Starting phenix.real_space_refine on Wed Mar 4 19:04:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7upa_26659/03_2026/7upa_26659.cif Found real_map, /net/cci-nas-00/data/ceres_data/7upa_26659/03_2026/7upa_26659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7upa_26659/03_2026/7upa_26659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7upa_26659/03_2026/7upa_26659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7upa_26659/03_2026/7upa_26659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7upa_26659/03_2026/7upa_26659.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.141 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 87 5.16 5 C 9940 2.51 5 N 2586 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15745 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3462 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 16, 'TRANS': 433} Chain breaks: 1 Chain: "D" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3446 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "G" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3446 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 16, 'TRANS': 430} Chain breaks: 1 Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "C" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 924 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.32, per 1000 atoms: 0.21 Number of scatterers: 15745 At special positions: 0 Unit cell: (145.2, 132, 122.1, 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 87 16.00 O 3132 8.00 N 2586 7.00 C 9940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.04 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.04 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 610.8 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3754 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 21 sheets defined 30.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.851A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.836A pdb=" N LYS H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.828A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.651A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.644A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.896A pdb=" N CYS A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 72' Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.854A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.953A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.952A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.601A pdb=" N SER A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.611A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.918A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 removed outlier: 4.002A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.639A pdb=" N CYS A 363 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.695A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 480 removed outlier: 3.838A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.703A pdb=" N LYS D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.750A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.938A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 86 " --> pdb=" O ARG D 82 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.942A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 145 removed outlier: 4.374A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP D 142 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 182 removed outlier: 3.666A pdb=" N ILE D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 215 removed outlier: 4.006A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.776A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.648A pdb=" N CYS D 363 " --> pdb=" O THR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.741A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 480 removed outlier: 3.763A pdb=" N SER D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 477 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.683A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.986A pdb=" N SER G 69 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 99 removed outlier: 3.587A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.814A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 145 removed outlier: 4.389A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA G 141 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP G 142 " --> pdb=" O MET G 138 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 182 removed outlier: 3.626A pdb=" N ILE G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.692A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.855A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.554A pdb=" N CYS G 363 " --> pdb=" O THR G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.740A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 