Starting phenix.real_space_refine on Sun May 3 11:17:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v3f_64754/05_2026/9v3f_64754.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v3f_64754/05_2026/9v3f_64754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v3f_64754/05_2026/9v3f_64754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v3f_64754/05_2026/9v3f_64754.map" model { file = "/net/cci-nas-00/data/ceres_data/9v3f_64754/05_2026/9v3f_64754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v3f_64754/05_2026/9v3f_64754.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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 81 5.16 5 C 7996 2.51 5 N 2040 2.21 5 O 2418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12535 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3232 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 15, 'TRANS': 405} Chain: "E" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 904 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 101} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3232 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 15, 'TRANS': 405} Chain: "F" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 907 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3228 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 405} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 906 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.56, per 1000 atoms: 0.28 Number of scatterers: 12535 At special positions: 0 Unit cell: (94.05, 138.7, 129.2, 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 81 16.00 O 2418 8.00 N 2040 7.00 C 7996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.02 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 105 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 85 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.02 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 25 " - pdb=" SG CYS G 85 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 602 " - " ASN A 99 " " NAG A 603 " - " ASN A 414 " " NAG B 602 " - " ASN B 99 " " NAG B 603 " - " ASN B 414 " " NAG C 602 " - " ASN C 99 " " NAG C 603 " - " ASN C 414 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 635.9 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3018 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 21 sheets defined 33.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 74 through 100 Proline residue: A 89 - end of helix removed outlier: 3.840A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 146 removed outlier: 4.179A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.280A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 4.018A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.667A pdb=" N LEU A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.598A pdb=" N TYR E 37 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 74 through 100 Proline residue: B 89 - end of helix removed outlier: 3.840A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 4.179A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.280A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.018A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.668A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 33 through 37 removed outlier: 3.948A pdb=" N TYR F 37 " --> pdb=" O PRO F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 79 removed outlier: 3.828A pdb=" N ASN F 79 " --> pdb=" O GLN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 98 removed outlier: 4.206A pdb=" N TYR F 97 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 74 through 100 Proline residue: C 89 - end of helix removed outlier: 3.841A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 146 removed outlier: 4.179A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 184 through 187 Processing helix chain 'C' and resid 191 through 215 removed outlier: 4.281A pdb=" N PHE C 212 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.018A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.667A pdb=" N LEU C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 358 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'G' and resid 10 through 16 removed outlier: 4.267A pdb=" N MET G 16 " --> pdb=" O LYS G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 35 No H-bonds generated for 'chain 'G' and resid 33 through 35' Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.721A pdb=" N ASP G 99 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 10.154A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 270 removed outlier: 6.415A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.658A pdb=" N VAL A 113 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER C 428 