Starting phenix.real_space_refine on Thu Mar 5 11:32:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mlu_23910/03_2026/7mlu_23910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mlu_23910/03_2026/7mlu_23910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mlu_23910/03_2026/7mlu_23910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mlu_23910/03_2026/7mlu_23910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mlu_23910/03_2026/7mlu_23910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mlu_23910/03_2026/7mlu_23910.map" } resolution = 4.1 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= -0.002 sd= 0.986 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 145 5.16 5 C 14063 2.51 5 N 3630 2.21 5 O 4048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 21886 Number of models: 1 Model: "" Number of chains: 20 Chain: "K" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "O" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "N" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 15, 'TRANS': 316} Chain breaks: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.75, per 1000 atoms: 0.22 Number of scatterers: 21886 At special positions: 0 Unit cell: (155.288, 153.636, 125.552, 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 145 16.00 O 4048 8.00 N 3630 7.00 C 14063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.04 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 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 38 " " NAG B 501 " - " ASN B 38 " " NAG C 501 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 38 " Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.0 seconds 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 41 sheets defined 22.7% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.798A pdb=" N ASP K 82 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 79 through 83' Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.150A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.118A pdb=" N SER G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.928A pdb=" N ASP O 82 " --> pdb=" O GLN O 79 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU O 83 " --> pdb=" O ALA O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 83' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.036A pdb=" N SER N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.948A pdb=" N LEU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 4.118A pdb=" N SER L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.100A pdb=" N LEU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.634A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.769A pdb=" N ILE A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP A 243 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 269 removed outlier: 4.130A pdb=" N VAL A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 254 " --> pdb=" O PRO A 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.682A pdb=" N TRP A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.547A pdb=" N ASN A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 removed outlier: 3.633A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE E 225 " --> pdb=" O GLY E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 removed outlier: 3.770A pdb=" N ILE E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP E 243 " --> pdb=" O ILE E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 269 removed outlier: 4.129A pdb=" N VAL E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY E 254 " --> pdb=" O PRO E 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR E 258 " --> pdb=" O GLY E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 296 removed outlier: 3.682A pdb=" N TRP E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET E 287 " --> pdb=" O ILE E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 308 removed outlier: 3.692A pdb=" N TYR E 301 " --> pdb=" O ALA E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 398 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 417 removed outlier: 3.548A pdb=" N ASN E 410 " --> pdb=" O PHE E 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP E 414 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE E 415 " --> pdb=" O MET E 411 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR E 417 " --> pdb=" O TYR E 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 18 removed outlier: 3.634A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.768A pdb=" N ILE D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.692A pdb=" N TRP D 243 " --> pdb=" O ILE D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 269 removed outlier: 4.130A pdb=" N VAL D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 removed outlier: 3.683A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE D 394 " --> pdb=" O ARG D 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.547A pdb=" N ASN D 410 " --> pdb=" O PHE D 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 415 " --> pdb=" O MET D 411 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR D 417 " --> pdb=" O TYR D 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 removed outlier: 3.633A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 226 removed outlier: 4.335A pdb=" N ILE B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.770A pdb=" N ILE B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP B 243 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 269 removed outlier: 4.130A pdb=" N VAL B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY B 254 " --> pdb=" O PRO B 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 removed outlier: 3.683A pdb=" N TRP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.548A pdb=" N ASN B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 removed outlier: 3.633A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 4.236A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 226 removed outlier: 4.336A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.769A pdb=" N ILE C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.693A pdb=" N TRP C 243 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 269 removed outlier: 4.129A pdb=" N VAL C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY C 254 " --> pdb=" O PRO C 250 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.683A pdb=" N TRP C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 287 " --> pdb=" O ILE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 308 removed outlier: 3.693A pdb=" N TYR C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 400 removed outlier: 3.501A pdb=" N ILE C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 417 removed outlier: 3.547A pdb=" N ASN C 410 " --> pdb=" O PHE C 406 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 412 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 415 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR C 417 " --> pdb=" O TYR C 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.534A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.398A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'F' and resid 47 through 51 removed outlier: 6.555A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE F 34 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 19 through 22 Processing sheet with id=AA6, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.365A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'G' and resid 47 through 51 removed outlier: 6.592A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE G 34 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 19 through 21 removed outlier: 3.527A pdb=" N THR O 72 " --> pdb=" O SER O 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 44 through 48 removed outlier: 6.425A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU O 85 " --> pdb=" O GLN O 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'N' and resid 47 through 51 removed outlier: 6.585A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE N 34 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.537A pdb=" N LEU M 73 " --> pdb=" O ILE M 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.496A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN M 38 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 47 through 51 removed outlier: 6.602A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE L 34 " --> pdb=" O GLU L 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 20 through 22 Processing sheet with id=AB9, first strand: chain 'I' and resid 44 through 46 Processing sheet with id=AC1, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 47 through 51 removed outlier: 6.592A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN A 177 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 43 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET A 154 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 217 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET A 154 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP E 68 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL E 37 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU E 169 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL E 39 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP E 68 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLN E 177 " --> pdb=" O CYS E 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE E 43 " --> pdb=" O GLN E 177 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET E 154 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET E 154 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR E 208 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.545A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN D 177 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE D 43 " --> pdb=" O GLN D 177 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.974A pdb=" N MET D 154 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 217 " --> pdb=" O ILE D 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.974A pdb=" N MET D 154 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR D 208 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLN B 177 " --> pdb=" O CYS B 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 43 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET B 154 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 217 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET B 154 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N THR B 208 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL C 37 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU C 169 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL C 39 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.544A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN C 177 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE C 43 " --> pdb=" O GLN C 177 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET C 154 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 217 " --> pdb=" O ILE C 188 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.975A pdb=" N MET C 154 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR C 208 " --> pdb=" O SER C 158 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2091 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6813 1.34 - 1.46: 5653 1.46 - 1.58: 9722 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 22428 Sorted by residual: bond pdb=" C THR K 94 " pdb=" N PRO K 95 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.90e+00 bond pdb=" C THR J 94 " pdb=" N PRO J 95 " ideal model delta sigma weight residual 1.334 1.385 -0.052 2.34e-02 1.83e+03 4.85e+00 bond pdb=" C THR O 94 " pdb=" N PRO O 95 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.75e+00 bond pdb=" C THR I 94 " pdb=" N PRO I 95 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.40e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.99e+00 ... (remaining 22423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 30049 3.15 - 6.29: 300 6.29 - 9.44: 41 9.44 - 12.59: 3 12.59 - 15.74: 5 Bond angle restraints: 30398 Sorted by residual: angle pdb=" N GLY B 205 " pdb=" CA GLY B 205 " pdb=" C GLY B 205 " ideal model delta sigma weight residual 110.29 117.05 -6.76 1.28e+00 6.10e-01 2.79e+01 angle pdb=" N GLY A 205 " pdb=" CA GLY A 205 " pdb=" C GLY A 205 " ideal model delta sigma weight residual 110.29 117.05 -6.76 1.28e+00 6.10e-01 2.79e+01 angle pdb=" N GLY C 205 " pdb=" CA GLY C 205 " pdb=" C GLY C 205 " ideal model delta sigma weight residual 110.29 117.05 -6.76 1.28e+00 6.10e-01 2.79e+01 angle pdb=" N GLY D 205 " pdb=" CA GLY D 205 " pdb=" C GLY D 205 " ideal model delta sigma weight residual 110.29 117.02 -6.73 1.28e+00 6.10e-01 2.77e+01 angle pdb=" N GLY E 205 " pdb=" CA GLY E 205 " pdb=" C GLY E 205 " ideal model delta sigma weight residual 110.29 117.02 -6.73 1.28e+00 6.10e-01 2.76e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 12589 14.39 - 28.78: 563 28.78 - 43.17: 128 43.17 - 57.56: 27 57.56 - 71.95: 27 Dihedral angle restraints: 13334 sinusoidal: 5359 harmonic: 7975 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 28.34 64.66 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 32.55 60.45 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.77 45.23 1 1.00e+01 1.00e-02 2.84e+01 ... (remaining 13331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2872 0.076 - 0.152: 443 0.152 - 0.227: 38 0.227 - 0.303: 0 0.303 - 0.379: 5 Chirality restraints: 3358 Sorted by residual: chirality pdb=" C2 NAG D 501 " pdb=" C1 NAG D 501 " pdb=" C3 NAG D 501 " pdb=" N2 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C2 NAG C 501 " pdb=" C1 NAG C 501 " pdb=" C3 NAG C 501 " pdb=" N2 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C2 NAG A 501 " pdb=" C1 NAG A 501 " pdb=" C3 NAG A 501 " pdb=" N2 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 3355 not shown) Planarity restraints: 3813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 58 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO K 59 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO K 59 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 59 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 86 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO D 87 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 86 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO E 87 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " 0.029 5.00e-02 4.00e+02 ... (remaining 3810 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5580 2.80 - 3.32: 18770 3.32 - 3.85: 36511 3.85 - 4.37: 42175 4.37 - 4.90: 69745 Nonbonded interactions: 172781 Sorted by model distance: nonbonded pdb=" OG1 THR D 162 " pdb=" OD1 ASN D 164 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR E 162 " pdb=" OD1 ASN E 164 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR C 162 " pdb=" OD1 ASN C 164 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR B 162 " pdb=" OD1 ASN B 164 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR A 162 " pdb=" OD1 ASN A 164 " model vdw 2.271 3.040 ... (remaining 172776 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'I' and resid 2 through 102) selection = chain 'J' selection = (chain 'K' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) selection = (chain 'M' and resid 2 through 102) selection = (chain 'O' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.290 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 19.