Starting phenix.real_space_refine on Fri Jul 3 13:29:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yq6_73325/07_2026/9yq6_73325.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yq6_73325/07_2026/9yq6_73325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yq6_73325/07_2026/9yq6_73325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yq6_73325/07_2026/9yq6_73325.map" model { file = "/net/cci-nas-00/data/ceres_data/9yq6_73325/07_2026/9yq6_73325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yq6_73325/07_2026/9yq6_73325.cif" } resolution = 2.95 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= 0.017 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 66 5.16 5 C 8805 2.51 5 N 2371 2.21 5 O 2719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13961 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3436 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 410} Chain: "F" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3387 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 405} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "G" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "H" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 102} Chain: "D" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 945 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "J" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.56, per 1000 atoms: 0.18 Number of scatterers: 13961 At special positions: 0 Unit cell: (107.44, 165.11, 97.17, 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 66 16.00 O 2719 8.00 N 2371 7.00 C 8805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 401 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 431 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 116 " - pdb=" SG CYS F 129 " distance=2.03 Simple disulfide: pdb=" SG CYS F 210 " - pdb=" SG CYS F 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 215 " - pdb=" SG CYS F 329 " distance=2.03 Simple disulfide: pdb=" SG CYS F 323 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 395 " - pdb=" SG CYS F 404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 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 BETA1-4 " NAG K 1 " - " NAG K 2 " BETA1-6 " NAG K 1 " - " FUC K 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG L 1 " - " FUC L 2 " NAG-ASN " NAG L 1 " - " ASN A 389 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 449.2 milliseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 39 sheets defined 7.0% alpha, 45.7% 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 18 through 23 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.566A pdb=" N ASN A 118 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.518A pdb=" N CYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 6.942A pdb=" N TRP A 237 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 108 through 112 removed outlier: 3.558A pdb=" N ASP F 111 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN F 112 " --> pdb=" O ILE F 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 112' Processing helix chain 'F' and resid 135 through 142 removed outlier: 3.549A pdb=" N SER F 142 " --> pdb=" O SER F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 removed outlier: 3.533A pdb=" N ILE F 169 " --> pdb=" O ASN F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 227 removed outlier: 3.526A pdb=" N CYS F 223 " --> pdb=" O THR F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 6.948A pdb=" N TRP F 231 " --> pdb=" O HIS F 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.978A pdb=" N VAL C 88 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.551A pdb=" N GLN G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.731A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 removed outlier: 3.982A pdb=" N VAL H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.731A pdb=" N LYS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.678A pdb=" N ALA D 92 " --> pdb=" O SER D 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.167A pdb=" N PHE E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.655A pdb=" N LYS I 66 " --> pdb=" O PRO I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.692A pdb=" N ALA I 92 " --> pdb=" O SER I 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.143A pdb=" N PHE J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 removed outlier: 3.879A pdb=" N LYS A 15 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA A 394 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN A 417 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TYR A 396 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA4, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 64 removed outlier: 6.538A pdb=" N THR A 72 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU A 62 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA A 70 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 88 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR A 112 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 90 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 110 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A 92 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 127 removed outlier: 4.903A pdb=" N SER A 121 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER A 136 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 177 removed outlier: 4.008A pdb=" N ARG A 242 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 198 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 177 removed outlier: 4.008A pdb=" N ARG A 242 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 198 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 