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET A 115 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.731A pdb=" N VAL E 87 " --> pdb=" O ILE E 103 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 103 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 162 removed outlier: 10.154A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 338 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 45 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS B 340 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 47 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 263 through 270 removed outlier: 6.415A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 276 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 58 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 278 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP B 56 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 280 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 54 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N PHE B 282 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU B 295 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR B 43 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 293 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB4, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB5, first strand: chain 'B' and resid 393 through 394 Processing sheet with id=AB6, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.992A pdb=" N ILE F 103 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 162 removed outlier: 10.155A pdb=" N THR C 168 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP C 56 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 170 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 263 through 270 removed outlier: 6.415A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 276 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL C 58 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL C 278 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP C 56 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 280 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR C 54 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE C 282 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU C 295 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR C 43 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE C 293 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 42 removed outlier: 3.700A pdb=" N CYS G 105 " --> pdb=" O CYS G 85 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE G 103 " --> pdb=" O VAL G 87 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3968 1.34 - 1.46: 2805 1.46 - 1.58: 5881 1.58 - 1.70: 0 1.70 - 1.83: 114 Bond restraints: 12768 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.42e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.34e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.29e+00 bond pdb=" C TRP E 101 " pdb=" O TRP E 101 " ideal model delta sigma weight residual 1.244 1.221 0.022 1.00e-02 1.00e+04 4.85e+00 bond pdb=" CA LYS G 84 " pdb=" C LYS G 84 " ideal model delta sigma weight residual 1.524 1.496 0.027 1.31e-02 5.83e+03 4.27e+00 ... (remaining 12763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 16611 1.60 - 3.19: 622 3.19 - 4.79: 115 4.79 - 6.39: 20 6.39 - 7.99: 7 Bond angle restraints: 17375 Sorted by residual: angle pdb=" N ASP F 99 " pdb=" CA ASP F 99 " pdb=" C ASP F 99 " ideal model delta sigma weight residual 112.97 108.85 4.12 1.06e+00 8.90e-01 1.51e+01 angle pdb=" N ASN C 155 " pdb=" CA ASN C 155 " pdb=" C ASN C 155 " ideal model delta sigma weight residual 112.57 108.22 4.35 1.13e+00 7.83e-01 1.48e+01 angle pdb=" N MET E 98 " pdb=" CA MET E 98 " pdb=" C MET E 98 " ideal model delta sigma weight residual 111.71 107.52 4.19 1.15e+00 7.56e-01 1.33e+01 angle pdb=" N ILE F 103 " pdb=" CA ILE F 103 " pdb=" C ILE F 103 " ideal model delta sigma weight residual 106.61 112.80 -6.19 1.78e+00 3.16e-01 1.21e+01 angle pdb=" C TRP G 101 " pdb=" CA TRP G 101 " pdb=" CB TRP G 101 " ideal model delta sigma weight residual 113.04 107.50 5.54 1.63e+00 3.76e-01 1.16e+01 ... (remaining 17370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 7106 16.59 - 33.19: 613 33.19 - 49.78: 148 49.78 - 66.37: 29 66.37 - 82.96: 18 Dihedral angle restraints: 7914 sinusoidal: 3223 harmonic: 4691 Sorted by residual: dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual -86.00 -138.75 52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -138.75 52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -138.74 52.74 1 1.00e+01 1.00e-02 3.79e+01 ... (remaining 7911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1643 0.061 - 0.122: 406 0.122 - 