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22453 Z= 0.195 Angle : 0.881 15.737 30453 Z= 0.465 Chirality : 0.054 0.379 3358 Planarity : 0.006 0.056 3808 Dihedral : 9.815 71.951 8162 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.21 % Allowed : 2.77 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.13), residues: 2706 helix: -3.90 (0.13), residues: 380 sheet: -2.50 (0.17), residues: 675 loop : -2.99 (0.12), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 29 TYR 0.021 0.002 TYR I 49 PHE 0.022 0.002 PHE D 63 TRP 0.031 0.002 TRP E 94 HIS 0.006 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00406 (22428) covalent geometry : angle 0.87869 (30398) SS BOND : bond 0.00394 ( 20) SS BOND : angle 1.89391 ( 40) hydrogen bonds : bond 0.29336 ( 627) hydrogen bonds : angle 11.07045 ( 2091) link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 0.89988 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 590 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 78 VAL cc_start: 0.8066 (t) cc_final: 0.6736 (t) REVERT: F 45 LEU cc_start: 0.7573 (mm) cc_final: 0.6898 (mm) REVERT: F 114 LEU cc_start: 0.8669 (tp) cc_final: 0.8005 (mm) REVERT: G 12 MET cc_start: 0.8886 (mmt) cc_final: 0.8622 (tpp) REVERT: G 48 ILE cc_start: 0.8475 (mt) cc_final: 0.8272 (mt) REVERT: G 71 THR cc_start: 0.7931 (p) cc_final: 0.7675 (p) REVERT: G 83 LEU cc_start: 0.9030 (mt) cc_final: 0.8779 (pp) REVERT: O 20 SER cc_start: 0.8021 (m) cc_final: 0.7499 (p) REVERT: O 50 TRP cc_start: 0.7264 (m100) cc_final: 0.7058 (m100) REVERT: N 45 LEU cc_start: 0.7507 (mm) cc_final: 0.7065 (tp) REVERT: N 77 ASN cc_start: 0.8260 (m-40) cc_final: 0.7912 (p0) REVERT: N 95 TYR cc_start: 0.7068 (m-80) cc_final: 0.6626 (m-80) REVERT: N 114 LEU cc_start: 0.9074 (tp) cc_final: 0.8617 (mm) REVERT: M 78 VAL cc_start: 0.7580 (t) cc_final: 0.6923 (t) REVERT: L 103 ASN cc_start: 0.7453 (m-40) cc_final: 0.7152 (m-40) REVERT: I 2 ILE cc_start: 0.8314 (mt) cc_final: 0.8043 (mm) REVERT: I 4 MET cc_start: 0.7880 (mmm) cc_final: 0.7567 (mmm) REVERT: H 106 ASP cc_start: 0.8208 (p0) cc_final: 0.7925 (p0) REVERT: A 246 MET cc_start: 0.3527 (ptt) cc_final: 0.2975 (ptm) REVERT: A 287 MET cc_start: 0.8925 (mmm) cc_final: 0.8646 (ttp) REVERT: A 404 MET cc_start: 0.9189 (mmm) cc_final: 0.8926 (mmp) REVERT: E 404 MET cc_start: 0.8835 (mmm) cc_final: 0.8576 (mmt) REVERT: D 227 MET cc_start: 0.7951 (mmp) cc_final: 0.7069 (mmm) REVERT: D 233 LEU cc_start: 0.8807 (tp) cc_final: 0.8556 (tt) REVERT: D 246 MET cc_start: 0.6965 (ptt) cc_final: 0.6670 (ttm) REVERT: D 263 MET cc_start: 0.8700 (mmm) cc_final: 0.8045 (mmt) REVERT: D 404 MET cc_start: 0.8426 (mmm) cc_final: 0.8212 (mtt) REVERT: B 62 ILE cc_start: 0.8969 (pt) cc_final: 0.8420 (pt) REVERT: B 246 MET cc_start: 0.4050 (ptt) cc_final: 0.3328 (ppp) REVERT: B 404 MET cc_start: 0.8645 (mmm) cc_final: 0.8187 (mtt) REVERT: C 246 MET cc_start: 0.6158 (ptt) cc_final: 0.5370 (ppp) REVERT: C 404 MET cc_start: 0.8093 (mmm) cc_final: 0.7666 (mtt) outliers start: 5 outliers final: 0 residues processed: 595 average time/residue: 0.1651 time to fit residues: 146.7271 Evaluate side-chains 327 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 GLN K 91 HIS ** F 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 HIS O 37 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 HIS ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS A 67 GLN A 115 ASN A 125 ASN A 155 GLN A 164 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 305 ASN E 67 GLN E 107 HIS E 115 ASN E 125 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 155 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN B 125 ASN B 186 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 305 ASN C 67 GLN C 115 ASN C 125 ASN C 186 GLN C 226 GLN C 305 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.042790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.035333 restraints weight = 248563.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.036093 restraints weight = 178963.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.036680 restraints weight = 140419.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.037130 restraints weight = 115672.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.037465 restraints weight = 99277.565| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22453 Z= 0.237 Angle : 0.805 16.849 30453 Z= 0.411 Chirality : 0.046 0.239 3358 Planarity : 0.006 0.076 3808 Dihedral : 7.128 59.656 3083 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.17 % Allowed : 3.06 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.15), residues: 2706 helix: -1.81 (0.22), residues: 420 sheet: -2.09 (0.17), residues: 716 loop : -2.15 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 131 TYR 0.024 0.002 TYR O 49 PHE 0.027 0.002 PHE C 13 TRP 0.034 0.002 TRP B 94 HIS 0.009 0.002 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00500 (22428) covalent geometry : angle 0.80320 (30398) SS BOND : bond 0.00416 ( 20) SS BOND : angle 1.18833 ( 40) hydrogen bonds : bond 0.04907 ( 627) hydrogen bonds : angle 7.22238 ( 2091) link_NAG-ASN : bond 0.00464 ( 5) link_NAG-ASN : angle 2.14501 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 391 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 MET cc_start: 0.6213 (mmm) cc_final: 0.5814 (mmm) REVERT: K 82 ASP cc_start: 0.8993 (p0) cc_final: 0.8569 (p0) REVERT: F 114 LEU cc_start: 0.9296 (tp) cc_final: 0.8876 (mm) REVERT: J 62 PHE cc_start: 0.9154 (m-10) cc_final: 0.8904 (m-80) REVERT: G 12 MET cc_start: 0.8948 (mmt) cc_final: 0.8502 (mmm) REVERT: G 20 ILE cc_start: 0.6527 (tt) cc_final: 0.5997 (tt) REVERT: G 73 GLU cc_start: 0.8990 (tt0) cc_final: 0.8354 (tt0) REVERT: G 83 LEU cc_start: 0.9330 (mt) cc_final: 0.9012 (pp) REVERT: O 49 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7268 (p90) REVERT: N 45 LEU cc_start: 0.7629 (mm) cc_final: 0.7286 (tp) REVERT: N 114 LEU cc_start: 0.9587 (tp) cc_final: 0.9193 (mm) REVERT: L 13 LYS cc_start: 0.7113 (mppt) cc_final: 0.6606 (mmmt) REVERT: L 83 LEU cc_start: 0.9295 (mt) cc_final: 0.9008 (mp) REVERT: I 2 ILE cc_start: 0.8197 (mt) cc_final: 0.7437 (mt) REVERT: I 4 MET cc_start: 0.8376 (mmm) cc_final: 0.7651 (mmm) REVERT: I 11 MET cc_start: 0.7654 (mmm) cc_final: 0.7371 (mmm) REVERT: I 86 TYR cc_start: 0.8499 (m-10) cc_final: 0.8179 (m-10) REVERT: H 12 MET cc_start: 0.7101 (tpt) cc_final: 0.6697 (mmm) REVERT: H 39 GLN cc_start: 0.9035 (tt0) cc_final: 0.8678 (tp-100) REVERT: H 83 LEU cc_start: 0.9504 (mm) cc_final: 0.9053 (pp) REVERT: A 140 MET cc_start: 0.8650 (mtm) cc_final: 0.7439 (mtm) REVERT: A 164 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.9094 (p0) REVERT: A 246 MET cc_start: 0.3683 (ptt) cc_final: 0.3164 (ptm) REVERT: A 264 THR cc_start: 0.9265 (m) cc_final: 0.8968 (p) REVERT: A 287 MET cc_start: 0.9232 (mmm) cc_final: 0.8814 (tpp) REVERT: A 291 LEU cc_start: 0.9473 (mt) cc_final: 0.9166 (mt) REVERT: A 404 MET cc_start: 0.9084 (mmm) cc_final: 0.8841 (mmp) REVERT: E 32 PHE cc_start: 0.8804 (p90) cc_final: 0.8377 (p90) REVERT: E 130 ILE cc_start: 0.9526 (pt) cc_final: 0.9286 (mm) REVERT: E 287 MET cc_start: 0.8797 (ttp) cc_final: 0.8280 (ttm) REVERT: E 404 MET cc_start: 0.8736 (mmm) cc_final: 0.8514 (mmt) REVERT: E 411 MET cc_start: 0.9057 (ptp) cc_final: 0.8749 (ppp) REVERT: D 117 LEU cc_start: 0.9363 (tt) cc_final: 0.9000 (tp) REVERT: D 200 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6730 (mmtt) REVERT: D 227 MET cc_start: 0.8516 (mmp) cc_final: 0.8296 (mmm) REVERT: D 263 MET cc_start: 0.8785 (mmm) cc_final: 0.7965 (mmt) REVERT: D 404 MET cc_start: 0.8644 (mmm) cc_final: 0.8353 (mtt) REVERT: B 246 MET cc_start: 0.4398 (ptt) cc_final: 0.3826 (ppp) REVERT: B 261 LEU cc_start: 0.9375 (tt) cc_final: 0.9135 (pp) REVERT: B 263 MET cc_start: 0.9089 (ttt) cc_final: 0.8759 (ttt) REVERT: B 287 MET cc_start: 0.8827 (tmm) cc_final: 0.8624 (tmm) REVERT: B 291 LEU cc_start: 0.9543 (mt) cc_final: 0.9305 (mt) REVERT: B 404 MET cc_start: 0.8746 (mmm) cc_final: 0.8315 (mtt) REVERT: C 56 MET cc_start: 0.9243 (ttp) cc_final: 0.9031 (ttm) REVERT: C 147 MET cc_start: 0.7953 (mtm) cc_final: 0.7606 (tpp) REVERT: C 246 MET cc_start: 0.6265 (ptt) cc_final: 0.5580 (ppp) REVERT: C 263 MET cc_start: 0.8811 (mmt) cc_final: 0.7618 (mmm) REVERT: C 404 MET cc_start: 0.8422 (mmm) cc_final: 0.7948 (mtt) outliers start: 4 outliers final: 1 residues processed: 395 average time/residue: 0.1529 time to fit residues: 94.1901 Evaluate side-chains 287 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 284 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 200 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 235 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 0.0470 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 GLN K 91 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN A 305 ASN E 177 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN B 67 GLN B 177 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.043806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.036108 restraints weight = 238203.