Starting phenix.real_space_refine on Mon Aug 25 22:12:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1n_62749/08_2025/9l1n_62749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1n_62749/08_2025/9l1n_62749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l1n_62749/08_2025/9l1n_62749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1n_62749/08_2025/9l1n_62749.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1n_62749/08_2025/9l1n_62749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1n_62749/08_2025/9l1n_62749.cif" } resolution = 3.3 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= 0.000 sd= 0.008 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 190 5.16 5 C 20089 2.51 5 N 5457 2.21 5 O 5952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31688 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3310 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "B" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3240 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "C" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1153 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 9, 'TRANS': 140} Chain: "D" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3310 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "E" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3240 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "F" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1153 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 9, 'TRANS': 140} Chain: "G" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3310 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "H" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3240 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "I" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1153 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 9, 'TRANS': 140} Chain: "J" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3310 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "K" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3240 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 28, 'TRANS': 386} Chain: "L" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1153 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 9, 'TRANS': 140} Chain: "M" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} 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: "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: "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: "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: "G" 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: "H" 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: "J" 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: "K" 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: 7.23, per 1000 atoms: 0.23 Number of scatterers: 31688 At special positions: 0 Unit cell: (172.86, 198.32, 205.02, 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 190 16.00 O 5952 8.00 N 5457 7.00 C 20089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.02 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.02 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.04 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.04 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 124 " distance=2.02 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 91 " - pdb=" SG CYS E 105 " distance=2.04 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 266 " distance=2.04 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 226 " distance=2.03 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.02 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.04 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.03 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.04 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.02 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.03 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.04 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.04 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 124 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.04 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 85 " - pdb=" SG CYS M 91 " distance=1.86 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 139 " " NAG B 501 " - " ASN B 196 " " NAG D 501 " - " ASN D 139 " " NAG E 501 " - " ASN E 196 " " NAG G 501 " - " ASN G 139 " " NAG H 501 " - " ASN H 196 " " NAG J 501 " - " ASN J 139 " " NAG K 501 " - " ASN K 196 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.4 microseconds 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7580 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 11.