0.183: 46 0.183 - 0.243: 3 0.243 - 0.304: 1 Chirality restraints: 2099 Sorted by residual: chirality pdb=" CB ILE G 54 " pdb=" CA ILE G 54 " pdb=" CG1 ILE G 54 " pdb=" CG2 ILE G 54 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB VAL C 369 " pdb=" CA VAL C 369 " pdb=" CG1 VAL C 369 " pdb=" CG2 VAL C 369 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 369 " pdb=" CA VAL B 369 " pdb=" CG1 VAL B 369 " pdb=" CG2 VAL B 369 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2096 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 101 " -0.036 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP G 101 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP G 101 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 101 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP G 101 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 101 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 101 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 101 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 101 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 101 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 446 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO C 447 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 447 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 447 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 446 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 447 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " 0.020 5.00e-02 4.00e+02 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 175 2.60 - 3.18: 11082 3.18 - 3.75: 19288 3.75 - 4.33: 29021 4.33 - 4.90: 46580 Nonbonded interactions: 106146 Sorted by model distance: nonbonded pdb=" O ASN B 67 " pdb=" OD1 ASN B 67 " model vdw 2.029 3.040 nonbonded pdb=" O ASN A 67 " pdb=" OD1 ASN A 67 " model vdw 2.031 3.040 nonbonded pdb=" O ASN C 67 " pdb=" OD1 ASN C 67 " model vdw 2.032 3.040 nonbonded pdb=" OH TYR F 57 " pdb=" NZ LYS F 69 " model vdw 2.201 3.120 nonbonded pdb=" OH TYR G 37 " pdb=" OD2 ASP G 93 " model vdw 2.211 3.040 ... (remaining 106141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 257 or (resid 258 and (name N or name CA or nam \ e C or name O or name CB )) or resid 259 through 603)) selection = (chain 'B' and (resid 27 through 257 or (resid 258 and (name N or name CA or nam \ e C or name O or name CB )) or resid 259 through 603)) selection = chain 'C' } ncs_group { reference = (chain 'E' and (resid 1 through 61 or (resid 62 and (name N or name CA or name C \ or name O or name CB )) or resid 63 through 111)) selection = (chain 'F' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 61 or (resid 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 through 111)) selection = (chain 'G' and (resid 1 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 34 or (resid 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 111)) } 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: 6.440 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.550 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12795 Z= 0.244 Angle : 0.748 7.987 17435 Z= 0.414 Chirality : 0.051 0.304 2099 Planarity : 0.004 0.039 2174 Dihedral : 13.581 82.963 4833 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.21), residues: 1584 helix: 0.06 (0.25), residues: 393 sheet: -0.74 (0.24), residues: 387 loop : -1.38 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 353 TYR 0.013 0.002 TYR G 42 PHE 0.011 0.002 PHE B 376 TRP 0.064 0.003 TRP G 101 HIS 0.002 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00546 (12768) covalent geometry : angle 0.74240 (17375) SS BOND : bond 0.00590 ( 21) SS BOND : angle 1.36204 ( 42) hydrogen bonds : bond 0.15040 ( 502) hydrogen bonds : angle 7.38710 ( 1305) link_NAG-ASN : bond 0.00581 ( 6) link_NAG-ASN : angle 2.31479 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.6698 (mmm) cc_final: 0.6103 (mmm) REVERT: A 352 MET cc_start: 0.7941 (tpp) cc_final: 0.7579 (tpt) REVERT: E 96 TYR cc_start: 0.7904 (t80) cc_final: 0.7662 (t80) REVERT: B 197 LEU cc_start: 0.8040 (mp) cc_final: 0.7710 (tt) REVERT: C 102 HIS cc_start: 0.7260 (p-80) cc_final: 0.6999 (p90) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.5234 time to fit residues: 136.1015 Evaluate side-chains 139 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 305 ASN A 351 ASN A 395 GLN E 74 HIS B 67 ASN B 143 ASN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 162 GLN C 302 ASN C 342 GLN G 79 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.169560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146680 restraints weight = 14802.260| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.00 r_work: 0.3770 