276 through 281 removed outlier: 3.629A pdb=" N LYS A 284 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE A 285 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU A 300 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 312 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AB2, first strand: chain 'F' and resid 8 through 10 removed outlier: 3.527A pdb=" N LYS F 9 " --> pdb=" O THR F 397 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA F 388 " --> pdb=" O ASN F 411 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN F 411 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR F 390 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 23 through 26 Processing sheet with id=AB4, first strand: chain 'F' and resid 50 through 58 removed outlier: 6.505A pdb=" N THR F 66 " --> pdb=" O PRO F 54 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU F 56 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA F 64 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 67 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN F 82 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR F 106 " --> pdb=" O GLN F 82 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU F 84 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER F 104 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE F 86 " --> pdb=" O ARG F 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 114 through 121 removed outlier: 4.912A pdb=" N SER F 115 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER F 130 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 170 through 171 removed outlier: 3.510A pdb=" N ARG F 236 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE F 192 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 170 through 171 removed outlier: 3.510A pdb=" N ARG F 236 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE F 192 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 270 through 275 removed outlier: 3.590A pdb=" N LYS F 278 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE F 279 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU F 294 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG F 306 " --> pdb=" O ASP F 298 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 341 through 343 Processing sheet with id=AC1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.622A pdb=" N SER B 71 " --> pdb=" O TYR B 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.619A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N CYS B 96 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP B 111 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS B 98 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.619A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B 92 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.652A pdb=" N GLU C 109 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 53 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 42 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU C 51 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.521A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.898A pdb=" N ALA G 92 " --> pdb=" O GLY G 117 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.898A pdb=" N ALA G 92 " --> pdb=" O GLY G 117 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.516A pdb=" N CYS H 23 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE H 76 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.709A pdb=" N GLU H 109 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR H 54 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TRP H 40 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN H 58 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.697A pdb=" N GLY D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG D 40 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.804A pdb=" N TYR D 112 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER D 101 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE D 110 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.522A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.697A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD8, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.187A pdb=" N TRP I 36 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP I 52 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP I 38 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 11 through 12 removed outlier: 4.018A pdb=" N TYR I 109 " --> pdb=" O SER I 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.535A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.646A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA J 84 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.646A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA J 84 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1431 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: 1.80 Time building geometry restraints manager: 1.14 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: 4488 1.34 - 1.46: 3463 1.46 - 1.58: 6263 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 14302 Sorted by residual: bond pdb=" CB ASP C 33 " pdb=" CG ASP C 33 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.48e+00 bond pdb=" CB LYS A 85 " pdb=" CG LYS A 85 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB GLU I 16 " pdb=" CG GLU I 16 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CB LYS F 79 " pdb=" CG LYS F 79 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CA GLN H 50 " pdb=" CB GLN H 50 " ideal model delta sigma weight residual 1.533 1.552 -0.019 1.66e-02 3.63e+03 1.24e+00 ... (remaining 14297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 