480 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.862A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.731A pdb=" N LYS B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.707A pdb=" N SER B 87 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.706A pdb=" N ILE E 83 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.796A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.682A pdb=" N LYS C 64 " --> pdb=" O GLN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.730A pdb=" N SER C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.653A pdb=" N ASP F 82 " --> pdb=" O GLU F 79 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE F 83 " --> pdb=" O GLN F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 56 through 59 current: chain 'H' and resid 100B through 103 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 100B through 103 current: chain 'A' and resid 168 through 173 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 173 current: chain 'A' and resid 263 through 270 removed outlier: 3.905A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 288 current: chain 'A' and resid 315 through 319 removed outlier: 6.483A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 322 through 326 current: chain 'A' and resid 337 through 340 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 12 current: chain 'L' and resid 44 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.564A pdb=" N VAL A 113 " --> pdb=" O ILE G 426 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N SER G 428 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET A 115 " --> pdb=" O SER G 428 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G 399 " --> pdb=" O CYS G 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.944A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 60 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 167 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 167 through 173 current: chain 'D' and resid 263 through 270 removed outlier: 6.023A pdb=" N GLY D 264 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR D 281 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE D 266 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG D 279 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR D 268 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR D 275 " --> pdb=" O ASP D 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 288 current: chain 'D' and resid 315 through 319 removed outlier: 6.474A pdb=" N PHE D 315 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE D 326 " --> pdb=" O PHE D 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 322 through 326 current: chain 'D' and resid 337 through 340 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 337 through 340 current: chain 'C' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 59 current: chain 'C' and resid 100B through 103 Processing sheet with id=AB2, first strand: chain 'D' and resid 301 through 303 Processing sheet with id=AB3, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'D' and resid 399 through 400 removed outlier: 3.523A pdb=" N ARG D 399 " --> pdb=" O CYS D 394 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 38 through 60 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 168 through 173 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 168 through 173 current: chain 'G' and resid 263 through 270 removed outlier: 5.971A pdb=" N GLY G 264 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR G 281 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE G 266 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG G 279 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR G 268 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR G 275 " --> pdb=" O ASP G 270 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 288 current: chain 'G' and resid 315 through 319 removed outlier: 6.486A pdb=" N PHE G 315 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE G 326 " --> pdb=" O PHE G 315 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 322 through 326 current: chain 'G' and resid 337 through 340 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 337 through 340 current: chain 'B' and resid 44 through 52 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 59 current: chain 'B' and resid 100B through 103 Processing sheet with id=AB6, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.734A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 10 through 12 current: chain 'F' and resid 44 through 49 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 53 through 54 current: chain 'F' and resid 97 through 98 493 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5065 1.35 - 1.47: 3722 1.47 - 1.59: 7096 1.59 - 1.71: 0 1.71 - 1.83: 126 Bond restraints: 16009 