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 12795 Z= 0.235 Angle : 0.673 7.230 17435 Z= 0.349 Chirality : 0.052 0.183 2099 Planarity : 0.005 0.042 2174 Dihedral : 5.994 37.602 1905 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.40 % Allowed : 11.15 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.20), residues: 1584 helix: 0.09 (0.25), residues: 420 sheet: -0.63 (0.24), residues: 381 loop : -1.33 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 399 TYR 0.016 0.002 TYR B 438 PHE 0.014 0.002 PHE B 376 TRP 0.040 0.003 TRP G 101 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00558 (12768) covalent geometry : angle 0.66781 (17375) SS BOND : bond 0.00409 ( 21) SS BOND : angle 1.21885 ( 42) hydrogen bonds : bond 0.04372 ( 502) hydrogen bonds : angle 5.85863 ( 1305) link_NAG-ASN : bond 0.00479 ( 6) link_NAG-ASN : angle 2.07504 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 258 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: E 90 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.8026 (mtt90) REVERT: E 96 TYR cc_start: 0.8413 (t80) cc_final: 0.7990 (t80) REVERT: B 335 LYS cc_start: 0.8038 (tppt) cc_final: 0.7591 (tppt) REVERT: B 425 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8308 (p) REVERT: F 73 LEU cc_start: 0.6412 (mp) cc_final: 0.6072 (tm) REVERT: F 98 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.5165 (mpm) REVERT: C 102 HIS cc_start: 0.7658 (p-80) cc_final: 0.7381 (p90) REVERT: C 142 ASP cc_start: 0.7212 (m-30) cc_final: 0.6906 (m-30) REVERT: C 224 ASN cc_start: 0.7805 (p0) cc_final: 0.7474 (p0) REVERT: C 252 ASP cc_start: 0.7237 (p0) cc_final: 0.6916 (p0) REVERT: C 336 ARG cc_start: 0.8414 (pmm-80) cc_final: 0.8170 (ptp-110) REVERT: G 13 ASP cc_start: 0.6423 (t0) cc_final: 0.6221 (t0) REVERT: G 86 LYS cc_start: 0.8883 (ttpp) cc_final: 0.8444 (ttmm) outliers start: 34 outliers final: 11 residues processed: 189 average time/residue: 0.5478 time to fit residues: 113.4783 Evaluate side-chains 151 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 128 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 67 ASN A 182 ASN A 302 ASN A 395 GLN B 67 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN C 155 ASN G 79 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.167801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144664 restraints weight = 15033.685| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.03 r_work: 0.3750 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.005 0.047 12795 Z= 0.228 Angle : 0.643 7.275 17435 Z= 0.334 Chirality : 0.050 0.183 2099 Planarity : 0.005 0.042 2174 Dihedral : 5.806 34.414 1905 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.68 % Allowed : 14.40 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1584 helix: 0.38 (0.25), residues: 402 sheet: -0.68 (0.25), residues: 366 loop : -1.41 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 399 TYR 0.014 0.002 TYR F 97 PHE 0.015 0.002 PHE B 376 TRP 0.036 0.003 TRP G 101 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00541 (12768) covalent geometry : angle 0.63627 (17375) SS BOND : bond 0.00413 ( 21) SS BOND : angle 1.46182 ( 42) hydrogen bonds : bond 0.04255 ( 502) hydrogen bonds : angle 5.74733 ( 1305) link_NAG-ASN : bond 0.00488 ( 6) link_NAG-ASN : angle 2.14016 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 219 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: E 90 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.8055 (mtt90) REVERT: E 96 TYR cc_start: 0.8440 (t80) cc_final: 0.7972 (t80) REVERT: B 103 ASP cc_start: 0.7972 (t70) cc_final: 0.7701 (t0) REVERT: B 288 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7558 (mm) REVERT: B 335 LYS cc_start: 0.8148 (tppt) cc_final: 0.7632 (tppt) REVERT: F 73 LEU cc_start: 0.6364 (mp) cc_final: 0.6042 (tm) REVERT: F 81 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6168 (mtmt) REVERT: F 86 LYS cc_start: 0.8272 (tttm) cc_final: 0.7819 (tttt) REVERT: F 98 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.5319 (mpm) REVERT: C 102 HIS cc_start: 0.7673 (p-80) cc_final: 0.7421 (p90) REVERT: C 142 ASP cc_start: 0.7090 (m-30) cc_final: 0.6877 (m-30) REVERT: C 224 ASN cc_start: 0.7709 (p0) cc_final: 0.7490 (p0) REVERT: G 13 ASP cc_start: 0.6440 (t0) cc_final: 0.6143 (t0) REVERT: G 86 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8384 (ttmm) outliers start: 38 outliers final: 15 residues processed: 186 average time/residue: 0.5693 time to fit residues: 115.7928 Evaluate side-chains 162 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 120 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 395 GLN B 290 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN G 75 GLN G 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147683 