19187 2.27 - 4.54: 242 4.54 - 6.80: 26 6.80 - 9.07: 2 9.07 - 11.34: 5 Bond angle restraints: 19462 Sorted by residual: angle pdb=" N LEU D 107 " pdb=" CA LEU D 107 " pdb=" C LEU D 107 " ideal model delta sigma weight residual 110.91 116.47 -5.56 1.17e+00 7.31e-01 2.26e+01 angle pdb=" CB LYS A 85 " pdb=" CG LYS A 85 " pdb=" CD LYS A 85 " ideal model delta sigma weight residual 111.30 121.51 -10.21 2.30e+00 1.89e-01 1.97e+01 angle pdb=" CB LYS F 79 " pdb=" CG LYS F 79 " pdb=" CD LYS F 79 " ideal model delta sigma weight residual 111.30 120.47 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" CB MET F 237 " pdb=" CG MET F 237 " pdb=" SD MET F 237 " ideal model delta sigma weight residual 112.70 124.04 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" CB MET A 243 " pdb=" CG MET A 243 " pdb=" SD MET A 243 " ideal model delta sigma weight residual 112.70 124.04 -11.34 3.00e+00 1.11e-01 1.43e+01 ... (remaining 19457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 7695 17.73 - 35.45: 656 35.45 - 53.18: 209 53.18 - 70.91: 40 70.91 - 88.64: 6 Dihedral angle restraints: 8606 sinusoidal: 3450 harmonic: 5156 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 37.75 55.25 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 97 " pdb=" CB CYS I 97 " ideal model delta sinusoidal sigma weight residual 93.00 38.98 54.02 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CA TYR D 106 " pdb=" C TYR D 106 " pdb=" N LEU D 107 " pdb=" CA LEU D 107 " ideal model delta harmonic sigma weight residual 180.00 151.48 28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 8603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1344 0.030 - 0.059: 504 0.059 - 0.089: 145 0.089 - 0.119: 146 0.119 - 0.148: 23 Chirality restraints: 2162 Sorted by residual: chirality pdb=" CB ILE F 77 " pdb=" CA ILE F 77 " pdb=" CG1 ILE F 77 " pdb=" CG2 ILE F 77 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA LEU D 107 " pdb=" N LEU D 107 " pdb=" C LEU D 107 " pdb=" CB LEU D 107 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE C 53 " pdb=" N ILE C 53 " pdb=" C ILE C 53 " pdb=" CB ILE C 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2159 not shown) Planarity restraints: 2494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 102 " 0.015 2.00e-02 2.50e+03 1.46e-02 5.31e+00 pdb=" CG TRP I 102 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP I 102 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP I 102 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 102 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 102 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 102 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP I 102 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 18 " -0.163 9.50e-02 1.11e+02 7.35e-02 4.13e+00 pdb=" NE ARG J 18 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG J 18 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG J 18 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG J 18 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 99 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C SER A 99 " 0.033 2.00e-02 2.50e+03 pdb=" O SER A 99 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 100 " -0.011 2.00e-02 2.50e+03 ... (remaining 2491 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 480 2.71 - 3.25: 12807 3.25 - 3.80: 21827 3.80 - 4.35: 27911 4.35 - 4.90: 49171 Nonbonded interactions: 112196 Sorted by model distance: nonbonded pdb=" N ASP H 33 " pdb=" OD1 ASP H 33 " model vdw 2.156 3.120 nonbonded pdb=" OE1 GLN A 1 " pdb=" OG SER F 158 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASN F 167 " pdb=" OH TYR J 32 " model vdw 2.169 3.040 nonbonded pdb=" O GLY G 52 " pdb=" NH1 ARG G 72 " model vdw 2.176 3.120 nonbonded pdb=" OG SER A 274 " pdb=" OG1 THR A 292 " model vdw 2.206 3.040 ... (remaining 112191 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 7 through 438) selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.830 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 0.003 0.047 14328 Z= 0.126 Angle : 0.628 11.341 19518 Z= 0.325 Chirality : 0.043 0.148 2162 Planarity : 0.004 0.074 2493 Dihedral : 14.861 88.636 5260 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.50 % Allowed : 20.81 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: 0.06 (0.20), residues: 1774 helix: -1.05 (0.77), residues: 44 sheet: 0.53 (0.19), residues: 791 loop : -0.25 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 18 TYR 0.016 0.001 TYR A 396 PHE 0.025 0.002 PHE E 83 TRP 0.038 0.002 TRP I 102 HIS 0.013 0.001 HIS F 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14302) covalent geometry : angle 0.62608 / 0.32 (19462) SS BOND : bond 0.00286 / 0.21 ( 22) SS BOND : angle 0.83227 / 0.55 ( 44) hydrogen bonds : bond 0.25082 / 16.97 ( 507) hydrogen bonds : angle 9.63173 / 6.62 ( 1431) link_BETA1-4 : bond 0.00254 / 0.13 ( 1) link_BETA1-4 : angle 0.82652 / 0.46 ( 3) link_BETA1-6 : bond 0.00282 / 0.15 ( 2) link_BETA1-6 : angle 1.26457 / 0.86 ( 6) link_NAG-ASN : bond 0.00104 / 0.05 ( 1) link_NAG-ASN : angle 2.50897 / 1.