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 removed outlier: 6.889A pdb=" N ILE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 117' Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 404 through 436 removed outlier: 4.175A pdb=" N LEU A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 358 through 361 No H-bonds generated for 'chain 'B' and resid 358 through 361' Processing helix chain 'B' and resid 366 through 395 Processing helix chain 'B' and resid 409 through 415 Processing helix chain 'C' and resid 144 through 147 No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 166 through 171 removed outlier: 5.631A pdb=" N SER C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 171' Processing helix chain 'D' and resid 112 through 117 removed outlier: 6.475A pdb=" N ILE D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 404 through 436 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 366 through 395 Processing helix chain 'E' and resid 409 through 415 Processing helix chain 'F' and resid 144 through 147 No H-bonds generated for 'chain 'F' and resid 144 through 147' Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 166 through 171 removed outlier: 5.668A pdb=" N SER F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP F 171 " --> pdb=" O ASN F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 171' Processing helix chain 'G' and resid 112 through 117 removed outlier: 6.250A pdb=" N ILE G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 245 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 256 through 258 No H-bonds generated for 'chain 'G' and resid 256 through 258' Processing helix chain 'G' and resid 404 through 436 removed outlier: 3.936A pdb=" N LEU G 410 " --> pdb=" O SER G 406 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 82 No H-bonds generated for 'chain 'H' and resid 80 through 82' Processing helix chain 'H' and resid 223 through 225 No H-bonds generated for 'chain 'H' and resid 223 through 225' Processing helix chain 'H' and resid 358 through 361 No H-bonds generated for 'chain 'H' and resid 358 through 361' Processing helix chain 'H' and resid 366 through 395 Processing helix chain 'H' and resid 409 through 415 Processing helix chain 'I' and resid 144 through 147 No H-bonds generated for 'chain 'I' and resid 144 through 147' Processing helix chain 'I' and resid 155 through 157 No H-bonds generated for 'chain 'I' and resid 155 through 157' Processing helix chain 'I' and resid 166 through 171 removed outlier: 7.348A pdb=" N SER I 170 " --> pdb=" O GLN I 166 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASP I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 171' Processing helix chain 'J' and resid 112 through 117 removed outlier: 6.448A pdb=" N ILE J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 112 through 117' Processing helix chain 'J' and resid 239 through 245 Processing helix chain 'J' and resid 251 through 253 No H-bonds generated for 'chain 'J' and resid 251 through 253' Processing helix chain 'J' and resid 256 through 258 No H-bonds generated for 'chain 'J' and resid 256 through 258' Processing helix chain 'J' and resid 404 through 436 removed outlier: 4.321A pdb=" N ALA J 412 " --> pdb=" O ASN J 408 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE J 421 " --> pdb=" O ALA J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 82 No H-bonds generated for 'chain 'K' and resid 80 through 82' Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'K' and resid 358 through 361 No H-bonds generated for 'chain 'K' and resid 358 through 