restraints weight = 14811.937| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.02 r_work: 0.3789 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12795 Z= 0.143 Angle : 0.557 6.819 17435 Z= 0.290 Chirality : 0.048 0.158 2099 Planarity : 0.004 0.037 2174 Dihedral : 5.327 29.681 1905 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.39 % Allowed : 15.46 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1584 helix: 0.65 (0.25), residues: 402 sheet: -0.50 (0.26), residues: 366 loop : -1.32 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 336 TYR 0.012 0.001 TYR G 96 PHE 0.014 0.001 PHE B 376 TRP 0.020 0.002 TRP F 101 HIS 0.005 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00334 (12768) covalent geometry : angle 0.55150 (17375) SS BOND : bond 0.00330 ( 21) SS BOND : angle 1.11160 ( 42) hydrogen bonds : bond 0.03580 ( 502) hydrogen bonds : angle 5.44781 ( 1305) link_NAG-ASN : bond 0.00273 ( 6) link_NAG-ASN : angle 2.13413 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 258 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7325 (pt0) REVERT: E 96 TYR cc_start: 0.8394 (t80) cc_final: 0.7916 (t80) REVERT: B 103 ASP cc_start: 0.7937 (t70) cc_final: 0.7650 (t0) REVERT: B 177 ASP cc_start: 0.6904 (t70) cc_final: 0.6696 (t70) REVERT: B 335 LYS cc_start: 0.8058 (tppt) cc_final: 0.7602 (tppt) REVERT: B 425 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8283 (p) REVERT: F 16 MET cc_start: 0.5826 (mtm) cc_final: 0.5114 (pmm) REVERT: F 73 LEU cc_start: 0.6286 (mp) cc_final: 0.6009 (tm) REVERT: F 81 LYS cc_start: 0.6520 (OUTLIER) cc_final: 0.6067 (mtmt) REVERT: F 86 LYS cc_start: 0.8224 (tttm) cc_final: 0.7799 (tttt) REVERT: F 98 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.5350 (mpm) REVERT: C 102 HIS cc_start: 0.7684 (p-80) cc_final: 0.7438 (p90) REVERT: G 13 ASP cc_start: 0.6357 (t0) cc_final: 0.6108 (t0) REVERT: G 86 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8406 (ttmm) outliers start: 48 outliers final: 20 residues processed: 201 average time/residue: 0.4926 time to fit residues: 109.6790 Evaluate side-chains 172 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 147 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 395 GLN B 84 ASN B 380 ASN C 380 ASN G 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.149763 restraints weight = 14882.574| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.03 r_work: 0.3807 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12795 Z= 0.122 Angle : 0.534 6.405 17435 Z= 0.278 Chirality : 0.047 0.147 2099 Planarity : 0.004 0.038 2174 Dihedral : 4.995 26.773 1905 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.18 % Allowed : 17.08 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1584 helix: 0.78 (0.26), residues: 405 sheet: -0.37 (0.26), residues: 366 loop : -1.26 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 336 TYR 0.017 0.001 TYR B 206 PHE 0.013 0.001 PHE B 376 TRP 0.018 0.002 TRP F 101 HIS 0.008 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00283 (12768) covalent geometry : angle 0.52743 (17375) SS BOND : bond 0.00273 ( 21) SS BOND : angle 1.11136 ( 42) hydrogen bonds : bond 0.03312 ( 502) hydrogen bonds : angle 5.27762 ( 1305) link_NAG-ASN : bond 0.00199 ( 6) link_NAG-ASN : angle 2.08585 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: E 96 TYR cc_start: 0.8347 (t80) cc_final: 0.7936 (t80) REVERT: B 103 ASP cc_start: 0.7955 (t70) cc_final: 0.7687 (t0) REVERT: B 177 ASP cc_start: 0.6865 (t70) cc_final: 0.6635 (t70) REVERT: B 197 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7471 (tt) REVERT: B 288 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7207 (mm) REVERT: B 335 LYS cc_start: 0.8058 (tppt) cc_final: 0.7603 (tppt) REVERT: B 425 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 431 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7804 (tttm) REVERT: F 86 LYS cc_start: 0.8231 (tttm) cc_final: 0.7855 (tttt) REVERT: F 98 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.5241 (mpm) REVERT: C 102 HIS cc_start: 0.7676 (p-80) cc_final: 0.7445 (p90) REVERT: C 335 LYS cc_start: 0.8525 (tppt) cc_final: 0.7752 (ttmm) REVERT: C 380 ASN cc_start: 0.8142 (m-40) cc_final: 0.7140 (t0) REVERT: G 13 ASP cc_start: 0.6413 (t0) cc_final: 0.6151 (t0) REVERT: G 86 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8268 (ttmm) outliers start: 45 outliers final: 23 residues processed: 203 average time/residue: 0.5162 time to fit residues: 115.4292 Evaluate side-chains 182 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 42 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 395 GLN B 84 ASN G 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.173632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150549 