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8556 (p) cc_final: 0.8274 (t) REVERT: A 34 LYS cc_start: 0.7549 (tmtt) cc_final: 0.6880 (tmtt) REVERT: A 37 LYS cc_start: 0.7039 (mmtt) cc_final: 0.6602 (mmtt) REVERT: A 195 LYS cc_start: 0.7217 (mmmm) cc_final: 0.6833 (tppp) REVERT: A 261 LYS cc_start: 0.7673 (tttt) cc_final: 0.7122 (tmtt) REVERT: A 307 ASP cc_start: 0.7012 (t0) cc_final: 0.6549 (t0) REVERT: A 427 MET cc_start: 0.7712 (mtt) cc_final: 0.7334 (mmm) REVERT: F 25 SER cc_start: 0.8469 (p) cc_final: 0.8183 (t) REVERT: F 26 LEU cc_start: 0.8139 (mm) cc_final: 0.7759 (mt) REVERT: F 27 MET cc_start: 0.7857 (mtm) cc_final: 0.7520 (mtt) REVERT: F 189 LYS cc_start: 0.7300 (mmmm) cc_final: 0.6853 (tppt) REVERT: F 255 LYS cc_start: 0.7784 (tttt) cc_final: 0.7127 (tmtt) REVERT: F 278 LYS cc_start: 0.8068 (mttp) cc_final: 0.7691 (mtpp) REVERT: F 306 ARG cc_start: 0.7260 (mtt90) cc_final: 0.7031 (mtm-85) REVERT: F 421 MET cc_start: 0.7735 (mtt) cc_final: 0.7373 (mmm) REVERT: B 58 THR cc_start: 0.7515 (p) cc_final: 0.7209 (p) REVERT: G 38 ARG cc_start: 0.6887 (ttm110) cc_final: 0.6403 (ttm110) REVERT: D 3 GLN cc_start: 0.6995 (mp10) cc_final: 0.6749 (mp10) REVERT: D 50 ILE cc_start: 0.7808 (mt) cc_final: 0.7570 (mt) REVERT: E 31 THR cc_start: 0.7864 (p) cc_final: 0.7256 (t) REVERT: J 33 LEU cc_start: 0.7414 (tt) cc_final: 0.7075 (tt) outliers start: 39 outliers final: 13 residues processed: 232 average time/residue: 0.4310 time to fit residues: 111.5162 Evaluate side-chains 194 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 149 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 HIS A 172 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 115 ASN H 43 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN E 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.173928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156251 restraints weight = 19919.323| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.19 r_work: 0.3963 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14328 Z= 0.202 Angle : 0.712 12.774 19518 Z= 0.363 Chirality : 0.047 0.177 2162 Planarity : 0.005 0.055 2493 Dihedral : 5.895 45.356 2086 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.99 % Allowed : 19.33 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.08 (0.20), residues: 1774 helix: -0.38 (0.87), residues: 32 sheet: 0.43 (0.18), residues: 798 loop : -0.40 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 38 TYR 0.037 0.002 TYR I 106 PHE 0.020 0.003 PHE G 27 TRP 0.023 0.002 TRP I 102 HIS 0.010 0.002 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (14302) covalent geometry : angle 0.70842 / 0.36 (19462) SS BOND : bond 0.00706 / 0.54 ( 22) SS BOND : angle 1.31748 / 0.92 ( 44) hydrogen bonds : bond 0.04498 / 3.02 ( 507) hydrogen bonds : angle 6.38209 / 4.33 ( 1431) link_BETA1-4 : bond 0.00983 / 0.52 ( 1) link_BETA1-4 : angle 1.10037 / 0.57 ( 3) link_BETA1-6 : bond 0.00317 / 0.16 ( 2) link_BETA1-6 : angle 1.89517 / 1.09 ( 6) link_NAG-ASN : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : angle 2.22914 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7965 (tmtt) cc_final: 0.7528 (tmtt) REVERT: A 37 LYS cc_start: 0.7296 (mmtt) cc_final: 0.7002 (mmtt) REVERT: A 41 MET cc_start: 0.6572 (mmm) cc_final: 0.6224 (mmm) REVERT: A 193 TYR cc_start: 0.7997 (t80) cc_final: 0.7784 (t80) REVERT: A 307 ASP cc_start: 0.7059 (t0) cc_final: 0.6771 (t0) REVERT: F 26 LEU cc_start: 0.8467 (mm) cc_final: 0.8170 (mt) REVERT: F 421 MET cc_start: 0.7435 (mtt) cc_final: 0.7125 (mmm) REVERT: B 58 THR cc_start: 0.7799 (p) cc_final: 0.7549 (p) REVERT: G 96 CYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6878 (p) REVERT: G 100 PHE cc_start: 0.2645 (OUTLIER) cc_final: -0.0558 (t80) REVERT: G 115 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6933 (t0) REVERT: H 95 GLN cc_start: 0.2992 (OUTLIER) cc_final: 0.2722 (tm-30) REVERT: D 50 ILE cc_start: 0.8104 (mt) cc_final: 0.7689 (mt) REVERT: D 78 ASN cc_start: 0.7288 (m-40) cc_final: 0.6948 (t0) REVERT: I 82 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7226 (tp) outliers start: 78 outliers final: 29 residues processed: 239 average time/residue: 0.3821 time to fit residues: 102.8088 Evaluate side-chains 202 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain J residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 100 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 133 optimal weight: 0.0270 chunk 97 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN A 406 ASN F 166 ASN G 39 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.175423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.158112 restraints weight = 20161.343| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.18 r_work: 0.3977 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14328 Z= 0.126 Angle : 0.606 10.641 19518 Z= 0.308 Chirality : 0.044 0.155 2162 Planarity : 0.005 0.052 2493 Dihedral : 5.381 46.255 2078 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.74 % Allowed : 20.68 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.01 (0.20), residues: 1774 helix: 0.34 (0.95), residues: 32 sheet: 0.49 (0.18), residues: 795 loop : -0.40 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 24 TYR 0.035 0.002 TYR I 106 PHE 0.013 0.002 PHE I 80 TRP 0.020 0.002 TRP I 102 HIS 0.006 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (14302) covalent geometry : angle 0.60335 / 0.31 (19462) SS BOND : bond 0.00425 / 0.32 ( 22) SS BOND : angle 0.86684 / 0.58 ( 44) hydrogen bonds : bond 0.03596 / 2.46 ( 507) hydrogen bonds : angle 5.84390 / 3.98 ( 1431) link_BETA1-4 : bond 0.00142 / 0.07 ( 1) link_BETA1-4 : angle 1.16873 / 0.63 ( 3) link_BETA1-6 : bond 0.00271 / 0.13 ( 2) link_BETA1-6 : angle 1.48675 / 0.90 ( 6) link_NAG-ASN : bond 0.00121 / 0.06 ( 1) link_NAG-ASN : angle 2.66758 / 1.