361' Processing helix chain 'K' and resid 366 through 395 Processing helix chain 'K' and resid 409 through 415 Processing helix chain 'L' and resid 144 through 148 removed outlier: 5.005A pdb=" N ALA L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 144 through 148' Processing helix chain 'L' and resid 166 through 171 removed outlier: 6.658A pdb=" N SER L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP L 171 " --> pdb=" O ASN L 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 166 through 171' Processing helix chain 'M' and resid 37 through 40 No H-bonds generated for 'chain 'M' and resid 37 through 40' Processing helix chain 'M' and resid 45 through 51 removed outlier: 4.589A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA M 50 " --> pdb=" O THR M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 59 No H-bonds generated for 'chain 'M' and resid 57 through 59' Processing helix chain 'M' and resid 81 through 85 241 hydrogen bonds defined for protein. 723 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: 3.65 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10214 1.34 - 1.47: 8044 1.47 - 1.59: 14005 1.59 - 1.72: 0 1.72 - 1.85: 242 Bond restraints: 32505 Sorted by residual: bond pdb=" C ALA H 403 " pdb=" N PRO H 404 " ideal model delta sigma weight residual 1.328 1.362 -0.034 1.25e-02 6.40e+03 7.25e+00 bond pdb=" C TRP H 351 " pdb=" N PRO H 352 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.16e+00 bond pdb=" CA ILE M 79 " pdb=" C ILE M 79 " ideal model delta sigma weight residual 1.526 1.498 0.028 1.13e-02 7.83e+03 5.99e+00 bond pdb=" N ILE M 79 " pdb=" CA ILE M 79 " ideal model delta sigma weight residual 1.460 1.434 0.026 1.10e-02 8.26e+03 5.46e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.15e+00 ... (remaining 32500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 43087 2.78 - 5.57: 1015 5.57 - 8.35: 119 8.35 - 11.13: 32 11.13 - 13.92: 7 Bond angle restraints: 44260 Sorted by residual: angle pdb=" C LEU H 397 " pdb=" N THR H 398 " pdb=" CA THR H 398 " ideal model delta sigma weight residual 120.09 132.98 -12.89 1.25e+00 6.40e-01 1.06e+02 angle pdb=" N GLU M 100 " pdb=" CA GLU M 100 " pdb=" C GLU M 100 " ideal model delta sigma weight residual 113.38 123.56 -10.18 1.23e+00 6.61e-01 6.85e+01 angle pdb=" O LEU H 397 " pdb=" C LEU H 397 " pdb=" N THR H 398 " ideal model delta sigma weight residual 121.63 112.03 9.60 1.52e+00 4.33e-01 3.99e+01 angle pdb=" N CYS M 85 " pdb=" CA CYS M 85 " pdb=" C CYS M 85 " ideal model delta sigma weight residual 111.07 104.71 6.36 1.07e+00 8.73e-01 3.54e+01 angle pdb=" C THR G 217 " pdb=" N ASP G 218 " pdb=" CA ASP G 218 " ideal model delta sigma weight residual 122.82 130.48 -7.66 1.42e+00 4.96e-01 2.91e+01 ... (remaining 44255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 18344 17.41 - 34.81: 1004 34.81 - 52.22: 214 52.22 - 69.62: 15 69.62 - 87.03: 17 Dihedral angle restraints: 19594 sinusoidal: 7757 harmonic: 11837 Sorted by residual: dihedral pdb=" CB CYS J 62 " pdb=" SG CYS J 62 " pdb=" SG CYS J 94 " pdb=" CB CYS J 94 " ideal model delta sinusoidal sigma weight residual -86.00 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS J 306 " pdb=" SG CYS J 306 " pdb=" SG CYS J 380 " pdb=" CB CYS J 380 " ideal model delta sinusoidal sigma weight residual -86.00 -4.71 -81.29 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -165.11 79.11 1 1.00e+01 1.00e-02 7.79e+01 ... (remaining 19591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3883 0.075 - 0.150: 932 0.150 - 0.225: 156 0.225 - 0.299: 25 0.299 - 0.374: 4 Chirality restraints: 5000 Sorted by residual: chirality pdb=" CA GLU M 100 " pdb=" N GLU M 100 " pdb=" C GLU M 100 " pdb=" CB GLU M 100 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB ILE D 307 " pdb=" CA ILE D 307 " pdb=" CG1 ILE D 307 " pdb=" CG2 ILE D 307 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB ILE J 366 " pdb=" CA ILE J 366 " pdb=" CG1 ILE J 366 " pdb=" CG2 ILE J 366 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 4997 not shown) Planarity restraints: 5679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 264 " -0.058 5.00e-02 