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.036916 restraints weight = 171774.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.037531 restraints weight = 134062.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.037986 restraints weight = 110291.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.038337 restraints weight = 94735.042| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22453 Z= 0.122 Angle : 0.670 14.254 30453 Z= 0.332 Chirality : 0.044 0.241 3358 Planarity : 0.004 0.045 3808 Dihedral : 6.401 56.323 3083 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.13 % Allowed : 1.85 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.15), residues: 2706 helix: -1.33 (0.22), residues: 465 sheet: -1.75 (0.17), residues: 773 loop : -1.85 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 18 TYR 0.030 0.001 TYR F 80 PHE 0.018 0.001 PHE C 99 TRP 0.012 0.001 TRP E 239 HIS 0.003 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00269 (22428) covalent geometry : angle 0.66744 (30398) SS BOND : bond 0.00375 ( 20) SS BOND : angle 1.56779 ( 40) hydrogen bonds : bond 0.03970 ( 627) hydrogen bonds : angle 6.03203 ( 2091) link_NAG-ASN : bond 0.00285 ( 5) link_NAG-ASN : angle 0.91126 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 376 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 MET cc_start: 0.6322 (mmm) cc_final: 0.5971 (mmm) REVERT: F 19 LYS cc_start: 0.7592 (tmtt) cc_final: 0.7288 (tmtt) REVERT: F 81 MET cc_start: 0.8679 (tmm) cc_final: 0.8377 (tmm) REVERT: J 62 PHE cc_start: 0.9159 (m-10) cc_final: 0.8786 (m-80) REVERT: G 12 MET cc_start: 0.8855 (mmt) cc_final: 0.8561 (mmm) REVERT: G 71 THR cc_start: 0.8209 (p) cc_final: 0.7849 (p) REVERT: G 73 GLU cc_start: 0.8875 (tt0) cc_final: 0.8608 (tt0) REVERT: G 83 LEU cc_start: 0.9389 (mt) cc_final: 0.8992 (pp) REVERT: N 39 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8413 (tp-100) REVERT: N 114 LEU cc_start: 0.9621 (tp) cc_final: 0.9341 (mm) REVERT: L 12 MET cc_start: 0.8358 (mmm) cc_final: 0.7482 (mmm) REVERT: L 69 THR cc_start: 0.8796 (m) cc_final: 0.8547 (m) REVERT: L 89 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8813 (mm-30) REVERT: L 114 LEU cc_start: 0.9405 (mm) cc_final: 0.9099 (mm) REVERT: I 4 MET cc_start: 0.8170 (mmm) cc_final: 0.7486 (mmm) REVERT: I 11 MET cc_start: 0.7779 (mmm) cc_final: 0.7153 (mmm) REVERT: I 86 TYR cc_start: 0.8607 (m-10) cc_final: 0.8246 (m-10) REVERT: H 20 ILE cc_start: 0.5954 (pt) cc_final: 0.5728 (pt) REVERT: H 39 GLN cc_start: 0.8982 (tt0) cc_final: 0.8696 (tp-100) REVERT: A 246 MET cc_start: 0.3587 (ptt) cc_final: 0.3078 (ptm) REVERT: A 264 THR cc_start: 0.9224 (m) cc_final: 0.8957 (p) REVERT: A 287 MET cc_start: 0.9210 (mmm) cc_final: 0.8941 (tpt) REVERT: A 291 LEU cc_start: 0.9456 (mt) cc_final: 0.9237 (mt) REVERT: A 404 MET cc_start: 0.9120 (mmm) cc_final: 0.8854 (mmp) REVERT: E 32 PHE cc_start: 0.8793 (p90) cc_final: 0.8362 (p90) REVERT: E 140 MET cc_start: 0.8308 (mtm) cc_final: 0.8045 (mtt) REVERT: E 204 THR cc_start: 0.7543 (p) cc_final: 0.7296 (p) REVERT: E 287 MET cc_start: 0.8758 (ttp) cc_final: 0.8493 (ttt) REVERT: E 404 MET cc_start: 0.8828 (mmm) cc_final: 0.8554 (mmt) REVERT: E 411 MET cc_start: 0.8989 (ptp) cc_final: 0.8686 (ppp) REVERT: D 117 LEU cc_start: 0.9325 (tt) cc_final: 0.8978 (tp) REVERT: D 140 MET cc_start: 0.7773 (mtm) cc_final: 0.7168 (mtt) REVERT: D 157 GLU cc_start: 0.9110 (pt0) cc_final: 0.8734 (pt0) REVERT: D 246 MET cc_start: 0.6934 (ptp) cc_final: 0.6451 (ptp) REVERT: D 263 MET cc_start: 0.8775 (mmm) cc_final: 0.8002 (mmt) REVERT: D 404 MET cc_start: 0.8740 (mmm) cc_final: 0.8365 (mtt) REVERT: B 157 GLU cc_start: 0.9008 (pt0) cc_final: 0.8559 (mt-10) REVERT: B 246 MET cc_start: 0.4370 (ptt) cc_final: 0.3613 (ppp) REVERT: B 261 LEU cc_start: 0.9426 (tt) cc_final: 0.9151 (pp) REVERT: B 263 MET cc_start: 0.8954 (ttt) cc_final: 0.8680 (ttt) REVERT: B 291 LEU cc_start: 0.9541 (mt) cc_final: 0.9293 (mt) REVERT: B 404 MET cc_start: 0.8722 (mmm) cc_final: 0.8262 (mtt) REVERT: C 147 MET cc_start: 0.7900 (mtm) cc_final: 0.7608 (tpp) REVERT: C 157 GLU cc_start: 0.9147 (pt0) cc_final: 0.8244 (mt-10) REVERT: C 246 MET cc_start: 0.6171 (ptt) cc_final: 0.5498 (ppp) REVERT: C 263 MET cc_start: 0.8865 (mmt) cc_final: 0.7795 (mmt) REVERT: C 404 MET cc_start: 0.8349 (mmm) cc_final: 0.7801 (mtt) outliers start: 3 outliers final: 2 residues processed: 378 average time/residue: 0.1523 time to fit residues: 89.6843 Evaluate side-chains 287 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 38 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 HIS M 27 GLN M 37 GLN M 89 GLN L 3 GLN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN A 31 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN B 46 ASN B 203 ASN C 46 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 177 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.038014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.031083 restraints weight = 270150.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.031817 restraints weight = 192459.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.032360 restraints weight = 148028.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.032747 restraints weight = 121236.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.033027 restraints weight = 104165.271| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.7246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.173 22453 Z= 0.327 Angle : 0.934 18.322 30453 Z= 0.474 Chirality : 0.050 0.241 3358 Planarity : 0.006 0.074 3808 Dihedral : 7.594 58.273 3083 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 32.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.15), residues: 2706 helix: -1.70 (0.21), residues: 430 sheet: -2.09 (0.17), residues: 776 loop : -1.92 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 252 TYR 0.046 0.003 TYR E 223 PHE 0.027 0.003 PHE F 64 TRP 0.027 0.003 TRP A 414 HIS 0.012 0.003 HIS E 201 Details of bonding type rmsd covalent geometry : bond 0.00696 (22428) covalent geometry : angle 0.93290 (30398) SS BOND : bond 0.00582 ( 20) SS BOND : angle 1.74651 ( 40) hydrogen bonds : bond 0.05140 ( 627) hydrogen bonds : angle 7.06030 ( 2091) link_NAG-ASN : bond 0.00260 ( 5) link_NAG-ASN : angle 0.74224 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 92 TYR cc_start: 0.8400 (t80) cc_final: 0.8181 (t80) REVERT: F 114 LEU cc_start: 0.9423 (mm) cc_final: 0.8827 (mm) REVERT: J 9 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8527 (mmtm) REVERT: J 62 PHE cc_start: 0.8995 (m-10) cc_final: 0.8464 (m-80) REVERT: J 85 LEU cc_start: 0.9664 (mt) cc_final: 0.9394 (mt) REVERT: J 87 TYR cc_start: 0.8282 (m-10) cc_final: 0.7971 (m-80) REVERT: G 12 MET cc_start: 0.8808 (mmt) cc_final: 0.8370 (mmm) REVERT: O 92 TYR cc_start: 0.8588 (t80) cc_final: 0.8305 (t80) REVERT: N 45 LEU cc_start: 0.7526 (tp) cc_final: 0.7319 (mm) REVERT: N 114 LEU cc_start: 0.9615 (tp) cc_final: 0.9330 (tp) REVERT: M 78 VAL cc_start: 0.7095 (t) cc_final: 0.6778 (t) REVERT: L 11 LEU cc_start: 0.8700 (tp) cc_final: 0.8207 (tp) REVERT: L 19 LYS cc_start: 0.9052 (pptt) cc_final: 0.8771 (tmmt) REVERT: L 81 MET cc_start: 0.8911 (tmm) cc_final: 0.8645 (tmm) REVERT: L 114 LEU cc_start: 0.9428 (mm) cc_final: 0.9195 (mm) REVERT: I 4 MET cc_start: 0.7962 (mmm) cc_final: 0.7279 (mmm) REVERT: I 86 TYR cc_start: 0.8808 (m-10) cc_final: 0.8457 (m-10) REVERT: I 104 LEU cc_start: 0.8816 (tp) cc_final: 0.8570 (tp) REVERT: H 12 MET cc_start: 0.8208 (tpp) cc_final: 0.7991 (mmm) REVERT: A 91 ASP cc_start: 0.9577 (m-30) cc_final: 0.9362 (p0) REVERT: A 140 MET cc_start: 0.8221 (mtm) cc_final: 0.7465 (mtt) REVERT: A 246 MET cc_start: 0.3805 (ptt) cc_final: 0.3405 (ptm) REVERT: A 263 MET cc_start: 0.9017 (mmp) cc_final: 0.8610 (mmm) REVERT: A 264 THR cc_start: 0.9406 (m) cc_final: 0.9165 (p) REVERT: A 287 MET cc_start: 0.9273 (mmm) cc_final: 0.8934 (tpp) REVERT: A 291 LEU cc_start: 0.9526 (mt) cc_final: 0.9102 (mt) REVERT: A 404 MET cc_start: 0.9159 (mmm) cc_final: 0.8892 (mmp) REVERT: E 56 MET cc_start: 0.9135 (tpp) cc_final: 0.8362 (tpp) REVERT: E 157 GLU cc_start: 0.9305 (pt0) cc_final: 0.8672 (pt0) REVERT: E 287 MET cc_start: 0.8976 (ttp) cc_final: 0.8750 (ttm) REVERT: E 404 MET cc_start: 0.9023 (mmm) cc_final: 0.8715 (mmt) REVERT: E 411 MET cc_start: 0.9101 (ptp) cc_final: 0.8810 (ppp) REVERT: D 56 MET cc_start: 0.9258 (tpp) cc_final: 0.8893 (tpt) REVERT: D 140 MET cc_start: 0.8033 (mtm) cc_final: 0.6983 (mtp) REVERT: D 246 MET cc_start: 0.6709 (ptp) cc_final: 0.6481 (ptp) REVERT: D 263 MET cc_start: 0.9214 (mmm) cc_final: 0.8360 (mmt) REVERT: D 404 MET cc_start: 0.8888 (mmm) cc_final: 0.8545 (mtt) REVERT: B 91 ASP cc_start: 0.9516 (m-30) cc_final: 0.9278 (p0) REVERT: B 246 MET cc_start: 0.4779 (ptt) cc_final: 0.4149 (ppp) REVERT: B 263 MET cc_start: 0.9310 (ttt) cc_final: 0.8839 (ttt) REVERT: B 291 LEU cc_start: 0.9578 (mt) cc_final: 0.9268 (mt) REVERT: B 404 MET cc_start: 0.8891 (mmm) cc_final: 0.8509 (mtt) REVERT: C 56 MET cc_start: 0.9148 (tpp) cc_final: 0.8435 (tpt) REVERT: C 173 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7842 (pp30) REVERT: C 246 MET cc_start: 0.6432 (ptt) cc_final: 0.5781 (ppp) REVERT: C 263 MET cc_start: 0.9137 (mmt) cc_final: 0.8146 (mmt) REVERT: C 404 MET cc_start: 0.8657 (mmm) cc_final: 0.8224 (mtt) outliers start: 2 outliers final: 0 residues processed: 312 average time/residue: 0.1596 time to fit residues: 76.7902 Evaluate side-chains 248 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 202 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 241 optimal weight: 1.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.039775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032366 restraints weight = 249582.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.033137 restraints weight = 178739.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.033690 restraints weight = 138609.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.034090 restraints weight = 114300.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.034384 restraints weight = 98610.034| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22453 Z= 0.152 Angle : 0.723 15.870 30453 Z= 0.358 Chirality : 0.046 0.230 3358 Planarity : 0.004 0.051 3808 Dihedral : 6.814 56.455 3083 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.04 % Allowed : 2.43 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.16), residues: 2706 helix: -0.94 (0.23), residues: 455 sheet: -1.84 (0.18), residues: 766 loop : -1.66 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 252 TYR 0.022 0.002 TYR A 228 PHE 0.035 0.002 PHE C 295 TRP 0.032 0.002 TRP E 239 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00331 (22428) covalent geometry : angle 0.72111 (30398) SS BOND : bond 0.00415 ( 20) SS BOND : angle 1.46596 ( 40) hydrogen bonds : bond 0.03706 ( 627) hydrogen bonds : angle 6.19651 ( 2091) link_NAG-ASN : bond 0.00229 ( 5) link_NAG-ASN : angle 0.61650 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 92 TYR cc_start: 0.8277 (t80) cc_final: 0.8022 (t80) REVERT: F 19 LYS cc_start: 0.8173 (tmmt) cc_final: 0.7846 (tmtt) REVERT: F 81 MET cc_start: 0.8761 (tmm) cc_final: 0.8387 (tmm) REVERT: J 9 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8515 (mmtm) REVERT: J 46 LEU cc_start: 0.8919 (tp) cc_final: 0.8703 (tp) REVERT: J 62 PHE cc_start: 0.9032 (m-10) cc_final: 0.8442 (m-80) REVERT: J 87 TYR cc_start: 0.8075 (m-10) cc_final: 0.7733 (m-80) REVERT: G 12 MET cc_start: 0.8852 (mmt) cc_final: 0.8466 (mmm) REVERT: O 37 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8622 (tp40) REVERT: O 92 TYR cc_start: 0.8534 (t80) cc_final: 0.8206 (t80) REVERT: N 52 LEU cc_start: 0.9291 (mt) cc_final: 0.8933 (mt) REVERT: N 114 LEU cc_start: 0.9613 (tp) cc_final: 0.9198 (mm) REVERT: M 59 PRO cc_start: 0.8837 (Cg_exo) cc_final: 0.8474 (Cg_endo) REVERT: L 11 LEU cc_start: 0.8823 (tp) cc_final: 0.8531 (tp) REVERT: L 12 MET cc_start: 0.7973 (mmp) cc_final: 0.7603 (mmm) REVERT: L 19 LYS cc_start: 0.8976 (pptt) cc_final: 0.8686 (tmmt) REVERT: L 45 LEU cc_start: 0.7882 (mm) cc_final: 0.7639 (mm) REVERT: L 81 MET cc_start: 0.9050 (tmm) cc_final: 0.8723 (tmm) REVERT: I 4 MET cc_start: 0.8031 (mmm) cc_final: 0.7429 (mmm) REVERT: I 11 MET cc_start: 0.7683 (mmm) cc_final: 0.6857 (mmm) REVERT: I 86 TYR cc_start: 0.8845 (m-10) cc_final: 0.8423 (m-10) REVERT: H 12 MET cc_start: 0.8172 (tpp) cc_final: 0.7742 (mmm) REVERT: A 91 ASP cc_start: 0.9584 (m-30) cc_final: 0.9343 (p0) REVERT: A 140 MET cc_start: 0.8391 (mtm) cc_final: 0.8191 (mtm) REVERT: A 246 MET cc_start: 0.3912 (ptt) cc_final: 0.3443 (ptm) REVERT: A 287 MET cc_start: 0.9287 (mmm) cc_final: 0.9085 (tpp) REVERT: A 291 LEU cc_start: 0.9503 (mt) cc_final: 0.9288 (mt) REVERT: A 404 MET cc_start: 0.9181 (mmm) cc_final: 0.8908 (mmp) REVERT: E 157 GLU cc_start: 0.9179 (pt0) cc_final: 0.8642 (pt0) REVERT: E 163 MET cc_start: 0.8773 (mmm) cc_final: 0.8201 (mmm) REVERT: E 287 MET cc_start: 0.9064 (ttp) cc_final: 0.8732 (ttm) REVERT: E 404 MET cc_start: 0.9106 (mmm) cc_final: 0.8686 (mmt) REVERT: E 411 MET cc_start: 0.9023 (ptp) cc_final: 0.8740 (ppp) REVERT: D 56 MET cc_start: 0.9199 (tpp) cc_final: 0.8751 (tpp) REVERT: D 140 MET cc_start: 0.8047 (mtm) cc_final: 0.7816 (mtm) REVERT: D 263 MET cc_start: 0.9115 (mmm) cc_final: 0.8190 (mmt) REVERT: D 404 MET cc_start: 0.8944 (mmm) cc_final: 0.8567 (mtt) REVERT: B 91 ASP cc_start: 0.9542 (m-30) cc_final: 0.9298 (p0) REVERT: B 246 MET cc_start: 0.4856 (ptt) cc_final: 0.4296 (ppp) REVERT: B 261 LEU cc_start: 0.9502 (tt) cc_final: 0.9180 (pp) REVERT: B 263 MET cc_start: 0.9238 (ttt) cc_final: 0.8766 (ttt) REVERT: B 291 LEU cc_start: 0.9549 (mt) cc_final: 0.9217 (mt) REVERT: B 404 MET cc_start: 0.8866 (mmm) cc_final: 0.8466 (mtt) REVERT: C 117 LEU cc_start: 0.9511 (tp) cc_final: 0.9279 (tp) REVERT: C 246 MET cc_start: 0.6398 (ptt) cc_final: 0.5773 (ppp) REVERT: C 263 MET cc_start: 0.9088 (mmt) cc_final: 0.8132 (mmt) REVERT: C 404 MET cc_start: 0.8615 (mmm) cc_final: 0.8149 (mtt) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.1513 time to fit residues: 75.5372 Evaluate side-chains 253 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 252 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 184 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 67 GLN A 155 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 155 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN B 186 GLN B 203 ASN C 46 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.038375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.031298 restraints weight = 262473.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.032048 restraints weight = 187022.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.032580 restraints weight = 144390.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.032971 restraints weight = 118666.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.033242 restraints weight = 102168.410| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.8145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22453 Z= 0.217 Angle : 0.775 15.215 30453 Z= 0.387 Chirality : 0.046 0.228 3358 Planarity : 0.005 0.081 3808 Dihedral : 6.981 57.122 3083 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.16), residues: 2706 helix: -0.93 (0.23), residues: 420 sheet: -1.99 (0.17), residues: 793 loop : -1.58 (0.17), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 18 TYR 0.022 0.002 TYR G 94 PHE 0.032 0.002 PHE C 295 TRP 0.035 0.002 TRP O 50 HIS 0.007 0.002 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00463 (22428) covalent geometry : angle 0.77237 (30398) SS BOND : bond 0.00367 ( 20) SS BOND : angle 1.90356 ( 40) hydrogen bonds : bond 0.03973 ( 627) hydrogen bonds : angle 6.27680 ( 2091) link_NAG-ASN : bond 0.00244 ( 5) link_NAG-ASN : angle 0.55647 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7400 (mpp) cc_final: 0.6635 (mpp) REVERT: K 50 TRP cc_start: 0.9011 (m100) cc_final: 0.8491 (m-90) REVERT: K 92 TYR cc_start: 0.8410 (t80) cc_final: 0.8121 (t80) REVERT: F 19 LYS cc_start: 0.8182 (tmmt) cc_final: 0.7779 (tmmt) REVERT: F 81 MET cc_start: 0.8934 (tmm) cc_final: 0.8620 (tmm) REVERT: J 9 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8645 (mmtm) REVERT: J 62 PHE cc_start: 0.9009 (m-10) cc_final: 0.8466 (m-80) REVERT: J 87 TYR cc_start: 0.8183 (m-10) cc_final: 0.7598 (m-80) REVERT: G 12 MET cc_start: 