Sorted by residual: bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG D 503 " pdb=" O5 NAG D 503 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG G 502 " pdb=" O5 NAG G 502 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 16004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 21158 1.66 - 3.33: 477 3.33 - 4.99: 46 4.99 - 6.65: 30 6.65 - 8.32: 13 Bond angle restraints: 21724 Sorted by residual: angle pdb=" CG ARG A 399 " pdb=" CD ARG A 399 " pdb=" NE ARG A 399 " ideal model delta sigma weight residual 112.00 120.05 -8.05 2.20e+00 2.07e-01 1.34e+01 angle pdb=" CA GLU H 85 " pdb=" CB GLU H 85 " pdb=" CG GLU H 85 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CG ARG G 399 " pdb=" CD ARG G 399 " pdb=" NE ARG G 399 " ideal model delta sigma weight residual 112.00 119.74 -7.74 2.20e+00 2.07e-01 1.24e+01 angle pdb=" CB GLU H 85 " pdb=" CG GLU H 85 " pdb=" CD GLU H 85 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.70e+00 3.46e-01 1.14e+01 angle pdb=" CA GLU C 85 " pdb=" CB GLU C 85 " pdb=" CG GLU C 85 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 ... (remaining 21719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8821 17.90 - 35.81: 760 35.81 - 53.71: 221 53.71 - 71.61: 45 71.61 - 89.52: 13 Dihedral angle restraints: 9860 sinusoidal: 4006 harmonic: 5854 Sorted by residual: dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -169.16 83.16 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -164.95 78.95 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 392 " pdb=" CB CYS A 392 " ideal model delta sinusoidal sigma weight residual 93.00 43.70 49.30 1 1.00e+01 1.00e-02 3.34e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2123 0.061 - 0.121: 411 0.121 - 0.182: 53 0.182 - 0.243: 4 0.243 - 0.303: 1 Chirality restraints: 2592 Sorted by residual: chirality pdb=" C1 NAG D 502 " pdb=" ND2 ASN D 99 " pdb=" C2 NAG D 502 " pdb=" O5 NAG D 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C1 NAG G 501 " pdb=" ND2 ASN G 67 " pdb=" C2 NAG G 501 " pdb=" O5 NAG G 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA ASN L 77 " pdb=" N ASN L 77 " pdb=" C ASN L 77 " pdb=" CB ASN L 77 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2589 not shown) Planarity restraints: 2751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 336 " -0.155 9.50e-02 1.11e+02 7.02e-02 3.99e+00 pdb=" NE ARG G 336 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG G 336 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G 336 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 336 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 85 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" CD GLU C 85 " 0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU C 85 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU C 85 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 399 " -0.153 9.50e-02 1.11e+02 6.91e-02 3.77e+00 pdb=" NE ARG D 399 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 399 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 399 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 399 " -0.000 2.00e-02 2.50e+03 ... (remaining 2748 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2052 2.76 - 3.30: 13544 3.30 - 3.83: 23921 3.83 - 4.37: 28183 4.37 - 4.90: 50626 Nonbonded interactions: 118326 Sorted by model distance: nonbonded pdb=" OD2 ASP B 72 " pdb=" OG SER B 75 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLU D 327 " pdb=" OG1 THR D 346 " model vdw 2.229 3.040 nonbonded pdb=" OE1 GLU G 327 " pdb=" OG1 THR G 346 " model vdw 2.251 3.040 nonbonded pdb=" N GLU A 251 " pdb=" OE1 GLU A 251 " model vdw 2.252 3.120 nonbonded pdb=" OE1 GLU A 327 " pdb=" OG1 THR A 346 " model vdw 2.261 3.040 ... (remaining 118321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 104 or resid 112 through 504)) selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.420 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.070 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 0.042 16045 Z= 0.162 Angle : 0.660 10.771 21808 Z= 0.350 Chirality : 0.048 0.303 2592 Planarity : 0.005 0.070 2739 Dihedral : 14.864 89.515 6034 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.96 % Allowed : 11.80 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.34 (0.19), residues: 1992 helix: 1.88 (0.27), residues: 411 sheet: 0.74 (0.20), residues: 647 loop : -0.92 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 336 TYR 0.014 0.001 TYR D 473 PHE 0.009 0.001 PHE D 301 TRP 0.006 0.001 TRP C 103 HIS 0.002 0.000 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00336 (16009) covalent geometry : angle 0.64514 (21724) SS BOND : bond 0.00587 ( 24) SS BOND : angle 1.28701 ( 48) hydrogen bonds : bond 0.18368 ( 493) hydrogen bonds : angle 5.03401 ( 1305) link_NAG-ASN : bond 0.00620 ( 12) link_NAG-ASN : angle 