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 174 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8003 (tmtt) cc_final: 0.7567 (tmtt) REVERT: A 37 LYS cc_start: 0.7253 (mmtt) cc_final: 0.6915 (mmtt) REVERT: A 41 MET cc_start: 0.6640 (mmm) cc_final: 0.6187 (mmm) REVERT: A 241 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7544 (mmm160) REVERT: A 307 ASP cc_start: 0.6965 (t0) cc_final: 0.6694 (t0) REVERT: A 427 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6937 (mtt) REVERT: F 26 LEU cc_start: 0.8335 (mm) cc_final: 0.8108 (mt) REVERT: F 235 ARG cc_start: 0.7996 (mmt180) cc_final: 0.7752 (mmt180) REVERT: F 302 TYR cc_start: 0.7676 (m-80) cc_final: 0.7429 (m-80) REVERT: F 306 ARG cc_start: 0.7449 (mtt90) cc_final: 0.7107 (mtt90) REVERT: F 421 MET cc_start: 0.7460 (mtt) cc_final: 0.7133 (mmm) REVERT: F 424 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7593 (mttm) REVERT: B 58 THR cc_start: 0.7742 (p) cc_final: 0.7490 (p) REVERT: G 100 PHE cc_start: 0.2632 (OUTLIER) cc_final: -0.0518 (t80) REVERT: G 115 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6491 (p0) REVERT: D 50 ILE cc_start: 0.7997 (mt) cc_final: 0.7602 (mt) REVERT: E 91 ARG cc_start: 0.5797 (OUTLIER) cc_final: 0.4932 (mtt180) outliers start: 74 outliers final: 32 residues processed: 224 average time/residue: 0.3770 time to fit residues: 95.4264 Evaluate side-chains 199 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 21 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 159 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 157 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 143 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 166 ASN F 167 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.174584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157521 restraints weight = 19838.858| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.15 r_work: 0.3971 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14328 Z= 0.140 Angle : 0.609 10.366 19518 Z= 0.307 Chirality : 0.044 0.151 2162 Planarity : 0.005 0.050 2493 Dihedral : 5.348 46.959 2078 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.55 % Allowed : 20.81 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.07 (0.20), residues: 1774 helix: 0.36 (0.93), residues: 32 sheet: 0.50 (0.18), residues: 800 loop : -0.49 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 375 TYR 0.034 0.002 TYR I 106 PHE 0.014 0.002 PHE B 29 TRP 0.022 0.002 TRP I 102 HIS 0.007 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14302) covalent geometry : angle 0.60717 / 0.31 (19462) SS BOND : bond 0.00517 / 0.38 ( 22) SS BOND : angle 0.90799 / 0.63 ( 44) hydrogen bonds : bond 0.03367 / 2.30 ( 507) hydrogen bonds : angle 5.61577 / 3.82 ( 1431) link_BETA1-4 : bond 0.00184 / 0.10 ( 1) link_BETA1-4 : angle 1.11260 / 0.60 ( 3) link_BETA1-6 : bond 0.00164 / 0.08 ( 2) link_BETA1-6 : angle 1.54559 / 0.93 ( 6) link_NAG-ASN : bond 0.00047 / 0.02 ( 1) link_NAG-ASN : angle 2.63635 / 1.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8014 (tmtt) cc_final: 0.7596 (tmtt) REVERT: A 37 LYS cc_start: 0.7245 (mmtt) cc_final: 0.6924 (mmtt) REVERT: A 41 MET cc_start: 0.6699 (mmm) cc_final: 0.6206 (mmm) REVERT: A 307 ASP cc_start: 0.6970 (t0) cc_final: 0.6721 (t0) REVERT: A 427 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6927 (mtt) REVERT: F 26 LEU cc_start: 0.8321 (mm) cc_final: 0.8117 (mt) REVERT: F 31 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7000 (mmtt) REVERT: F 232 PHE cc_start: 0.6648 (m-80) cc_final: 0.6141 (m-80) REVERT: F 284 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7474 (ttp80) REVERT: F 302 TYR cc_start: 0.7692 (m-80) cc_final: 0.7444 (m-80) REVERT: F 306 ARG cc_start: 0.7446 (mtt90) cc_final: 0.7126 (mtt90) REVERT: F 421 MET cc_start: 0.7471 (mtt) cc_final: 0.7151 (mmm) REVERT: B 58 THR cc_start: 0.7744 (p) cc_final: 0.7503 (p) REVERT: G 100 PHE cc_start: 0.2630 (OUTLIER) cc_final: -0.0682 (t80) REVERT: G 115 ASN cc_start: 0.7078 (OUTLIER) cc_final: 0.6413 (p0) REVERT: H 97 LEU cc_start: 0.2610 (OUTLIER) cc_final: 0.2150 (mp) REVERT: D 50 ILE cc_start: 0.8013 (mt) cc_final: 0.7584 (mt) REVERT: D 108 LYS cc_start: 0.5064 (OUTLIER) cc_final: 0.4652 (ptpt) REVERT: E 91 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5107 (mtt180) outliers start: 71 outliers final: 36 residues processed: 219 average time/residue: 0.3552 time to fit residues: 88.2828 Evaluate side-chains 202 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 171 optimal weight: 0.0020 chunk 36 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN F 167 ASN F 377 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN G 39 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.172679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155715 restraints weight = 19787.703| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.14 r_work: 0.3948 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14328 Z= 0.189 Angle : 0.664 11.495 19518 Z= 0.333 Chirality : 0.045 0.157 2162 Planarity : 0.005 0.051 2493 Dihedral : 5.523 48.195 2077 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.57 % Allowed : 20.17 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.24 (0.19), residues: 1774 helix: -0.00 (0.88), residues: 32 sheet: 0.46 (0.18), residues: 797 loop : -0.69 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 45 TYR 0.035 0.002 TYR J 32 PHE 0.017 0.002 PHE B 29 TRP 0.025 0.002 TRP I 102 HIS 0.008 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (14302) covalent geometry : angle 0.66121 / 0.33 (19462) SS BOND : bond 0.00647 / 0.49 ( 22) SS BOND : angle 1.08618 / 0.76 ( 44) hydrogen bonds : bond 0.03641 / 2.50 ( 507) hydrogen bonds : angle 5.64511 / 3.82 ( 1431) link_BETA1-4 : bond 0.00034 / 0.02 ( 1) link_BETA1-4 : angle 1.00688 / 0.54 ( 3) link_BETA1-6 : bond 0.00892 / 0.43 ( 2) link_BETA1-6 : angle 1.47204 / 0.85 ( 6) link_NAG-ASN : bond 0.00033 / 0.02 ( 1) link_NAG-ASN : angle 2.57692 / 1.