4.00e+02 8.72e-02 1.22e+01 pdb=" N PRO D 265 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 99 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C LEU M 99 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU M 99 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU M 100 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU G 264 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO G 265 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO G 265 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 265 " -0.045 5.00e-02 4.00e+02 ... (remaining 5676 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 281 2.62 - 3.19: 25878 3.19 - 3.76: 46733 3.76 - 4.33: 60802 4.33 - 4.90: 101497 Nonbonded interactions: 235191 Sorted by model distance: nonbonded pdb=" O CYS M 85 " pdb=" O SER M 88 " model vdw 2.046 3.040 nonbonded pdb=" OH TYR D 76 " pdb=" OE1 GLU D 105 " model vdw 2.248 3.040 nonbonded pdb=" OG1 THR H 277 " pdb=" OG1 THR H 284 " model vdw 2.257 3.040 nonbonded pdb=" O TYR K 359 " pdb=" OG1 THR K 367 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU H 138 " pdb=" OG1 THR H 293 " model vdw 2.281 3.040 ... (remaining 235186 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.600 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 : 0.007 0.167 32569 Z= 0.314 Angle : 1.079 32.036 44396 Z= 0.579 Chirality : 0.067 0.374 5000 Planarity : 0.009 0.087 5671 Dihedral : 10.983 82.649 11846 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.62 (0.10), residues: 4081 helix: -2.78 (0.18), residues: 401 sheet: -2.95 (0.13), residues: 1191 loop : -3.31 (0.10), residues: 2489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 44 TYR 0.050 0.003 TYR B 18 PHE 0.037 0.004 PHE E 100 TRP 0.027 0.004 TRP A 407 HIS 0.021 0.002 HIS E 349 Details of bonding type rmsd covalent geometry : bond 0.00740 (32505) covalent geometry : angle 1.06104 (44260) SS BOND : bond 0.02296 ( 56) SS BOND : angle 4.00063 ( 112) hydrogen bonds : bond 0.06174 ( 241) hydrogen bonds : angle 5.73830 ( 723) link_NAG-ASN : bond 0.00277 ( 8) link_NAG-ASN : angle 2.06636 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 716 time to evaluate : 1.247 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: A 24 TYR cc_start: 0.8443 (m-10) cc_final: 0.8218 (m-80) REVERT: A 218 ASP cc_start: 0.8579 (t0) cc_final: 0.8312 (t0) REVERT: A 237 VAL cc_start: 0.8952 (p) cc_final: 0.8520 (m) REVERT: A 288 VAL cc_start: 0.9191 (p) cc_final: 0.8843 (m) REVERT: A 324 ARG cc_start: 0.7826 (ttp-110) cc_final: 0.7383 (ptm160) REVERT: A 381 LYS cc_start: 0.7846 (mtmp) cc_final: 0.7548 (mttp) REVERT: A 407 TRP cc_start: 0.6699 (OUTLIER) cc_final: 0.6279 (m-10) REVERT: B 217 MET cc_start: 0.7110 (mmp) cc_final: 0.6226 (mmt) REVERT: B 365 VAL cc_start: 0.8546 (t) cc_final: 0.8080 (m) REVERT: D 61 LYS cc_start: 0.8390 (tttp) cc_final: 0.8044 (ttmt) REVERT: D 124 VAL cc_start: 0.8753 (m) cc_final: 0.8417 (p) REVERT: D 207 SER cc_start: 0.8764 (p) cc_final: 0.8511 (p) REVERT: D 234 THR cc_start: 0.8951 (t) cc_final: 0.8718 (m) REVERT: D 328 CYS cc_start: 0.5596 (m) cc_final: 0.5172 (m) REVERT: D 346 VAL cc_start: 0.8096 (p) cc_final: 0.7769 (m) REVERT: E 239 ASN cc_start: 0.8006 (p0) cc_final: 0.7712 (p0) REVERT: F 126 VAL cc_start: 0.8084 (m) cc_final: 0.7876 (t) REVERT: F 132 MET cc_start: 0.7267 (mpt) cc_final: 0.7017 (mpt) REVERT: G 146 THR cc_start: 0.8558 (p) cc_final: 0.8358 (p) REVERT: G 338 VAL cc_start: 0.8842 (t) cc_final: 0.8620 (t) REVERT: G 341 GLU cc_start: 0.8377 (mp0) cc_final: 0.7750 (mp0) REVERT: G 373 LYS cc_start: 0.7926 (mttp) cc_final: 0.7680 (mttt) REVERT: H 158 LEU cc_start: 0.8760 (mt) cc_final: 0.8399 (mm) REVERT: J 10 VAL cc_start: 0.8361 (t) cc_final: 0.8159 (t) REVERT: J 66 LEU cc_start: 0.6373 (mm) cc_final: 0.5964 (mt) REVERT: J 241 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6845 (pt0) REVERT: J 297 LEU cc_start: 0.7619 (mm) cc_final: 0.7352 (mp) REVERT: J 298 GLU cc_start: 0.7426 (pm20) cc_final: 0.6999 (pm20) REVERT: J 404 LYS cc_start: 0.7644 (ttpm) cc_final: 0.7026 (tppt) REVERT: K 80 MET cc_start: 0.8339 (tpp) cc_final: 0.7816 (mmm) REVERT: K 199 TYR