3.28557 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.599 Fit side-chains REVERT: L 23 CYS cc_start: 0.6180 (t) cc_final: 0.5810 (t) REVERT: A 244 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7633 (mmt90) REVERT: E 24 ARG cc_start: 0.7133 (mtp-110) cc_final: 0.6579 (ttm110) REVERT: E 105 GLU cc_start: 0.7827 (pp20) cc_final: 0.7333 (pm20) outliers start: 17 outliers final: 15 residues processed: 180 average time/residue: 0.7753 time to fit residues: 150.6711 Evaluate side-chains 179 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 186 THR Chi-restraints excluded: chain G residue 252 ASP Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 321 THR Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN E 3 GLN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074130 restraints weight = 25580.294| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.73 r_work: 0.2930 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16045 Z= 0.128 Angle : 0.557 10.298 21808 Z= 0.296 Chirality : 0.046 0.291 2592 Planarity : 0.004 0.038 2739 Dihedral : 6.237 59.581 2435 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.54 % Allowed : 10.45 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.55 (0.19), residues: 1992 helix: 2.09 (0.27), residues: 424 sheet: 0.76 (0.21), residues: 634 loop : -0.73 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 24 TYR 0.012 0.001 TYR D 473 PHE 0.009 0.001 PHE E 87 TRP 0.006 0.001 TRP B 103 HIS 0.001 0.001 HIS G 29 Details of bonding type rmsd covalent geometry : bond 0.00284 (16009) covalent geometry : angle 0.53702 (21724) SS BOND : bond 0.00606 ( 24) SS BOND : angle 1.32886 ( 48) hydrogen bonds : bond 0.05369 ( 493) hydrogen bonds : angle 4.22689 ( 1305) link_NAG-ASN : bond 0.00580 ( 12) link_NAG-ASN : angle 3.38006 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: H 95 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: L 23 CYS cc_start: 0.7296 (t) cc_final: 0.6722 (t) REVERT: L 79 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7318 (mp0) REVERT: D 322 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7536 (mm) REVERT: B 73 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8494 (mttt) REVERT: B 95 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: E 105 GLU cc_start: 0.7836 (pp20) cc_final: 0.7135 (pm20) REVERT: F 77 ASN cc_start: 0.7971 (p0) cc_final: 0.7498 (p0) REVERT: F 105 GLU cc_start: 0.8078 (pp20) cc_final: 0.7853 (pp20) outliers start: 45 outliers final: 22 residues processed: 191 average time/residue: 0.7356 time to fit residues: 152.1953 Evaluate side-chains 190 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 136 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 6 GLN B 61 GLN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073326 restraints weight = 25720.861| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.75 r_work: 0.2914 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16045 Z= 0.133 Angle : 0.560 10.473 21808 Z= 0.298 Chirality : 0.046 0.284 2592 Planarity : 0.004 0.040 2739 Dihedral : 6.045 89.224 2418 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.16 % Allowed : 11.41 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.54 (0.19), residues: 1992 helix: 2.28 (0.27), residues: 420 sheet: 0.68 (0.20), residues: 647 loop : -0.79 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 24 TYR 0.013 0.001 TYR D 473 PHE 0.010 0.001 PHE E 87 TRP 0.006 0.001 TRP B 103 HIS 0.002 0.001 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00300 (16009) covalent geometry : angle 0.54192 (21724) SS BOND : bond 0.00641 ( 24) SS BOND : angle 1.36424 ( 48) hydrogen bonds : bond 0.05398 ( 493) hydrogen bonds : angle 4.10994 ( 1305) link_NAG-ASN : bond 0.00509 ( 12) link_NAG-ASN : angle 3.24351 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8444 (t0) cc_final: 0.8229 (t0) REVERT: H 95 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: L 23 CYS cc_start: 0.7320 (t) cc_final: 0.6758 (t) REVERT: L 79 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7364 (mp0) REVERT: A 463 MET cc_start: 0.8714 (mtp) cc_final: 0.8143 (mtm) REVERT: D 322 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7509 (mm) REVERT: B 73 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8488 (mttt) REVERT: E 11 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7731 (tt) REVERT: E 105 GLU cc_start: 0.7918 (pp20) cc_final: 0.7218 (pm20) REVERT: C 10 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: F 77 ASN cc_start: 0.8004 (p0) cc_final: 0.7476 (p0) REVERT: F 105 GLU cc_start: 0.8092 (pp20) cc_final: 0.7588 (pp20) outliers start: 56 outliers final: 28 residues processed: 201 average time/residue: 0.7348 time to fit residues: 160.4805 Evaluate side-chains 192 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 61 GLN E 3 GLN C 