: 580 sheet: 0.73 (0.27), residues: 395 loop : -0.80 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 302 HIS 0.002 0.001 HIS C 125 PHE 0.014 0.002 PHE C 115 TYR 0.012 0.001 TYR B 317 ARG 0.005 0.001 ARG D 147 ********************** 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 210 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 169 time to evaluate : 1.672 Fit side-chains REVERT: A 179 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8731 (tpt) REVERT: A 206 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8446 (mmmm) REVERT: A 287 ARG cc_start: 0.7895 (ptp-170) cc_final: 0.7393 (mtm180) REVERT: A 400 LYS cc_start: 0.8257 (mttm) cc_final: 0.7881 (mmmt) REVERT: A 402 ILE cc_start: 0.8439 (tt) cc_final: 0.7947 (mt) REVERT: A 403 ASP cc_start: 0.8313 (t0) cc_final: 0.7956 (t0) REVERT: B 243 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8400 (mtm) REVERT: B 287 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.7356 (mtm180) REVERT: B 400 LYS cc_start: 0.8189 (mttm) cc_final: 0.7854 (mmmt) REVERT: B 402 ILE cc_start: 0.8332 (tt) cc_final: 0.7982 (mt) REVERT: B 403 ASP cc_start: 0.8318 (t0) cc_final: 0.8038 (t0) REVERT: C 72 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.7866 (mtp) REVERT: C 276 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9073 (m) REVERT: C 400 LYS cc_start: 0.8266 (mttm) cc_final: 0.7976 (mmmt) REVERT: C 402 ILE cc_start: 0.8549 (tt) cc_final: 0.8117 (mt) REVERT: D 83 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8498 (mt0) REVERT: D 109 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8394 (tt) REVERT: D 243 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8514 (mtt) REVERT: D 287 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.7350 (mtm180) REVERT: D 400 LYS cc_start: 0.8193 (mttm) cc_final: 0.7914 (mmmt) REVERT: D 401 ARG cc_start: 0.7357 (tpt-90) cc_final: 0.6647 (tpm-80) REVERT: D 402 ILE cc_start: 0.8506 (tt) cc_final: 0.7989 (mt) REVERT: E 126 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: E 400 LYS cc_start: 0.8170 (mttm) cc_final: 0.7936 (mmmt) REVERT: E 401 ARG cc_start: 0.7545 (tpt90) cc_final: 0.6761 (tpm-80) REVERT: E 402 ILE cc_start: 0.8373 (tt) cc_final: 0.7928 (mt) outliers start: 41 outliers final: 30 residues processed: 201 average time/residue: 1.4176 time to fit residues: 309.9211 Evaluate side-chains 204 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 412 LEU 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 261 ASN Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 261 ASN Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 261 ASN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 418 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0570 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN D 82 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.089250 restraints weight = 18263.940| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.93 r_work: 0.2799 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14470 Z= 0.158 Angle : 0.541 8.655 19630 Z= 0.279 Chirality : 0.044 0.288 2230 Planarity : 0.003 0.031 2430 Dihedral : 4.323 22.089 2095 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.15 % Allowed : 19.74 % Favored : 78.11 % 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: 0.61 (0.21), residues: 1705 helix: 1.60 (0.22), residues: 580 sheet: 0.74 (0.27), residues: 395 loop : -0.74 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 84 HIS 0.002 0.001 HIS B 327 PHE 0.010 0.001 PHE E 417 TYR 0.012 0.001 TYR C 317 ARG 0.004 0.000 ARG B 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5860.89 seconds wall clock time: 104 minutes 26.35 seconds (6266.35 seconds total)