cc_start: 0.5995 (p90) cc_final: 0.5675 (p90) REVERT: K 252 GLN cc_start: 0.7316 (mm110) cc_final: 0.6889 (mm-40) REVERT: K 305 ASP cc_start: 0.7987 (t70) cc_final: 0.7653 (t70) REVERT: M 68 LEU cc_start: 0.6453 (mm) cc_final: 0.5771 (tt) outliers start: 6 outliers final: 2 residues processed: 722 average time/residue: 0.2227 time to fit residues: 253.1942 Evaluate side-chains 420 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 417 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain H residue 105 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 125 HIS A 230 HIS A 392 HIS B 104 GLN B 157 HIS B 246 HIS B 349 HIS ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 HIS C 188 HIS C 217 ASN D 125 HIS D 246 ASN D 392 HIS E 50 GLN E 55 GLN E 157 HIS E 246 HIS E 361 HIS ** F 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN G 125 HIS G 143 HIS ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 GLN H 73 HIS H 246 HIS I 188 HIS ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS J 125 HIS J 143 HIS J 270 ASN J 377 ASN J 392 HIS K 73 HIS K 157 HIS ** K 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 HIS L 230 ASN M 19 GLN M 25 GLN M 30 HIS M 58 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.200339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.158202 restraints weight = 39302.535| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.50 r_work: 0.3451 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32569 Z= 0.134 Angle : 0.646 8.514 44396 Z= 0.332 Chirality : 0.046 0.209 5000 Planarity : 0.006 0.077 5671 Dihedral : 6.376 58.506 4596 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.59 % Allowed : 11.64 % Favored : 85.77 % 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 aren not related in a simple way. whole: -3.80 (0.11), residues: 4081 helix: -0.91 (0.23), residues: 401 sheet: -2.60 (0.13), residues: 1263 loop : -2.85 (0.11), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 220 TYR 0.022 0.001 TYR G 308 PHE 0.022 0.002 PHE G 414 TRP 0.017 0.001 TRP G 243 HIS 0.014 0.001 HIS G 3 Details of bonding type rmsd covalent geometry : bond 0.00317 (32505) covalent geometry : angle 0.63942 (44260) SS BOND : bond 0.00464 ( 56) SS BOND : angle 1.71041 ( 112) hydrogen bonds : bond 0.03996 ( 241) hydrogen bonds : angle 4.46470 ( 723) link_NAG-ASN : bond 0.00360 ( 8) link_NAG-ASN : angle 2.12886 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 471 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8645 (m-10) cc_final: 0.8284 (m-80) REVERT: A 237 VAL cc_start: 0.9136 (p) cc_final: 0.8829 (t) REVERT: A 288 VAL cc_start: 0.9167 (p) cc_final: 0.8877 (m) REVERT: A 324 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7717 (ptm160) REVERT: A 407 TRP cc_start: 0.7150 (OUTLIER) cc_final: 0.6199 (t60) REVERT: B 77 GLU cc_start: 0.8354 (mp0) cc_final: 0.7841 (mp0) REVERT: B 217 MET cc_start: 0.6919 (mmp) cc_final: 0.6055 (mmt) REVERT: B 312 THR cc_start: 0.9139 (t) cc_final: 0.8895 (m) REVERT: D 62 CYS cc_start: 0.7614 (m) cc_final: 0.7328 (m) REVERT: D 207 SER cc_start: 0.9037 (p) cc_final: 0.8787 (p) REVERT: D 284 ASP cc_start: 0.8024 (m-30) cc_final: 0.7758 (m-30) REVERT: D 328 CYS cc_start: 0.7160 (m) cc_final: 0.6682 (m) REVERT: D 346 VAL cc_start: 0.8240 (p) cc_final: 0.7904 (m) REVERT: D 352 ILE cc_start: 0.7430 (pp) cc_final: 0.7158 (pp) REVERT: E 305 ASP cc_start: 0.8090 (t0) cc_final: 0.7880 (t0) REVERT: E 412 LEU cc_start: 0.1266 (OUTLIER) cc_final: 0.0970 (tm) REVERT: G 108 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9090 (m) REVERT: H 305 ASP cc_start: 0.8281 (p0) cc_final: 0.7979 (p0) REVERT: H 311 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8109 (pt) REVERT: J 49 CYS cc_start: 0.8693 (p) cc_final: 0.8461 (p) REVERT: J 220 ARG cc_start: 0.5168 (pmt170) cc_final: 0.3708 (ptp-170) REVERT: J 404 LYS cc_start: 0.7952 (ttpm) cc_final: 0.7402 (tppt) REVERT: K 141 LEU cc_start: 0.8420 (tt) cc_final: 0.7494 (tt) REVERT: K 199 TYR cc_start: 0.6031 (p90) cc_final: 0.5831 (p90) REVERT: K 305 ASP cc_start: 0.8231 (t70) cc_final: 0.7887 (t70) REVERT: L 168 MET cc_start: 0.5115 (mtt) cc_final: 