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 170 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7649 (tmtt) REVERT: A 37 LYS cc_start: 0.7273 (mmtt) cc_final: 0.6933 (mmtt) REVERT: A 41 MET cc_start: 0.6587 (mmm) cc_final: 0.6224 (mmm) REVERT: A 307 ASP cc_start: 0.7005 (t0) cc_final: 0.6755 (t0) REVERT: A 427 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6922 (mtt) REVERT: F 232 PHE cc_start: 0.6727 (m-80) cc_final: 0.6243 (m-80) REVERT: F 306 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7159 (mtt90) REVERT: F 377 ASN cc_start: 0.4891 (OUTLIER) cc_final: 0.4545 (m-40) REVERT: F 421 MET cc_start: 0.7439 (mtt) cc_final: 0.7119 (mmm) REVERT: G 32 TYR cc_start: 0.4440 (OUTLIER) cc_final: 0.3695 (m-80) REVERT: G 100 PHE cc_start: 0.2959 (OUTLIER) cc_final: -0.0595 (t80) REVERT: G 115 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6966 (t0) REVERT: D 50 ILE cc_start: 0.8085 (mt) cc_final: 0.7658 (mt) REVERT: E 91 ARG cc_start: 0.5924 (OUTLIER) cc_final: 0.5078 (mtt180) REVERT: I 107 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6546 (mt) outliers start: 87 outliers final: 47 residues processed: 237 average time/residue: 0.3743 time to fit residues: 100.5297 Evaluate side-chains 223 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 17 GLU Chi-restraints excluded: chain J residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 92 optimal weight: 0.9990 chunk 158 optimal weight: 0.0970 chunk 161 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.172440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155739 restraints weight = 19537.763| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.11 r_work: 0.3947 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14328 Z= 0.171 Angle : 0.650 11.466 19518 Z= 0.325 Chirality : 0.045 0.156 2162 Planarity : 0.005 0.053 2493 Dihedral : 5.518 51.505 2077 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.12 % Allowed : 21.00 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.29 (0.19), residues: 1774 helix: 0.02 (0.89), residues: 32 sheet: 0.52 (0.18), residues: 774 loop : -0.78 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 101 TYR 0.038 0.002 TYR J 32 PHE 0.016 0.002 PHE I 80 TRP 0.023 0.002 TRP I 102 HIS 0.008 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (14302) covalent geometry : angle 0.64701 / 0.32 (19462) SS BOND : bond 0.00591 / 0.44 ( 22) SS BOND : angle 1.22591 / 0.86 ( 44) hydrogen bonds : bond 0.03502 / 2.40 ( 507) hydrogen bonds : angle 5.55347 / 3.76 ( 1431) link_BETA1-4 : bond 0.00186 / 0.10 ( 1) link_BETA1-4 : angle 1.02767 / 0.55 ( 3) link_BETA1-6 : bond 0.00069 / 0.03 ( 2) link_BETA1-6 : angle 1.54498 / 0.93 ( 6) link_NAG-ASN : bond 0.00054 / 0.03 ( 1) link_NAG-ASN : angle 2.74825 / 1.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 169 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7673 (tmtt) REVERT: A 37 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6943 (mmtt) REVERT: A 41 MET cc_start: 0.6512 (mmm) cc_final: 0.6210 (mmm) REVERT: A 78 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.7002 (ttp80) REVERT: A 307 ASP cc_start: 0.7060 (t0) cc_final: 0.6795 (t0) REVERT: A 381 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6877 (mtp180) REVERT: A 427 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6916 (mtt) REVERT: F 232 PHE cc_start: 0.6722 (m-80) cc_final: 0.6283 (m-80) REVERT: F 306 ARG cc_start: 0.7434 (mtt90) cc_final: 0.7115 (mtt90) REVERT: F 421 MET cc_start: 0.7448 (mtt) cc_final: 0.7134 (mmm) REVERT: G 32 TYR cc_start: 0.4620 (OUTLIER) cc_final: 0.3546 (m-80) REVERT: G 100 PHE cc_start: 0.2808 (OUTLIER) cc_final: -0.0552 (t80) REVERT: G 115 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6661 (p0) REVERT: H 97 LEU cc_start: 0.2969 (OUTLIER) cc_final: 0.2517 (mp) REVERT: D 50 ILE cc_start: 0.7982 (mt) cc_final: 0.7549 (mt) REVERT: E 91 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5167 (mtt180) REVERT: I 107 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6545 (mt) outliers start: 80 outliers final: 51 residues processed: 232 average time/residue: 0.3688 time to fit residues: 97.3612 Evaluate side-chains 222 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 163 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 36 ASN Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 150 optimal weight: 0.0170 chunk 174 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 44 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 117 optimal weight: 0.1980 chunk 162 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN F 167 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.174316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157588 restraints weight = 19500.176| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.12 r_work: 0.3973 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14328 Z= 0.109 Angle : 0.591 10.818 19518 Z= 0.294 Chirality : 0.044 0.242 2162 Planarity : 0.005 0.046 2493 Dihedral : 5.276 54.482 2077 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.97 % Allowed : 22.15 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.14 (0.19), residues: 1774 helix: 0.65 (0.97), residues: 32 sheet: 0.64 (0.19), residues: 762 loop : -0.71 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 45 TYR 0.026 0.001 TYR J 32 PHE 0.015 0.001 PHE I 80 TRP 0.021 0.002 TRP I 102 HIS 0.005 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (14302) covalent geometry : angle 0.58829 / 0.29 (19462) SS BOND : bond 0.00419 / 0.30 ( 22) SS BOND : angle 0.85416 / 0.60 ( 44) hydrogen bonds : bond 0.03001 / 2.07 ( 507) hydrogen bonds : angle 5.32207 / 3.62 ( 1431) link_BETA1-4 : bond 0.00151 / 0.08 ( 1) link_BETA1-4 : angle 1.15556 / 0.62 ( 3) link_BETA1-6 : bond 0.00142 / 0.07 ( 2) link_BETA1-6 : angle 1.41263 / 0.89 ( 6) link_NAG-ASN : bond 0.00104 / 0.05 ( 1) link_NAG-ASN : angle 3.02590 / 1.