restraints weight = 14809.606| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.03 r_work: 0.3816 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12795 Z= 0.121 Angle : 0.538 9.207 17435 Z= 0.278 Chirality : 0.046 0.155 2099 Planarity : 0.004 0.038 2174 Dihedral : 4.879 27.859 1905 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.11 % Allowed : 18.21 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.21), residues: 1584 helix: 0.83 (0.25), residues: 411 sheet: -0.28 (0.26), residues: 366 loop : -1.20 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 90 TYR 0.019 0.001 TYR B 206 PHE 0.013 0.001 PHE B 376 TRP 0.019 0.002 TRP F 101 HIS 0.009 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00280 (12768) covalent geometry : angle 0.53174 (17375) SS BOND : bond 0.00289 ( 21) SS BOND : angle 1.13994 ( 42) hydrogen bonds : bond 0.03202 ( 502) hydrogen bonds : angle 5.18455 ( 1305) link_NAG-ASN : bond 0.00226 ( 6) link_NAG-ASN : angle 2.11680 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 65 ARG cc_start: 0.7081 (mtm-85) cc_final: 0.6795 (mtm180) REVERT: E 96 TYR cc_start: 0.8338 (t80) cc_final: 0.7986 (t80) REVERT: B 103 ASP cc_start: 0.7966 (t70) cc_final: 0.7702 (t0) REVERT: B 177 ASP cc_start: 0.6777 (t70) cc_final: 0.6561 (t70) REVERT: B 197 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7376 (tt) REVERT: B 288 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7065 (mm) REVERT: B 333 ILE cc_start: 0.8538 (mt) cc_final: 0.8242 (mt) REVERT: B 335 LYS cc_start: 0.8035 (tppt) cc_final: 0.7594 (tppt) REVERT: B 425 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 431 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7712 (tttm) REVERT: F 16 MET cc_start: 0.5748 (mtm) cc_final: 0.5065 (pmm) REVERT: F 73 LEU cc_start: 0.7132 (tm) cc_final: 0.6696 (pp) REVERT: F 86 LYS cc_start: 0.8178 (tttm) cc_final: 0.7655 (tttt) REVERT: F 98 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.5316 (mpm) REVERT: F 104 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: C 102 HIS cc_start: 0.7693 (p-80) cc_final: 0.7460 (p90) REVERT: C 335 LYS cc_start: 0.8573 (tppt) cc_final: 0.7850 (ttmm) REVERT: C 380 ASN cc_start: 0.8140 (m-40) cc_final: 0.7124 (t0) REVERT: G 13 ASP cc_start: 0.6486 (t0) cc_final: 0.6250 (t0) REVERT: G 86 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8265 (ttmm) outliers start: 44 outliers final: 26 residues processed: 198 average time/residue: 0.4685 time to fit residues: 103.0108 Evaluate side-chains 186 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 75 optimal weight: 0.0030 chunk 101 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 395 GLN B 342 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.173341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150273 restraints weight = 14826.095| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.03 r_work: 0.3813 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12795 Z= 0.127 Angle : 0.539 8.229 17435 Z= 0.278 Chirality : 0.047 0.162 2099 Planarity : 0.004 0.038 2174 Dihedral : 4.832 28.656 1905 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.32 % Allowed : 18.63 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1584 helix: 0.88 (0.25), residues: 411 sheet: -0.20 (0.26), residues: 366 loop : -1.19 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.020 0.001 TYR B 206 PHE 0.012 0.001 PHE B 376 TRP 0.020 0.002 TRP F 101 HIS 0.009 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00296 (12768) covalent geometry : angle 0.53353 (17375) SS BOND : bond 0.00270 ( 21) SS BOND : angle 1.07992 ( 42) hydrogen bonds : bond 0.03201 ( 502) hydrogen bonds : angle 5.16111 ( 1305) link_NAG-ASN : bond 0.00218 ( 6) link_NAG-ASN : angle 2.04350 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 65 ARG cc_start: 0.7118 (mtm-85) cc_final: 0.6907 (mtm180) REVERT: E 96 TYR cc_start: 0.8341 (t80) cc_final: 0.8003 (t80) REVERT: B 103 ASP cc_start: 0.7964 (t70) cc_final: 0.7696 (t0) REVERT: B 197 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7384 (tt) REVERT: B 288 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.6977 (mm) REVERT: B 335 LYS cc_start: 0.8036 (tppt) cc_final: 0.7603 (tppt) REVERT: B 425 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 431 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7731 (tttm) REVERT: F 16 MET cc_start: 0.5765 (mtm) cc_final: 0.5043 (pmm) REVERT: F 86 LYS cc_start: 0.8189 (tttm) cc_final: 0.7675 (tttt) REVERT: F 98 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.5218 (mpm) REVERT: F 104 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: C 102 HIS cc_start: 0.7720 (p-80) cc_final: 0.7483 (p90) REVERT: C 224 ASN cc_start: 