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071490 restraints weight = 25538.070| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.74 r_work: 0.2877 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16045 Z= 0.179 Angle : 0.631 11.567 21808 Z= 0.337 Chirality : 0.049 0.275 2592 Planarity : 0.005 0.042 2739 Dihedral : 6.227 88.350 2418 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.22 % Allowed : 12.08 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.38 (0.19), residues: 1992 helix: 2.20 (0.27), residues: 420 sheet: 0.62 (0.21), residues: 594 loop : -0.87 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.015 0.002 TYR B 98 PHE 0.013 0.001 PHE E 87 TRP 0.008 0.001 TRP B 103 HIS 0.002 0.001 HIS G 29 Details of bonding type rmsd covalent geometry : bond 0.00424 (16009) covalent geometry : angle 0.61083 (21724) SS BOND : bond 0.00846 ( 24) SS BOND : angle 1.79914 ( 48) hydrogen bonds : bond 0.06541 ( 493) hydrogen bonds : angle 4.17775 ( 1305) link_NAG-ASN : bond 0.00412 ( 12) link_NAG-ASN : angle 3.41093 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 165 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: L 23 CYS cc_start: 0.7627 (t) cc_final: 0.7161 (t) REVERT: L 79 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7344 (mp0) REVERT: A 322 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7109 (mm) REVERT: A 463 MET cc_start: 0.8761 (mtp) cc_final: 0.8120 (mtm) REVERT: D 70 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: D 322 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7509 (mm) REVERT: B 73 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8521 (mttt) REVERT: B 95 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: E 11 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7783 (tt) REVERT: E 105 GLU cc_start: 0.7880 (pp20) cc_final: 0.7212 (pm20) REVERT: C 10 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7992 (mm-30) REVERT: F 77 ASN cc_start: 0.8072 (p0) cc_final: 0.7628 (p0) outliers start: 57 outliers final: 33 residues processed: 203 average time/residue: 0.7336 time to fit residues: 161.3335 Evaluate side-chains 203 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain G residue 71 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 61 GLN E 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.097321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.070602 restraints weight = 25566.049| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.74 r_work: 0.2859 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16045 Z= 0.207 Angle : 0.680 12.174 21808 Z= 0.362 Chirality : 0.050 0.273 2592 Planarity : 0.005 0.043 2739 Dihedral : 6.427 87.710 2418 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.67 % Allowed : 12.20 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.27 (0.19), residues: 1992 helix: 2.22 (0.26), residues: 412 sheet: 0.57 (0.21), residues: 594 loop : -0.99 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.017 0.002 TYR B 98 PHE 0.014 0.002 PHE E 87 TRP 0.009 0.001 TRP B 103 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00498 (16009) covalent geometry : angle 0.65633 (21724) SS BOND : bond 0.00938 ( 24) SS BOND : angle 2.05054 ( 48) hydrogen bonds : bond 0.07097 ( 493) hydrogen bonds : angle 4.23651 ( 1305) link_NAG-ASN : bond 0.00537 ( 12) link_NAG-ASN : angle 3.76308 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 163 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: L 23 CYS cc_start: 0.7502 (t) cc_final: 0.6909 (t) REVERT: L 79 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7465 (mp0) REVERT: A 244 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8357 (mmt90) REVERT: A 322 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7164 (mm) REVERT: A 361 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: A 463 MET cc_start: 0.8791 (mtp) cc_final: 0.8169 (mtm) REVERT: D 70 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: D 166 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: D 322 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7524 (mm) REVERT: D 417 CYS cc_start: 0.5419 (OUTLIER) cc_final: 0.5039 (t) REVERT: D 453 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7678 (tttm) REVERT: B 73 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8518 (mttt) REVERT: B 95 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: E 11 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7808 (tt) REVERT: E 105 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: C 10 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8002 (mm-30) REVERT: F 77 ASN cc_start: 0.8127 (p0) cc_final: 0.7808 (p0) outliers start: 65 outliers final: 34 residues processed: 209 average time/residue: 0.7390 time to fit residues: 167.2282 Evaluate side-chains 208 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 167 optimal