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7661 (tmtt) REVERT: A 37 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6885 (mmtt) REVERT: A 41 MET cc_start: 0.6527 (mmm) cc_final: 0.6228 (mmm) REVERT: A 307 ASP cc_start: 0.7026 (t0) cc_final: 0.6757 (t0) REVERT: A 427 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6879 (mtt) REVERT: F 232 PHE cc_start: 0.6714 (m-80) cc_final: 0.6299 (m-80) REVERT: F 306 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7191 (mtt90) REVERT: F 421 MET cc_start: 0.7415 (mtt) cc_final: 0.7072 (mmm) REVERT: G 32 TYR cc_start: 0.4561 (OUTLIER) cc_final: 0.3570 (m-80) REVERT: G 100 PHE cc_start: 0.2511 (OUTLIER) cc_final: -0.0699 (t80) REVERT: G 115 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6647 (p0) REVERT: D 50 ILE cc_start: 0.7962 (mt) cc_final: 0.7487 (mt) REVERT: D 108 LYS cc_start: 0.4986 (OUTLIER) cc_final: 0.4573 (ptpt) REVERT: E 91 ARG cc_start: 0.5831 (OUTLIER) cc_final: 0.5218 (mtt180) outliers start: 62 outliers final: 33 residues processed: 212 average time/residue: 0.3794 time to fit residues: 90.7101 Evaluate side-chains 199 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 87 optimal weight: 0.1980 chunk 113 optimal weight: 0.0870 chunk 160 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.173128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156541 restraints weight = 19446.060| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.10 r_work: 0.3962 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14328 Z= 0.143 Angle : 0.619 11.505 19518 Z= 0.307 Chirality : 0.044 0.220 2162 Planarity : 0.005 0.050 2493 Dihedral : 5.166 45.628 2073 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.52 % Allowed : 22.60 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.18 (0.19), residues: 1774 helix: 0.58 (0.95), residues: 32 sheet: 0.61 (0.18), residues: 765 loop : -0.73 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 45 TYR 0.031 0.002 TYR I 106 PHE 0.016 0.002 PHE I 80 TRP 0.023 0.002 TRP I 102 HIS 0.006 0.001 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (14302) covalent geometry : angle 0.61589 / 0.31 (19462) SS BOND : bond 0.00515 / 0.38 ( 22) SS BOND : angle 1.00187 / 0.71 ( 44) hydrogen bonds : bond 0.03192 / 2.20 ( 507) hydrogen bonds : angle 5.35721 / 3.64 ( 1431) link_BETA1-4 : bond 0.00197 / 0.10 ( 1) link_BETA1-4 : angle 1.05605 / 0.57 ( 3) link_BETA1-6 : bond 0.00096 / 0.05 ( 2) link_BETA1-6 : angle 1.39384 / 0.89 ( 6) link_NAG-ASN : bond 0.00042 / 0.02 ( 1) link_NAG-ASN : angle 2.93272 / 1.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 157 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8066 (tmtt) cc_final: 0.7658 (tmtt) REVERT: A 37 LYS cc_start: 0.7278 (mmtt) cc_final: 0.6925 (mmtt) REVERT: A 41 MET cc_start: 0.6508 (mmm) cc_final: 0.6218 (mmm) REVERT: A 307 ASP cc_start: 0.7041 (t0) cc_final: 0.6767 (t0) REVERT: A 427 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6883 (mtt) REVERT: F 232 PHE cc_start: 0.6719 (m-80) cc_final: 0.6311 (m-80) REVERT: F 306 ARG cc_start: 0.7426 (mtt90) cc_final: 0.7129 (mtt90) REVERT: F 421 MET cc_start: 0.7413 (mtt) cc_final: 0.7079 (mmm) REVERT: G 32 TYR cc_start: 0.4725 (OUTLIER) cc_final: 0.3458 (m-80) REVERT: G 34 MET cc_start: 0.6379 (ptp) cc_final: 0.5700 (ptp) REVERT: G 100 PHE cc_start: 0.2856 (OUTLIER) cc_final: -0.0417 (t80) REVERT: G 115 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.6704 (p0) REVERT: H 35 ASN cc_start: 0.0946 (OUTLIER) cc_final: -0.0977 (m-40) REVERT: D 50 ILE cc_start: 0.7950 (mt) cc_final: 0.7463 (mt) REVERT: D 108 LYS cc_start: 0.5028 (OUTLIER) cc_final: 0.4575 (ptpt) REVERT: E 91 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5287 (mtt180) outliers start: 55 outliers final: 37 residues processed: 200 average time/residue: 0.3737 time to fit residues: 84.5412 Evaluate side-chains 204 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 425 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 26 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN A 133 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.170494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153966 restraints weight = 19517.308| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.10 r_work: 0.3926 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 14328 Z= 0.229 Angle : 0.723 14.343 19518 Z= 0.360 Chirality : 0.047 0.292 2162 Planarity : 0.006 0.063 2493 Dihedral : 5.629 45.661 2073 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.16 % Allowed : 22.60 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.45 (0.19), residues: 1774 helix: -0.29 (0.85), residues: 32 sheet: 0.52 (0.18), residues: 757 loop : -0.97 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 101 TYR 0.032 0.002 TYR I 106 PHE 0.021 0.003 PHE G 27 TRP 0.027 0.003 TRP I 102 HIS 0.011 0.002 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (14302) covalent geometry : angle 0.71890 / 0.36 (19462) SS BOND : bond 0.00752 / 0.58 ( 22) SS BOND : angle 1.43500 / 1.01 ( 44) hydrogen bonds : bond 0.03839 / 2.63 ( 507) hydrogen bonds : angle 5.73136 / 3.89 ( 1431) link_BETA1-4 : bond 0.00214 / 0.11 ( 1) link_BETA1-4 : angle 0.96018 / 0.52 ( 3) link_BETA1-6 : bond 0.00133 / 0.06 ( 2) link_BETA1-6 : angle 1.55663 / 1.00 ( 6) link_NAG-ASN : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : angle 2.77150 / 1.