0.7578 (p0) cc_final: 0.6938 (t0) REVERT: C 263 THR cc_start: 0.8873 (p) cc_final: 0.8460 (p) REVERT: C 380 ASN cc_start: 0.8109 (m-40) cc_final: 0.7103 (t0) REVERT: G 13 ASP cc_start: 0.6559 (t0) cc_final: 0.6309 (t0) REVERT: G 86 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8259 (ttmm) outliers start: 47 outliers final: 28 residues processed: 200 average time/residue: 0.4654 time to fit residues: 103.5571 Evaluate side-chains 186 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 16 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 HIS ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.144531 restraints weight = 14794.217| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.02 r_work: 0.3748 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12795 Z= 0.221 Angle : 0.641 11.398 17435 Z= 0.327 Chirality : 0.050 0.181 2099 Planarity : 0.004 0.040 2174 Dihedral : 5.380 31.052 1905 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.32 % Allowed : 19.05 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1584 helix: 0.69 (0.25), residues: 408 sheet: -0.41 (0.26), residues: 366 loop : -1.27 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 244 TYR 0.022 0.002 TYR B 206 PHE 0.014 0.002 PHE B 376 TRP 0.037 0.003 TRP F 101 HIS 0.009 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00530 (12768) covalent geometry : angle 0.63582 (17375) SS BOND : bond 0.00423 ( 21) SS BOND : angle 1.27045 ( 42) hydrogen bonds : bond 0.03747 ( 502) hydrogen bonds : angle 5.46318 ( 1305) link_NAG-ASN : bond 0.00492 ( 6) link_NAG-ASN : angle 2.09140 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 65 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.6966 (mtm180) REVERT: E 90 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7769 (mtt180) REVERT: E 96 TYR cc_start: 0.8410 (t80) cc_final: 0.8075 (t80) REVERT: B 103 ASP cc_start: 0.7937 (t70) cc_final: 0.7671 (t0) REVERT: B 197 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7350 (tt) REVERT: B 244 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7280 (ttp-110) REVERT: B 288 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7421 (mm) REVERT: B 335 LYS cc_start: 0.8109 (tppt) cc_final: 0.7650 (tppt) REVERT: F 16 MET cc_start: 0.5847 (mtm) cc_final: 0.5131 (pmm) REVERT: F 86 LYS cc_start: 0.8211 (tttm) cc_final: 0.7730 (tttt) REVERT: F 98 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.5211 (mpm) REVERT: F 104 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: C 102 HIS cc_start: 0.7765 (p-80) cc_final: 0.7502 (p90) REVERT: C 224 ASN cc_start: 0.7705 (p0) cc_final: 0.7008 (t0) REVERT: C 263 THR cc_start: 0.8939 (p) cc_final: 0.8541 (p) REVERT: G 13 ASP cc_start: 0.6544 (t0) cc_final: 0.6302 (t0) REVERT: G 86 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8291 (ttmm) outliers start: 47 outliers final: 29 residues processed: 196 average time/residue: 0.4626 time to fit residues: 100.8013 Evaluate side-chains 186 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN B 380 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 380 ASN G 79 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.146716 restraints weight = 14849.839| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.03 r_work: 0.3771 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12795 Z= 0.165 Angle : 0.597 12.219 17435 Z= 0.305 Chirality : 0.048 0.182 2099 Planarity : 0.004 0.038 2174 Dihedral : 5.228 30.957 1905 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.96 % Allowed : 19.97 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1584 helix: 0.71 (0.25), residues: 411 sheet: -0.40 (0.26), residues: 366 loop : -1.22 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 336 TYR 0.021 0.001 TYR B 206 PHE 0.013 0.002 PHE B 376 TRP 0.027 0.002 TRP F 101 HIS 0.011 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00392 (12768) covalent geometry : angle 0.59127 (17375) SS BOND : bond 0.00348 ( 21) SS BOND : angle 1.15358 ( 42) hydrogen bonds : bond 0.03495 ( 502) hydrogen bonds : angle 5.36835 ( 1305) link_NAG-ASN : bond 0.00372 ( 6) link_NAG-ASN : angle 2.04732 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6980 (mtm180) REVERT: E 90 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7705 (mtt180) REVERT: E 96 TYR cc_start: 0.8394 (t80) cc_final: 0.8066 (t80) REVERT: B 103 ASP cc_start: 0.7905 (t70) cc_final: 0.7619 (t0) REVERT: B 197 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7352 (tt) REVERT: B 288 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7331 (mm) REVERT: B 335 LYS cc_start: 0.8104 (tppt) cc_final: 0.7685 (tppt) REVERT: F 16 MET cc_start: 0.5882 (mtm) cc_final: 0.5283 (pmm) REVERT: F 86 LYS cc_start: 0.8219 (tttm) cc_final: 0.7733 (tttt) REVERT: F 98 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.5196 (mpm) REVERT: F 104 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: C 102 HIS cc_start: 0.7772 (p90) cc_final: 0.7511 (p90) REVERT: C 224 ASN cc_start: 0.7679 (p0) cc_final: 0.6932 (t0) REVERT: C 263 THR cc_start: 0.8908 (p) cc_final: 0.8506 (p) REVERT: G 13 ASP cc_start: 0.6531 (t0) cc_final: 0.6293 (t0) REVERT: G 86 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8239 (ttmm) outliers start: 42 outliers final: 28 residues processed: 188 average time/residue: 0.4485 time to fit residues: 93.9906 Evaluate side-chains 187 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 104 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 112 optimal weight: 0.0570 chunk 155 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 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 182 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149659 restraints weight = 14867.427| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.04 r_work: 0.3804 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12795 Z= 0.130 Angle : 0.565 12.578 17435 Z= 0.289 Chirality : 0.047 0.180 2099 Planarity : 0.004 0.040 2174 Dihedral : 4.972 29.844 1905 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.40 % Allowed : 20.54 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.21), residues: 1584 helix: 0.89 (0.26), residues: 411 sheet: -0.34 (0.26), residues: 366 loop : -1.19 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 90 TYR 0.020 0.001 TYR B 206 PHE 0.013 0.001 PHE B 376 TRP 0.018 0.002 TRP F 101 HIS 0.012 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00303 (12768) covalent geometry : angle 0.56036 (17375) SS BOND : bond 0.00281 ( 21) SS BOND : angle 1.05244 ( 42) hydrogen bonds : bond 0.03265 ( 502) hydrogen bonds : angle 5.23675 ( 1305) link_NAG-ASN : bond 0.00261 ( 6) link_NAG-ASN : angle 2.00696 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 65 ARG cc_start: 0.7186 (mtm-85) cc_final: 0.6928 (mtm180) REVERT: E 96 TYR cc_start: 0.8378 (t80) cc_final: 0.8019 (t80) REVERT: B 103 ASP cc_start: 0.7912 (t70) cc_final: 0.7636 (t0) REVERT: B 197 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7330 (tt) REVERT: B 288 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7169 (mm) REVERT: B 333 ILE cc_start: 0.8529 (mt) cc_final: 0.8250 (mt) REVERT: B 335 LYS cc_start: 0.8078 (tppt) cc_final: 0.7685 (tppt) REVERT: B 425 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 431 LYS cc_start: 0.8159 (ttmm) cc_final: 0.7833 (tttm) REVERT: F 16 MET cc_start: 0.5913 (mtm) cc_final: 0.5329 (pmm) REVERT: F 86 LYS cc_start: 0.8211 (tttm) cc_final: 0.7684 (tttt) REVERT: F 98 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.5354 (mpm) REVERT: F 104 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: C 102 HIS cc_start: 0.7755 (p90) cc_final: 0.7502 (p90) REVERT: C 224 ASN cc_start: 0.7636 (p0) cc_final: 0.6862 (t0) REVERT: C 263 THR cc_start: 0.8905 (p) cc_final: 0.8488 (p) REVERT: C 380 ASN cc_start: 0.8036 (m-40) cc_final: 0.7067 (t0) REVERT: C 417 CYS cc_start: 0.7057 (t) cc_final: 0.6485 (t) REVERT: G 13 ASP cc_start: 0.6642 (t0) cc_final: 0.6398 (t0) REVERT: G 86 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8283 (ttmm) outliers start: 34 outliers final: 24 residues processed: 196 average time/residue: 0.4858 time to fit residues: 105.4871 Evaluate side-chains 191 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 76 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 57 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.148014 restraints weight = 14890.814| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.04 r_work: 0.3787 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12795 Z= 0.153 Angle : 0.585 12.558 17435 Z= 0.298 Chirality : 0.048 0.194 2099 Planarity : 0.004 0.061 2174 Dihedral : 5.047 30.434 1905 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.75 % Allowed : 20.47 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.21), residues: 1584 helix: 0.91 (0.25), residues: 411 sheet: -0.31 (0.26), residues: 366 loop : -1.19 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 279 TYR 0.021 0.001 TYR B 206 PHE 0.015 0.002 PHE C 212 TRP 0.025 0.002 TRP F 101 HIS 0.011 0.001 HIS G 60 Details of bonding type rmsd covalent geometry : bond 0.00362 (12768) covalent geometry : angle 0.57985 (17375) SS BOND : bond 0.00325 ( 21) SS BOND : angle 1.09200 ( 42) hydrogen bonds : bond 0.03354 ( 502) hydrogen bonds : angle 5.24764 ( 1305) link_NAG-ASN : bond 0.00326 ( 6) link_NAG-ASN : angle 1.95810 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4561.88 seconds wall clock time: 78 minutes 41.41 seconds (4721.41 seconds total)