weight: 0.0770 chunk 39 optimal weight: 0.6980 chunk 164 optimal weight: 0.0980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.073410 restraints weight = 25628.114| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.75 r_work: 0.2917 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16045 Z= 0.114 Angle : 0.546 10.838 21808 Z= 0.291 Chirality : 0.046 0.274 2592 Planarity : 0.004 0.043 2739 Dihedral : 6.016 92.110 2418 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.77 % Allowed : 13.27 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.39 (0.19), residues: 1992 helix: 2.37 (0.27), residues: 418 sheet: 0.59 (0.21), residues: 617 loop : -0.95 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 336 TYR 0.013 0.001 TYR D 473 PHE 0.008 0.001 PHE E 49 TRP 0.004 0.001 TRP B 103 HIS 0.001 0.000 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00247 (16009) covalent geometry : angle 0.52538 (21724) SS BOND : bond 0.00508 ( 24) SS BOND : angle 1.50114 ( 48) hydrogen bonds : bond 0.04801 ( 493) hydrogen bonds : angle 3.98949 ( 1305) link_NAG-ASN : bond 0.00556 ( 12) link_NAG-ASN : angle 3.36801 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: L 23 CYS cc_start: 0.7274 (t) cc_final: 0.6742 (t) REVERT: L 79 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7362 (mp0) REVERT: A 244 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8412 (mmt180) REVERT: A 322 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7080 (mm) REVERT: A 361 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: A 383 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8784 (tp) REVERT: A 463 MET cc_start: 0.8797 (mtp) cc_final: 0.8567 (mtp) REVERT: D 70 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: D 322 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7583 (mm) REVERT: D 417 CYS cc_start: 0.5340 (OUTLIER) cc_final: 0.4948 (t) REVERT: B 73 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8452 (mttt) REVERT: E 11 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7698 (tt) REVERT: E 18 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7994 (mmm-85) REVERT: E 105 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: F 77 ASN cc_start: 0.8126 (p0) cc_final: 0.7845 (p0) outliers start: 49 outliers final: 26 residues processed: 199 average time/residue: 0.7377 time to fit residues: 158.9036 Evaluate side-chains 200 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 114 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 61 GLN C 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.070933 restraints weight = 25480.496| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.73 r_work: 0.2867 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16045 Z= 0.193 Angle : 0.676 11.861 21808 Z= 0.358 Chirality : 0.050 0.286 2592 Planarity : 0.005 0.054 2739 Dihedral : 6.352 94.285 2418 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.33 % Allowed : 13.27 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.28 (0.19), residues: 1992 helix: 2.31 (0.27), residues: 412 sheet: 0.57 (0.21), residues: 594 loop : -1.01 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 336 TYR 0.015 0.002 TYR B 98 PHE 0.012 0.001 PHE E 87 TRP 0.008 0.001 TRP B 103 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00464 (16009) covalent geometry : angle 0.65261 (21724) SS BOND : bond 0.00898 ( 24) SS BOND : angle 2.32379 ( 48) hydrogen bonds : bond 0.06687 ( 493) hydrogen bonds : angle 4.14536 ( 1305) link_NAG-ASN : bond 0.00485 ( 12) link_NAG-ASN : angle 3.55150 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 165 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: L 23 CYS cc_start: 0.7496 (t) cc_final: 0.6912 (t) REVERT: L 79 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7434 (mp0) REVERT: A 244 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8410 (mmt180) REVERT: A 322 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7134 (mm) REVERT: A 383 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8755 (tt) REVERT: A 463 MET cc_start: 0.8766 (mtp) cc_final: 0.8151 (mtm) REVERT: D 322 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7573 (mm) REVERT: D 417 CYS cc_start: 0.5608 (OUTLIER) cc_final: 0.5217 (t) REVERT: G 327 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: B 73 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8493 (mttt) REVERT: E 11 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7797 (tt) REVERT: E 105 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: C 10 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: F 77 ASN cc_start: 0.8266 (p0) cc_final: 0.7914 (p0) REVERT: F 79 GLU cc_start: 0.7687 (mp0) cc_final: 0.7448 (mp0) outliers start: 59 outliers final: 34 residues processed: 205 average time/residue: 0.7258 time to fit residues: 161.5693 Evaluate side-chains 208 