0.8799 (mmt) cc_final: 0.8359 (mmm) REVERT: O 37 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8588 (tp-100) REVERT: O 92 TYR cc_start: 0.8623 (t80) cc_final: 0.8375 (t80) REVERT: N 52 LEU cc_start: 0.9324 (mt) cc_final: 0.8954 (mt) REVERT: N 114 LEU cc_start: 0.9612 (tp) cc_final: 0.9319 (tp) REVERT: L 11 LEU cc_start: 0.8815 (tp) cc_final: 0.8486 (tp) REVERT: L 12 MET cc_start: 0.7794 (mmp) cc_final: 0.7535 (mmm) REVERT: L 19 LYS cc_start: 0.8917 (pptt) cc_final: 0.8533 (tmmt) REVERT: L 80 TYR cc_start: 0.7060 (m-10) cc_final: 0.6829 (m-80) REVERT: L 81 MET cc_start: 0.9132 (tmm) cc_final: 0.8646 (tmm) REVERT: I 4 MET cc_start: 0.8172 (mmm) cc_final: 0.7494 (mmm) REVERT: I 11 MET cc_start: 0.7701 (mmm) cc_final: 0.6854 (pmm) REVERT: I 86 TYR cc_start: 0.8829 (m-10) cc_final: 0.8403 (m-10) REVERT: H 12 MET cc_start: 0.8195 (tpp) cc_final: 0.7562 (mmm) REVERT: A 43 ILE cc_start: 0.9580 (pt) cc_final: 0.9148 (mm) REVERT: A 91 ASP cc_start: 0.9617 (m-30) cc_final: 0.9364 (p0) REVERT: A 147 MET cc_start: 0.8820 (tpp) cc_final: 0.8509 (ttp) REVERT: A 246 MET cc_start: 0.3998 (ptt) cc_final: 0.3539 (ptm) REVERT: A 263 MET cc_start: 0.8982 (mmp) cc_final: 0.8490 (mmm) REVERT: A 295 PHE cc_start: 0.9312 (m-80) cc_final: 0.8709 (m-80) REVERT: A 404 MET cc_start: 0.9239 (mmm) cc_final: 0.8970 (mmp) REVERT: E 56 MET cc_start: 0.9133 (tpp) cc_final: 0.8100 (tpp) REVERT: E 157 GLU cc_start: 0.9258 (pt0) cc_final: 0.8847 (pt0) REVERT: E 163 MET cc_start: 0.8725 (mmm) cc_final: 0.8273 (mmm) REVERT: E 287 MET cc_start: 0.9031 (ttp) cc_final: 0.8287 (tmm) REVERT: E 404 MET cc_start: 0.9156 (mmm) cc_final: 0.8888 (mmt) REVERT: E 411 MET cc_start: 0.9069 (ptp) cc_final: 0.8782 (ppp) REVERT: D 56 MET cc_start: 0.9291 (tpp) cc_final: 0.8870 (tpp) REVERT: D 89 MET cc_start: 0.7680 (ptt) cc_final: 0.7467 (ptt) REVERT: D 404 MET cc_start: 0.9040 (mmm) cc_final: 0.8676 (mtt) REVERT: B 56 MET cc_start: 0.9227 (tpp) cc_final: 0.8686 (tpp) REVERT: B 91 ASP cc_start: 0.9477 (m-30) cc_final: 0.9250 (p0) REVERT: B 246 MET cc_start: 0.5137 (ptt) cc_final: 0.4551 (ppp) REVERT: B 263 MET cc_start: 0.9298 (ttt) cc_final: 0.8917 (ttt) REVERT: B 404 MET cc_start: 0.8972 (mmm) cc_final: 0.8559 (mtt) REVERT: C 117 LEU cc_start: 0.9524 (tp) cc_final: 0.9314 (tp) REVERT: C 246 MET cc_start: 0.6503 (ptt) cc_final: 0.5883 (ppp) REVERT: C 263 MET cc_start: 0.9137 (mmt) cc_final: 0.8217 (mmt) REVERT: C 404 MET cc_start: 0.8725 (mmm) cc_final: 0.8269 (mtt) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1474 time to fit residues: 69.3735 Evaluate side-chains 247 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 21 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 211 optimal weight: 0.6980 chunk 163 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 193 optimal weight: 0.0770 chunk 112 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 127 optimal weight: 0.3980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 67 GLN A 125 ASN E 125 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 125 ASN C 67 GLN C 125 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.041012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.033410 restraints weight = 244414.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.034179 restraints weight = 175369.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.034751 restraints weight = 136728.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.035169 restraints weight = 113133.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.035415 restraints weight = 97767.272| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.8083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22453 Z= 0.114 Angle : 0.692 12.483 30453 Z= 0.339 Chirality : 0.045 0.237 3358 Planarity : 0.004 0.052 3808 Dihedral : 6.328 55.914 3083 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.16), residues: 2706 helix: -0.16 (0.25), residues: 420 sheet: -1.71 (0.17), residues: 814 loop : -1.44 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 18 TYR 0.022 0.001 TYR M 49 PHE 0.032 0.001 PHE C 295 TRP 0.028 0.001 TRP F 47 HIS 0.004 0.001 HIS M 91 Details of bonding type rmsd covalent geometry : bond 0.00249 (22428) covalent geometry : angle 0.69005 (30398) SS BOND : bond 0.00312 ( 20) SS BOND : angle 1.52421 ( 40) hydrogen bonds : bond 0.03183 ( 627) hydrogen bonds : angle 5.58300 ( 2091) link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 0.63807 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7373 (mpp) cc_final: 0.6248 (mpp) REVERT: K 92 TYR cc_start: 0.8246 (t80) cc_final: 0.7955 (t80) REVERT: F 19 LYS cc_start: 0.7969 (tmmt) cc_final: 0.7617 (tmmt) REVERT: F 81 MET cc_start: 0.8720 (tmm) cc_final: 0.8371 (tmm) REVERT: J 9 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8632 (mmtm) REVERT: J 61 ARG cc_start: 0.8269 (ptt-90) cc_final: 0.8052 (ttp-110) REVERT: J 62 PHE cc_start: 0.9097 (m-10) cc_final: 0.8698 (m-80) REVERT: J 87 TYR cc_start: 0.7946 (m-10) cc_final: 0.7326 (m-80) REVERT: G 12 MET cc_start: 0.8742 (mmt) cc_final: 0.8406 (mmm) REVERT: O 37 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8353 (tp-100) REVERT: O 92 TYR cc_start: 0.8537 (t80) cc_final: 0.8304 (t80) REVERT: N 39 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8245 (tp-100) REVERT: N 52 LEU cc_start: 0.9180 (mt) cc_final: 0.8878 (mt) REVERT: N 114 LEU cc_start: 0.9572 (tp) cc_final: 0.9129 (mm) REVERT: M 62 PHE cc_start: 0.9018 (m-80) cc_final: 0.8319 (m-80) REVERT: L 19 LYS cc_start: 0.8737 (pptt) cc_final: 0.8352 (tmmt) REVERT: L 45 LEU cc_start: 0.7927 (mm) cc_final: 0.7650 (mm) REVERT: L 69 THR cc_start: 0.9156 (m) cc_final: 0.8933 (m) REVERT: L 81 MET cc_start: 0.9143 (tmm) cc_final: 0.8737 (tmm) REVERT: I 4 MET cc_start: 0.8180 (mmm) cc_final: 0.7516 (mmm) REVERT: I 11 MET cc_start: 0.7804 (mmm) cc_final: 0.7104 (mmm) REVERT: I 86 TYR cc_start: 0.8844 (m-10) cc_final: 0.8452 (m-10) REVERT: H 114 LEU cc_start: 0.9511 (mm) cc_final: 0.9249 (mm) REVERT: A 91 ASP cc_start: 0.9638 (m-30) cc_final: 0.9391 (p0) REVERT: A 147 MET cc_start: 0.8764 (tpp) cc_final: 0.8503 (ttp) REVERT: A 246 MET cc_start: 0.3923 (ptt) cc_final: 0.3402 (ptm) REVERT: A 263 MET cc_start: 0.9002 (mmp) cc_final: 0.8562 (mmm) REVERT: A 287 MET cc_start: 0.9164 (tpt) cc_final: 0.8773 (tpt) REVERT: A 295 PHE cc_start: 0.9348 (m-80) cc_final: 0.8702 (m-80) REVERT: A 404 MET cc_start: 0.9232 (mmm) cc_final: 0.8933 (mmp) REVERT: E 157 GLU cc_start: 0.9056 (pt0) cc_final: 0.8680 (pt0) REVERT: E 163 MET cc_start: 0.8649 (mmm) cc_final: 0.8253 (mmm) REVERT: E 287 MET cc_start: 0.9050 (ttp) cc_final: 0.8831 (ttt) REVERT: E 404 MET cc_start: 0.9156 (mmm) cc_final: 0.8863 (mmt) REVERT: E 411 MET cc_start: 0.8922 (ptp) cc_final: 0.8697 (ppp) REVERT: D 56 MET cc_start: 0.9265 (tpp) cc_final: 0.8614 (tpp) REVERT: D 98 LEU cc_start: 0.9532 (tt) cc_final: 0.9275 (tp) REVERT: D 404 MET cc_start: 0.9034 (mmm) cc_final: 0.8637 (mtt) REVERT: B 91 ASP cc_start: 0.9531 (m-30) cc_final: 0.9314 (p0) REVERT: B 246 MET cc_start: 0.4925 (ptt) cc_final: 0.4397 (ppp) REVERT: B 263 MET cc_start: 0.9189 (ttt) cc_final: 0.8753 (ttt) REVERT: B 404 MET cc_start: 0.8870 (mmm) cc_final: 0.8444 (mtt) REVERT: C 56 MET cc_start: 0.9341 (tpp) cc_final: 0.8898 (tpp) REVERT: C 117 LEU cc_start: 0.9494 (tp) cc_final: 0.9253 (tp) REVERT: C 147 MET cc_start: 0.8900 (ttt) cc_final: 0.8556 (ttm) REVERT: C 246 MET cc_start: 0.6417 (ptt) cc_final: 0.5848 (ppp) REVERT: C 263 MET cc_start: 0.9026 (mmt) cc_final: 0.8076 (mmt) REVERT: C 404 MET cc_start: 0.8632 (mmm) cc_final: 0.8118 (mtt) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.1474 time to fit residues: 74.9503 Evaluate side-chains 264 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 211 optimal weight: 0.0030 chunk 133 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 238 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN A 67 GLN A 125 ASN E 31 ASN E 46 ASN E 125 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 203 ASN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.039104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.031837 restraints weight = 258571.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.032575 restraints weight = 185997.