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 0.333 Fit side-chains REVERT: A 34 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7665 (tmtt) REVERT: A 41 MET cc_start: 0.6482 (mmm) cc_final: 0.6271 (mmm) REVERT: A 133 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: A 307 ASP cc_start: 0.7112 (t0) cc_final: 0.6825 (t0) REVERT: A 427 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6941 (mtt) REVERT: F 232 PHE cc_start: 0.6781 (m-80) cc_final: 0.6387 (m-80) REVERT: F 306 ARG cc_start: 0.7421 (mtt90) cc_final: 0.7102 (mtt90) REVERT: F 421 MET cc_start: 0.7410 (mtt) cc_final: 0.7115 (mmm) REVERT: G 32 TYR cc_start: 0.4679 (OUTLIER) cc_final: 0.2982 (m-80) REVERT: G 100 PHE cc_start: 0.3159 (OUTLIER) cc_final: -0.0371 (t80) REVERT: G 115 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.6815 (p0) REVERT: H 35 ASN cc_start: 0.1038 (OUTLIER) cc_final: -0.0603 (m-40) REVERT: D 50 ILE cc_start: 0.8117 (mt) cc_final: 0.7648 (mp) REVERT: E 91 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5234 (mtt180) outliers start: 65 outliers final: 41 residues processed: 210 average time/residue: 0.3587 time to fit residues: 85.3120 Evaluate side-chains 207 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 143 SER Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 14 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.171863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.155367 restraints weight = 19520.881| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.10 r_work: 0.3944 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14328 Z= 0.156 Angle : 0.660 12.956 19518 Z= 0.327 Chirality : 0.045 0.164 2162 Planarity : 0.005 0.057 2493 Dihedral : 5.511 47.512 2073 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.59 % Allowed : 23.43 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.36 (0.19), residues: 1774 helix: 0.14 (0.93), residues: 32 sheet: 0.57 (0.19), residues: 749 loop : -0.90 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 45 TYR 0.029 0.002 TYR I 106 PHE 0.016 0.002 PHE I 80 TRP 0.025 0.002 TRP I 102 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (14302) covalent geometry : angle 0.65464 / 0.33 (19462) SS BOND : bond 0.00571 / 0.43 ( 22) SS BOND : angle 1.04952 / 0.73 ( 44) hydrogen bonds : bond 0.03370 / 2.32 ( 507) hydrogen bonds : angle 5.55327 / 3.79 ( 1431) link_BETA1-4 : bond 0.00214 / 0.11 ( 1) link_BETA1-4 : angle 1.07435 / 0.58 ( 3) link_BETA1-6 : bond 0.00399 / 0.21 ( 2) link_BETA1-6 : angle 1.26985 / 0.88 ( 6) link_NAG-ASN : bond 0.00955 / 0.50 ( 1) link_NAG-ASN : angle 5.61996 / 3.19 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 34 LYS cc_start: 0.8060 (tmtt) cc_final: 0.7664 (tmtt) REVERT: A 37 LYS cc_start: 0.7293 (mmtt) cc_final: 0.7018 (mmtt) REVERT: A 133 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: A 307 ASP cc_start: 0.7069 (t0) cc_final: 0.6791 (t0) REVERT: A 427 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6909 (mtt) REVERT: F 232 PHE cc_start: 0.6777 (m-80) cc_final: 0.6403 (m-80) REVERT: F 306 ARG cc_start: 0.7418 (mtt90) cc_final: 0.7131 (mtt90) REVERT: F 421 MET cc_start: 0.7376 (mtt) cc_final: 0.7063 (mmm) REVERT: G 32 TYR cc_start: 0.4626 (OUTLIER) cc_final: 0.2939 (m-80) REVERT: G 34 MET cc_start: 0.6256 (ptp) cc_final: 0.6047 (ptp) REVERT: G 100 PHE cc_start: 0.3063 (OUTLIER) cc_final: -0.0301 (t80) REVERT: G 115 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.6744 (p0) REVERT: H 35 ASN cc_start: 0.1016 (OUTLIER) cc_final: -0.0388 (m-40) REVERT: D 50 ILE cc_start: 0.8048 (mt) cc_final: 0.7571 (mt) REVERT: E 91 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5220 (mtt180) outliers start: 56 outliers final: 37 residues processed: 203 average time/residue: 0.3684 time to fit residues: 84.5461 Evaluate side-chains 201 residues out of total 1562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 397 THR Chi-restraints excluded: chain F residue 424 LYS Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 35 ASN Chi-restraints excluded: chain H residue 76 PHE Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 93 CYS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 102 TRP Chi-restraints excluded: chain I residue 120 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 145 optimal weight: 0.1980 chunk 64 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 104 optimal weight: 0.0030 chunk 119 optimal weight: 0.5980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.172676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156187 restraints weight = 19427.424| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.10 r_work: 0.3954 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14328 Z= 0.134 Angle : 0.641 13.059 19518 Z= 0.315 Chirality : 0.045 0.160 2162 Planarity : 0.005 0.056 2493 Dihedral : 5.398 48.978 2073 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.20 % Allowed : 23.82 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.77 % 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: -0.30 (0.19), residues: 1774 helix: 0.38 (0.97), residues: 32 sheet: 0.62 (0.19), residues: 749 loop : -0.88 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 45 TYR 0.026 0.002 TYR I 106 PHE 0.015 0.002 PHE I 80 TRP 0.024 0.002 TRP I 102 HIS 0.004 0.001 HIS G 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (14302) covalent geometry : angle 0.63466 / 0.31 (19462) SS BOND : bond 0.00501 / 0.37 ( 22) SS BOND : angle 0.96033 / 0.67 ( 44) hydrogen bonds : bond 0.03159 / 2.18 ( 507) hydrogen bonds : angle 5.43230 / 3.71 ( 1431) link_BETA1-4 : bond 0.00017 / 0.01 ( 1) link_BETA1-4 : angle 1.09351 / 0.58 ( 3) link_BETA1-6 : bond 0.00745 / 0.39 ( 2) link_BETA1-6 : angle 1.32580 / 0.96 ( 6) link_NAG-ASN : bond 0.00941 / 0.50 ( 1) link_NAG-ASN : angle 6.30801 / 3.60 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.74 seconds wall clock time: 68 minutes 12.65 seconds (4092.65 seconds total)