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 35 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071287 restraints weight = 25678.636| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.73 r_work: 0.2873 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16045 Z= 0.181 Angle : 0.655 11.784 21808 Z= 0.348 Chirality : 0.049 0.283 2592 Planarity : 0.005 0.054 2739 Dihedral : 6.304 80.521 2418 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.44 % Allowed : 13.44 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.23 (0.19), residues: 1992 helix: 2.29 (0.26), residues: 412 sheet: 0.54 (0.21), residues: 594 loop : -1.05 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 336 TYR 0.013 0.002 TYR B 98 PHE 0.012 0.001 PHE E 87 TRP 0.008 0.001 TRP B 103 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00432 (16009) covalent geometry : angle 0.63188 (21724) SS BOND : bond 0.00825 ( 24) SS BOND : angle 2.04971 ( 48) hydrogen bonds : bond 0.06400 ( 493) hydrogen bonds : angle 4.12989 ( 1305) link_NAG-ASN : bond 0.00505 ( 12) link_NAG-ASN : angle 3.64736 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 10 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8227 (mt-10) REVERT: L 23 CYS cc_start: 0.7431 (t) cc_final: 0.6864 (t) REVERT: L 79 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7313 (mp0) REVERT: L 81 GLU cc_start: 0.8114 (pm20) cc_final: 0.7799 (pm20) REVERT: A 244 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8411 (mmt180) REVERT: A 322 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7149 (mm) REVERT: A 383 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8763 (tt) REVERT: A 463 MET cc_start: 0.8764 (mtp) cc_final: 0.8159 (mtm) REVERT: D 166 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: D 322 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7585 (mm) REVERT: D 417 CYS cc_start: 0.5540 (OUTLIER) cc_final: 0.5090 (t) REVERT: G 327 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: B 73 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8497 (mttt) REVERT: B 95 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: E 11 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7734 (tt) REVERT: E 105 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: C 10 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: F 77 ASN cc_start: 0.8208 (p0) cc_final: 0.7955 (p0) REVERT: F 79 GLU cc_start: 0.7766 (mp0) cc_final: 0.7420 (mp0) outliers start: 61 outliers final: 37 residues processed: 209 average time/residue: 0.7267 time to fit residues: 164.7731 Evaluate side-chains 214 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 187 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.096849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070376 restraints weight = 25534.281| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.71 r_work: 0.2854 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16045 Z= 0.223 Angle : 0.730 12.042 21808 Z= 0.386 Chirality : 0.051 0.292 2592 Planarity : 0.005 0.061 2739 Dihedral : 6.566 90.727 2418 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.61 % Allowed : 13.38 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1992 helix: 2.19 (0.26), residues: 412 sheet: 0.50 (0.21), residues: 597 loop : -1.12 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 336 TYR 0.017 0.002 TYR B 98 PHE 0.014 0.002 PHE E 87 TRP 0.008 0.001 TRP B 103 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00543 (16009) covalent geometry : angle 0.70657 (21724) SS BOND : bond 0.00983 ( 24) SS BOND : angle 2.36745 ( 48) hydrogen bonds : bond 0.07341 ( 493) hydrogen bonds : angle 4.23347 ( 1305) link_NAG-ASN : bond 0.00485 ( 12) link_NAG-ASN : angle 3.76959 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 167 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: H 10 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8223 (mt-10) REVERT: L 23 CYS cc_start: 0.7524 (t) cc_final: 0.6933 (t) REVERT: L 79 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7428 (mp0) REVERT: L 81 GLU cc_start: 0.8148 (pm20) cc_final: 0.7886 (pm20) REVERT: L 82 ASP cc_start: 0.8525 (m-30) cc_final: 0.7975 (m-30) REVERT: A 244 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8404 (mmt180) REVERT: A 322 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7171 (mm) REVERT: A 383 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8750 (tt) REVERT: A 463 MET cc_start: 0.8796 (mtp) cc_final: 0.8194 (mtm) REVERT: D 166 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: D 322 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7524 (mm) REVERT: D 417 CYS cc_start: 0.5348 (OUTLIER) cc_final: 0.4796 (t) REVERT: D 453 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7727 (tttm) REVERT: G 327 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: B 43 LYS cc_start: 