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.033108 restraints weight = 144678.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.033496 restraints weight = 119684.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.033767 restraints weight = 103721.648| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.8589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22453 Z= 0.173 Angle : 0.731 14.321 30453 Z= 0.362 Chirality : 0.045 0.233 3358 Planarity : 0.005 0.083 3808 Dihedral : 6.547 57.156 3083 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2706 helix: -0.23 (0.25), residues: 430 sheet: -1.87 (0.17), residues: 821 loop : -1.42 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 65 TYR 0.028 0.002 TYR M 49 PHE 0.032 0.002 PHE C 295 TRP 0.029 0.002 TRP F 47 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00375 (22428) covalent geometry : angle 0.72903 (30398) SS BOND : bond 0.00360 ( 20) SS BOND : angle 1.54296 ( 40) hydrogen bonds : bond 0.03503 ( 627) hydrogen bonds : angle 5.78006 ( 2091) link_NAG-ASN : bond 0.00179 ( 5) link_NAG-ASN : angle 0.52310 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7553 (mpp) cc_final: 0.5837 (mtt) REVERT: K 50 TRP cc_start: 0.9026 (m100) cc_final: 0.8602 (m-90) REVERT: K 92 TYR cc_start: 0.8393 (t80) cc_final: 0.8045 (t80) REVERT: F 19 LYS cc_start: 0.8060 (tmmt) cc_final: 0.7747 (tmmt) REVERT: F 81 MET cc_start: 0.8925 (tmm) cc_final: 0.8497 (tmm) REVERT: J 9 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8705 (mmtm) REVERT: J 18 ARG cc_start: 0.9211 (ptm-80) cc_final: 0.8856 (ttp80) REVERT: J 62 PHE cc_start: 0.9064 (m-10) cc_final: 0.8453 (m-80) REVERT: J 87 TYR cc_start: 0.8154 (m-10) cc_final: 0.7657 (m-80) REVERT: G 12 MET cc_start: 0.8711 (mmt) cc_final: 0.8302 (mmm) REVERT: N 52 LEU cc_start: 0.9175 (mt) cc_final: 0.8757 (mt) REVERT: N 81 MET cc_start: 0.8863 (tmm) cc_final: 0.8581 (tmm) REVERT: N 114 LEU cc_start: 0.9619 (tp) cc_final: 0.9253 (tp) REVERT: M 103 LYS cc_start: 0.9202 (tptt) cc_final: 0.8956 (tppt) REVERT: L 11 LEU cc_start: 0.8985 (tp) cc_final: 0.8704 (tp) REVERT: L 12 MET cc_start: 0.7756 (mmp) cc_final: 0.7276 (mmm) REVERT: L 19 LYS cc_start: 0.8765 (pptt) cc_final: 0.8327 (tmmt) REVERT: L 45 LEU cc_start: 0.7832 (mm) cc_final: 0.7404 (mm) REVERT: L 80 TYR cc_start: 0.6777 (m-80) cc_final: 0.6203 (m-80) REVERT: L 89 GLU cc_start: 0.9072 (mp0) cc_final: 0.8711 (mp0) REVERT: I 4 MET cc_start: 0.8265 (mmm) cc_final: 0.7462 (mmm) REVERT: I 11 MET cc_start: 0.7723 (mmm) cc_final: 0.7202 (mmm) REVERT: I 86 TYR cc_start: 0.8917 (m-10) cc_final: 0.8597 (m-10) REVERT: H 12 MET cc_start: 0.7885 (tpp) cc_final: 0.7067 (mmm) REVERT: A 91 ASP cc_start: 0.9631 (m-30) cc_final: 0.9360 (p0) REVERT: A 220 MET cc_start: 0.8422 (mmt) cc_final: 0.7958 (mmp) REVERT: A 246 MET cc_start: 0.4044 (ptt) cc_final: 0.3563 (ptm) REVERT: A 263 MET cc_start: 0.9118 (mmp) cc_final: 0.8869 (mmm) REVERT: A 287 MET cc_start: 0.9141 (tpt) cc_final: 0.8779 (tpt) REVERT: A 295 PHE cc_start: 0.9219 (m-80) cc_final: 0.8931 (m-80) REVERT: A 404 MET cc_start: 0.9283 (mmm) cc_final: 0.9015 (mmp) REVERT: E 157 GLU cc_start: 0.9246 (pt0) cc_final: 0.8939 (pt0) REVERT: E 163 MET cc_start: 0.8662 (mmm) cc_final: 0.8117 (mmm) REVERT: E 287 MET cc_start: 0.8977 (ttp) cc_final: 0.8481 (tmm) REVERT: E 404 MET cc_start: 0.9234 (mmm) cc_final: 0.8925 (mmt) REVERT: E 411 MET cc_start: 0.8991 (ptp) cc_final: 0.8755 (ppp) REVERT: D 404 MET cc_start: 0.9106 (mmm) cc_final: 0.8730 (mtt) REVERT: B 91 ASP cc_start: 0.9531 (m-30) cc_final: 0.9317 (p0) REVERT: B 140 MET cc_start: 0.8856 (mmp) cc_final: 0.8537 (mmm) REVERT: B 163 MET cc_start: 0.8241 (mmm) cc_final: 0.7898 (mmm) REVERT: B 246 MET cc_start: 0.5276 (ptt) cc_final: 0.4653 (ppp) REVERT: B 263 MET cc_start: 0.9215 (ttt) cc_final: 0.8840 (tpp) REVERT: B 404 MET cc_start: 0.8977 (mmm) cc_final: 0.8538 (mtt) REVERT: C 56 MET cc_start: 0.9457 (tpp) cc_final: 0.9248 (tpp) REVERT: C 246 MET cc_start: 0.6481 (ptt) cc_final: 0.5866 (ppp) REVERT: C 404 MET cc_start: 0.8757 (mmm) cc_final: 0.8255 (mtt) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1456 time to fit residues: 69.3081 Evaluate side-chains 242 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 139 optimal weight: 0.0870 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 103 ASN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN C 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.040690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.033107 restraints weight = 245894.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.033902 restraints weight = 175281.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.034478 restraints weight = 135643.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.034895 restraints weight = 111506.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.035206 restraints weight = 96275.305| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.8670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22453 Z= 0.116 Angle : 0.684 14.347 30453 Z= 0.335 Chirality : 0.045 0.234 3358 Planarity : 0.004 0.064 3808 Dihedral : 6.217 56.390 3083 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2706 helix: -0.01 (0.27), residues: 385 sheet: -1.73 (0.17), residues: 855 loop : -1.24 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 18 TYR 0.020 0.001 TYR M 49 PHE 0.031 0.001 PHE C 295 TRP 0.021 0.001 TRP F 47 HIS 0.006 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00256 (22428) covalent geometry : angle 0.68280 (30398) SS BOND : bond 0.00374 ( 20) SS BOND : angle 1.47743 ( 40) hydrogen bonds : bond 0.03077 ( 627) hydrogen bonds : angle 5.39099 ( 2091) link_NAG-ASN : bond 0.00245 ( 5) link_NAG-ASN : angle 0.67527 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7528 (mpp) cc_final: 0.6302 (mpp) REVERT: K 50 TRP cc_start: 0.9066 (m100) cc_final: 0.8606 (m-90) REVERT: K 92 TYR cc_start: 0.8277 (t80) cc_final: 0.7957 (t80) REVERT: F 11 LEU cc_start: 0.9082 (tp) cc_final: 0.8524 (tp) REVERT: F 12 MET cc_start: 0.7629 (mmm) cc_final: 0.6808 (mmm) REVERT: F 19 LYS cc_start: 0.7701 (tmmt) cc_final: 0.7417 (tmmt) REVERT: F 81 MET cc_start: 0.8715 (tmm) cc_final: 0.8304 (tmm) REVERT: J 9 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8680 (mmtm) REVERT: J 18 ARG cc_start: 0.9162 (ptm-80) cc_final: 0.8819 (ttp80) REVERT: J 46 LEU cc_start: 0.8896 (tp) cc_final: 0.8576 (tt) REVERT: J 62 PHE cc_start: 0.9063 (m-10) cc_final: 0.8518 (m-80) REVERT: J 87 TYR cc_start: 0.8062 (m-10) cc_final: 0.7603 (m-80) REVERT: G 12 MET cc_start: 0.8699 (mmt) cc_final: 0.8348 (mmm) REVERT: O 11 MET cc_start: 0.5900 (pmm) cc_final: 0.5280 (mmt) REVERT: O 92 TYR cc_start: 0.8531 (t80) cc_final: 0.8293 (t80) REVERT: N 52 LEU cc_start: 0.9112 (mt) cc_final: 0.8741 (mt) REVERT: N 81 MET cc_start: 0.8814 (tmm) cc_final: 0.8551 (tmm) REVERT: N 114 LEU cc_start: 0.9618 (tp) cc_final: 0.9320 (tp) REVERT: M 11 MET cc_start: 0.5971 (mmt) cc_final: 0.5098 (pmm) REVERT: M 62 PHE cc_start: 0.9058 (m-80) cc_final: 0.8285 (m-80) REVERT: L 12 MET cc_start: 0.7617 (mmp) cc_final: 0.7293 (mmm) REVERT: L 19 LYS cc_start: 0.8618 (pptt) cc_final: 0.8302 (tmmt) REVERT: L 20 ILE cc_start: 0.7625 (mt) cc_final: 0.6958 (mp) REVERT: L 45 LEU cc_start: 0.7835 (mm) cc_final: 0.7389 (mm) REVERT: L 69 THR cc_start: 0.9108 (m) cc_final: 0.8777 (m) REVERT: L 80 TYR cc_start: 0.6543 (m-80) cc_final: 0.6243 (m-80) REVERT: L 89 GLU cc_start: 0.9051 (mp0) cc_final: 0.8685 (mp0) REVERT: I 4 MET cc_start: 0.8310 (mmm) cc_final: 0.7632 (mmm) REVERT: I 11 MET cc_start: 0.7750 (mmm) cc_final: 0.7119 (mmm) REVERT: I 86 TYR cc_start: 0.8959 (m-10) cc_final: 0.8662 (m-10) REVERT: H 12 MET cc_start: 0.8076 (tpp) cc_final: 0.7228 (mmm) REVERT: A 91 ASP cc_start: 0.9631 (m-30) cc_final: 0.9359 (p0) REVERT: A 147 MET cc_start: 0.8719 (tpp) cc_final: 0.8507 (ttt) REVERT: A 246 MET cc_start: 0.4098 (ptt) cc_final: 0.3553 (ptm) REVERT: A 263 MET cc_start: 0.9086 (mmp) cc_final: 0.8781 (mmm) REVERT: A 287 MET cc_start: 0.9206 (tpt) cc_final: 0.8875 (tpt) REVERT: A 295 PHE cc_start: 0.9213 (m-80) cc_final: 0.8935 (m-80) REVERT: A 404 MET cc_start: 0.9295 (mmm) cc_final: 0.9039 (mmp) REVERT: E 91 ASP cc_start: 0.9575 (m-30) cc_final: 0.9373 (p0) REVERT: E 157 GLU cc_start: 0.9173 (pt0) cc_final: 0.8890 (pt0) REVERT: E 163 MET cc_start: 0.8618 (mmm) cc_final: 0.8284 (mmm) REVERT: E 404 MET cc_start: 0.9228 (mmm) cc_final: 0.8897 (mmt) REVERT: E 411 MET cc_start: 0.8888 (ptp) cc_final: 0.8666 (ppp) REVERT: D 93 ILE cc_start: 0.9206 (mm) cc_final: 0.9004 (mm) REVERT: D 98 LEU cc_start: 0.9521 (tt) cc_final: 0.9259 (tp) REVERT: D 404 MET cc_start: 0.9050 (mmm) cc_final: 0.8666 (mtt) REVERT: D 411 MET cc_start: 0.8160 (ptp) cc_final: 0.7937 (ppp) REVERT: B 91 ASP cc_start: 0.9563 (m-30) cc_final: 0.9328 (p0) REVERT: B 163 MET cc_start: 0.8284 (mmm) cc_final: 0.7971 (mmm) REVERT: B 246 MET cc_start: 0.5236 (ptt) cc_final: 0.4763 (ptp) REVERT: B 263 MET cc_start: 0.9254 (ttt) cc_final: 0.8836 (ttt) REVERT: B 404 MET cc_start: 0.8928 (mmm) cc_final: 0.8459 (mtt) REVERT: C 56 MET cc_start: 0.9441 (tpp) cc_final: 0.9205 (tpp) REVERT: C 98 LEU cc_start: 0.9452 (tt) cc_final: 0.8900 (tp) REVERT: C 117 LEU cc_start: 0.9546 (tp) cc_final: 0.9309 (tp) REVERT: C 246 MET cc_start: 0.6461 (ptt) cc_final: 0.5859 (ppp) REVERT: C 263 MET cc_start: 0.9041 (mmt) cc_final: 0.8132 (mmt) REVERT: C 404 MET cc_start: 0.8722 (mmm) cc_final: 0.8204 (mtt) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.1490 time to fit residues: 73.3590 Evaluate side-chains 251 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 137 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 99 optimal weight: 0.0370 chunk 126 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 12 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN B 203 ASN C 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.038468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.031296 restraints weight = 264330.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.032049 restraints weight = 186849.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.032597 restraints weight = 144053.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.032985 restraints weight = 118338.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.033273 restraints weight = 101862.720| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.9263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22453 Z= 0.211 Angle : 0.786 15.000 30453 Z= 0.390 Chirality : 0.046 0.234 3358 Planarity : 0.005 0.053 3808 Dihedral : 6.711 57.693 3083 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2706 helix: -0.24 (0.26), residues: 385 sheet: -1.85 (0.18), residues: 793 loop : -1.32 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 18 TYR 0.031 0.002 TYR M 49 PHE 0.031 0.002 PHE C 295 TRP 0.032 0.002 TRP F 47 HIS 0.006 0.001 HIS E 201 Details of bonding type rmsd covalent geometry : bond 0.00454 (22428) covalent geometry : angle 0.78446 (30398) SS BOND : bond 0.00447 ( 20) SS BOND : angle 1.60055 ( 40) hydrogen bonds : bond 0.03754 ( 627) hydrogen bonds : angle 5.92635 ( 2091) link_NAG-ASN : bond 0.00190 ( 5) link_NAG-ASN : angle 0.57728 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5412 Ramachandran restraints generated. 2706 Oldfield, 0 Emsley, 2706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 4 MET cc_start: 0.7660 (mpp) cc_final: 0.5923 (mtt) REVERT: K 92 TYR cc_start: 0.8444 (t80) cc_final: 0.8197 (t80) REVERT: F 19 LYS cc_start: 0.7918 (tmmt) cc_final: 0.7566 (tmmt) REVERT: F 81 MET cc_start: 0.8903 (tmm) cc_final: 0.8451 (tmm) REVERT: J 9 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8735 (mmtm) REVERT: J 18 ARG cc_start: 0.9284 (ptm-80) cc_final: 0.8946 (ttp80) REVERT: J 62 PHE cc_start: 0.9056 (m-10) cc_final: 0.8441 (m-80) REVERT: J 87 TYR cc_start: 0.8253 (m-10) cc_final: 0.7746 (m-80) REVERT: G 12 MET cc_start: 0.8741 (mmt) cc_final: 0.8299 (mmm) REVERT: O 11 MET cc_start: 0.5971 (pmm) cc_final: 0.5005 (mmt) REVERT: O 39 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8484 (mmmt) REVERT: N 52 LEU cc_start: 0.9203 (mt) cc_final: 0.8791 (mt) REVERT: N 81 MET cc_start: 0.9010 (tmm) cc_final: 0.8710 (tmm) REVERT: N 114 LEU cc_start: 0.9668 (tp) cc_final: 0.9242 (tp) REVERT: L 12 MET cc_start: 0.7601 (mmp) cc_final: 0.7332 (mmm) REVERT: L 19 LYS cc_start: 0.8754 (pptt) cc_final: 0.8269 (tmmt) REVERT: L 45 LEU cc_start: 0.7623 (mm) cc_final: 0.7177 (mm) REVERT: L 81 MET cc_start: 0.9320 (ptm) cc_final: 0.8923 (ptm) REVERT: L 89 GLU cc_start: 0.9126 (mp0) cc_final: 0.8783 (mp0) REVERT: I 4 MET cc_start: 0.8289 (mmm) cc_final: 0.7511 (mmm) REVERT: I 11 MET cc_start: 0.7767 (mmm) cc_final: 0.7015 (pmm) REVERT: I 86 TYR cc_start: 0.8960 (m-10) cc_final: 0.8602 (m-10) REVERT: H 12 MET cc_start: 0.8044 (tpp) cc_final: 0.7231 (mmm) REVERT: A 91 ASP cc_start: 0.9614 (m-30) cc_final: 0.9316 (p0) REVERT: A 147 MET cc_start: 0.8745 (tpp) cc_final: 0.8378 (tpp) REVERT: A 220 MET cc_start: 0.8536 (mmt) cc_final: 0.8053 (mmp) REVERT: A 246 MET cc_start: 0.4156 (ptt) cc_final: 0.3653 (ptm) REVERT: A 263 MET cc_start: 0.9203 (mmp) cc_final: 0.8804 (mmm) REVERT: A 287 MET cc_start: 0.9192 (tpt) cc_final: 0.8843 (tpt) REVERT: A 295 PHE cc_start: 0.9231 (m-80) cc_final: 0.8959 (m-80) REVERT: A 404 MET cc_start: 0.9330 (mmm) cc_final: 0.9070 (mmp) REVERT: E 56 MET cc_start: 0.9152 (tpp) cc_final: 0.8438 (tpp) REVERT: E 91 ASP cc_start: 0.9562 (m-30) cc_final: 0.9309 (p0) REVERT: E 157 GLU cc_start: 0.9342 (pt0) cc_final: 0.9068 (pt0) REVERT: E 163 MET cc_start: 0.8636 (mmm) cc_final: 0.8217 (mmm) REVERT: E 287 MET cc_start: 0.9060 (ttp) cc_final: 0.8329 (tmm) REVERT: E 404 MET cc_start: 0.9271 (mmm) cc_final: 0.8960 (mmt) REVERT: E 411 MET cc_start: 0.9028 (ptp) cc_final: 0.8766 (ppp) REVERT: D 56 MET cc_start: 0.9272 (tpp) cc_final: 0.8520 (tpp) REVERT: D 404 MET cc_start: 0.9144 (mmm) cc_final: 0.8745 (mmt) REVERT: D 411 MET cc_start: 0.8319 (ptp) cc_final: 0.8098 (ppp) REVERT: B 91 ASP cc_start: 0.9545 (m-30) cc_final: 0.9300 (p0) REVERT: B 163 MET cc_start: 0.8231 (mmm) cc_final: 0.7890 (mmm) REVERT: B 246 MET cc_start: 0.5275 (ptt) cc_final: 0.4830 (ptp) REVERT: B 263 MET cc_start: 0.9370 (ttt) cc_final: 0.9105 (tpp) REVERT: B 404 MET cc_start: 0.9018 (mmm) cc_final: 0.8647 (mtt) REVERT: C 56 MET cc_start: 0.9495 (tpp) cc_final: 0.9238 (tpp) REVERT: C 246 MET cc_start: 0.6422 (ptt) cc_final: 0.5774 (ppp) REVERT: C 263 MET cc_start: 0.9126 (mmt) cc_final: 0.8230 (mmt) REVERT: C 404 MET cc_start: 0.8851 (mmm) cc_final: 0.8379 (mtt) REVERT: C 411 MET cc_start: 0.8429 (ptp) cc_final: 0.7892 (ppp) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1481 time to fit residues: 66.2862 Evaluate side-chains 232 residues out of total 2386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.037480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.030467 restraints weight = 269959.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.031185 restraints weight = 193025.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.031689 restraints weight = 149793.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.032063 restraints weight = 123851.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.032338 restraints weight = 107061.070| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.9936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22453 Z= 0.242 Angle : 0.825 15.619 30453 Z= 0.411 Chirality : 0.048 0.231 3358 Planarity : 0.005 0.056 3808 Dihedral : 7.174 58.034 3083 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 27.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.16), residues: 2706 helix: -0.48 (0.25), residues: 385 sheet: -2.10 (0.18), residues: 762 loop : -1.43 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 18 TYR 0.030 0.002 TYR M 49 PHE 0.032 0.002 PHE C 295 TRP 0.034 0.002 TRP F 47 HIS 0.007 0.002 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00515 (22428) covalent geometry : angle 0.82282 (30398) SS BOND : bond 0.00455 ( 20) SS BOND : angle 1.82225 ( 40) hydrogen bonds : bond 0.04086 ( 627) hydrogen bonds : angle 6.37871 ( 2091) link_NAG-ASN : bond 0.00255 ( 5) link_NAG-ASN : angle 0.63229 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3516.41 seconds wall clock time: 62 minutes 8.05 seconds (3728.05 seconds total)