0.8256 (mmpt) cc_final: 0.7849 (mmmm) REVERT: B 73 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8545 (mttt) REVERT: B 95 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: E 11 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7819 (tt) REVERT: E 105 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: C 10 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7928 (mm-30) REVERT: F 77 ASN cc_start: 0.8235 (p0) cc_final: 0.8008 (p0) REVERT: F 79 GLU cc_start: 0.7791 (mp0) cc_final: 0.7503 (mp0) outliers start: 64 outliers final: 39 residues processed: 212 average time/residue: 0.7328 time to fit residues: 168.5079 Evaluate side-chains 217 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 127 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071395 restraints weight = 25557.377| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.74 r_work: 0.2875 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16045 Z= 0.170 Angle : 0.655 11.749 21808 Z= 0.347 Chirality : 0.049 0.286 2592 Planarity : 0.005 0.059 2739 Dihedral : 6.340 89.924 2417 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.05 % Allowed : 14.06 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.21 (0.19), residues: 1992 helix: 2.31 (0.27), residues: 412 sheet: 0.50 (0.21), residues: 600 loop : -1.08 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 336 TYR 0.013 0.001 TYR G 473 PHE 0.011 0.001 PHE E 87 TRP 0.007 0.001 TRP B 103 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00404 (16009) covalent geometry : angle 0.63282 (21724) SS BOND : bond 0.00777 ( 24) SS BOND : angle 1.88151 ( 48) hydrogen bonds : bond 0.06190 ( 493) hydrogen bonds : angle 4.11507 ( 1305) link_NAG-ASN : bond 0.00546 ( 12) link_NAG-ASN : angle 3.66805 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 23 CYS cc_start: 0.7503 (t) cc_final: 0.6945 (t) REVERT: L 79 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7399 (mp0) REVERT: L 81 GLU cc_start: 0.8160 (pm20) cc_final: 0.7884 (pm20) REVERT: A 244 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8388 (mmt180) REVERT: A 322 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7093 (mm) REVERT: A 383 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8737 (tt) REVERT: A 463 MET cc_start: 0.8779 (mtp) cc_final: 0.8168 (mtm) REVERT: D 166 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: D 322 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7540 (mm) REVERT: D 417 CYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4933 (t) REVERT: G 327 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: B 43 LYS cc_start: 0.8228 (mmpt) cc_final: 0.8004 (mmmt) REVERT: B 73 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8446 (mttt) REVERT: E 11 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7745 (tt) REVERT: E 105 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: C 10 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: F 77 ASN cc_start: 0.8187 (p0) cc_final: 0.7915 (p0) REVERT: F 79 GLU cc_start: 0.7736 (mp0) cc_final: 0.7445 (mp0) outliers start: 54 outliers final: 38 residues processed: 203 average time/residue: 0.7666 time to fit residues: 168.4697 Evaluate side-chains 211 residues out of total 1771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 41 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 417 CYS Chi-restraints excluded: chain G residue 304 ASP Chi-restraints excluded: chain G residue 327 GLU Chi-restraints excluded: chain G residue 361 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 164 optimal weight: 0.0070 chunk 125 optimal weight: 0.0070 chunk 159 optimal weight: 1.9990 chunk 87 optimal weight: 0.0070 chunk 131 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074774 restraints weight = 25700.861| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.75 r_work: 0.2947 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16045 Z= 0.105 Angle : 0.552 10.601 21808 Z= 0.289 Chirality : 0.045 0.283 2592 Planarity : 0.004 0.053 2739 Dihedral : 5.733 79.206 2417 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.20 % Allowed : 14.85 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.39 (0.19), residues: 1992 helix: 2.50 (0.27), residues: 419 sheet: 0.61 (0.20), residues: 659 loop : -1.12 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 336 TYR 0.013 0.001 TYR D 473 PHE 0.008 0.001 PHE E 49 TRP 0.005 0.001 TRP G 308 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00227 (16009) covalent geometry : angle 0.53442 (21724) SS BOND : bond 0.00387 ( 24) SS BOND : angle 1.03196 ( 48) hydrogen bonds : bond 0.03967 ( 493) hydrogen bonds : angle 3.86718 ( 1305) link_NAG-ASN : bond 0.00560 ( 12) link_NAG-ASN : angle 3.25020 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6532.02 seconds wall clock time: 111 minutes 27.38 seconds (6687.38 seconds total)