0.4810 (mmp) REVERT: L 191 VAL cc_start: 0.5481 (p) cc_final: 0.5215 (t) REVERT: M 68 LEU cc_start: 0.6237 (mm) cc_final: 0.5762 (tt) outliers start: 90 outliers final: 39 residues processed: 538 average time/residue: 0.2062 time to fit residues: 179.8085 Evaluate side-chains 417 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 105 CYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 104 GLU Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 201 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 402 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 333 HIS A 345 HIS B 252 GLN B 361 HIS D 125 HIS D 246 ASN ** D 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 333 HIS G 52 HIS H 256 HIS H 349 HIS H 361 HIS ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 HIS J 275 HIS J 345 HIS K 363 HIS ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.187428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.130303 restraints weight = 38545.203| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.52 r_work: 0.3145 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 32569 Z= 0.278 Angle : 0.793 11.213 44396 Z= 0.404 Chirality : 0.052 0.226 5000 Planarity : 0.007 0.082 5671 Dihedral : 6.513 55.739 4596 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.10 % Allowed : 13.51 % Favored : 81.39 % 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 aren not related in a simple way. whole: -3.45 (0.12), residues: 4081 helix: -0.24 (0.26), residues: 397 sheet: -2.45 (0.13), residues: 1247 loop : -2.64 (0.11), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 220 TYR 0.036 0.002 TYR D 308 PHE 0.035 0.003 PHE E 100 TRP 0.016 0.002 TRP K 351 HIS 0.010 0.002 HIS E 169 Details of bonding type rmsd covalent geometry : bond 0.00706 (32505) covalent geometry : angle 0.78537 (44260) SS BOND : bond 0.00574 ( 56) SS BOND : angle 2.03446 ( 112) hydrogen bonds : bond 0.04616 ( 241) hydrogen bonds : angle 4.13245 ( 723) link_NAG-ASN : bond 0.00314 ( 8) link_NAG-ASN : angle 2.23741 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 377 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8927 (m-10) cc_final: 0.8636 (m-80) REVERT: A 42 THR cc_start: 0.8580 (m) cc_final: 0.8332 (m) REVERT: A 72 SER cc_start: 0.8669 (m) cc_final: 0.8446 (p) REVERT: A 237 VAL cc_start: 0.9355 (p) cc_final: 0.9082 (t) REVERT: A 288 VAL cc_start: 0.9206 (p) cc_final: 0.8986 (m) REVERT: A 362 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8260 (mm-40) REVERT: A 386 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8016 (p-80) REVERT: B 6 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8249 (t80) REVERT: B 8 LEU cc_start: 0.9175 (mp) cc_final: 0.8964 (mt) REVERT: B 217 MET cc_start: 0.7372 (mmp) cc_final: 0.6527 (mmt) REVERT: B 295 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8711 (tp) REVERT: D 97 ASP cc_start: 0.7256 (m-30) cc_final: 0.6861 (p0) REVERT: D 105 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8655 (pt0) REVERT: D 125 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7175 (p-80) REVERT: D 170 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.5427 (p90) REVERT: D 207 SER cc_start: 0.9177 (p) cc_final: 0.8905 (p) REVERT: D 218 ASP cc_start: 0.8881 (t0) cc_final: 0.8450 (t0) REVERT: D 284 ASP cc_start: 0.8226 (m-30) cc_final: 0.7850 (m-30) REVERT: D 321 LYS cc_start: 0.8194 (pptt) cc_final: 0.7962 (mmtm) REVERT: D 346 VAL cc_start: 0.8365 (OUTLIER) cc_final: 0.8020 (m) REVERT: D 352 ILE cc_start: 0.7586 (pp) cc_final: 0.7279 (pt) REVERT: E 129 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8292 (tptm) REVERT: E 169 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.8072 (p-80) REVERT: E 295 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8476 (tt) REVERT: E 412 LEU cc_start: 0.1327 (OUTLIER) cc_final: 0.1020 (tm) REVERT: G 226 VAL cc_start: 0.8826 (p) cc_final: 0.8623 (m) REVERT: H 202 LYS cc_start: 0.7484 (tttp) cc_final: 0.7052 (tttt) REVERT: H 254 LYS cc_start: 0.7557 (pptt) cc_final: 0.7115 (pptt) REVERT: H 311 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8081 (mt) REVERT: J 151 VAL cc_start: 0.7425 (m) cc_final: 0.6736 (p) REVERT: J 273 TYR cc_start: 0.7816 (p90) cc_final: 0.7392 (p90) REVERT: J 362 GLN cc_start: 0.7013 (mm-40) cc_final: 0.6785 (mm-40) REVERT: J 404 LYS cc_start: 0.7916 (ttpm) cc_final: 0.6987 (tppt) REVERT: J 433 MET cc_start: 0.6037 (tpt) cc_final: 0.5538 (tpt) REVERT: K 239 ASN cc_start: 0.7967 (t0) cc_final: 0.7736 (t0) REVERT: K 305 ASP cc_start: 0.8604 (t70) cc_final: 0.8247 (t70) REVERT: L 168 MET cc_start: 0.5616 (mtt) cc_final: 0.4918 (mmp) REVERT: M 77 GLU cc_start: 0.6570 (mp0) cc_final: 0.6336 (mp0) outliers start: 177 outliers final: 104 residues processed: 510 average time/residue: 0.1983 time to fit residues: 167.2992 Evaluate side-chains 427 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 312 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 407 TRP Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 169 HIS Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 363 HIS Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 363 HIS Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 214 VAL Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 402 VAL Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 240 VAL Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 320 optimal weight: 5.9990 chunk 358 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN E 349 HIS G 235 GLN G 275 HIS J 175 HIS J 377 ASN J 386 HIS K 50 GLN K 174 HIS K 363 HIS L 136 HIS M 25 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.191902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136826 restraints weight = 38260.730| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.55 r_work: 0.3218 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32569 Z= 0.110 Angle : 0.603 10.380 44396 Z= 0.306 Chirality : 0.045 0.310 5000 Planarity : 0.005 0.069 5671 Dihedral : 5.672 58.014 4594 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.37 % Allowed : 16.76 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.12), residues: 4081 helix: 0.26 (0.26), residues: 405 sheet: -2.13 (0.14), residues: 1224 loop : -2.38 (0.11), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 134 TYR 0.026 0.001 TYR D 308 PHE 0.019 0.001 PHE G 414 TRP 0.011 0.001 TRP E 279 HIS 0.016 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00259 (32505) covalent geometry : angle 0.59690 (44260) SS BOND : bond 0.00355 ( 56) SS BOND : angle 1.61776 ( 112) hydrogen bonds : bond 0.03649 ( 241) hydrogen bonds : angle 3.96750 ( 723) link_NAG-ASN : bond 0.00790 ( 8) link_NAG-ASN : angle 1.92673 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 377 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8825 (m-10) cc_final: 0.8416 (m-80) REVERT: A 42 THR cc_start: 0.8332 (m) cc_final: 0.8119 (m) REVERT: A 237 VAL cc_start: 0.9328 (p) cc_final: 0.9079 (t) REVERT: A 288 VAL cc_start: 0.9241 (p) cc_final: 0.8962 (m) REVERT: A 386 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8150 (p-80) REVERT: B 217 MET cc_start: 0.7484 (mmp) cc_final: 0.6673 (mmt) REVERT: B 225 GLN cc_start: 0.7935 (mt0) cc_final: 0.7607 (mt0) REVERT: C 176 THR cc_start: 0.7642 (t) cc_final: 0.7199 (p) REVERT: D 89 TRP cc_start: 0.8854 (t-100) cc_final: 0.8521 (t-100) REVERT: D 97 ASP cc_start: 0.7179 (m-30) cc_final: 0.6739 (p0) REVERT: D 170 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.5235 (p90) REVERT: D 207 SER cc_start: 0.9069 (p) cc_final: 0.8847 (p) REVERT: D 273 TYR cc_start: 0.8469 (p90) cc_final: 0.8193 (p90) REVERT: D 284 ASP cc_start: 0.8192 (m-30) cc_final: 0.7853 (m-30) REVERT: D 321 LYS cc_start: 0.8214 (pptt) cc_final: 0.7980 (mmtm) REVERT: D 328 CYS cc_start: 0.7282 (m) cc_final: 0.6930 (m) REVERT: D 346 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8134 (m) REVERT: E 20 ARG cc_start: 0.8137 (ptm160) cc_final: 0.7677 (ptm160) REVERT: E 129 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8154 (tptm) REVERT: E 285 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8164 (pt) REVERT: E 295 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8299 (tt) REVERT: E 311 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8730 (pt) REVERT: E 412 LEU cc_start: 0.1295 (OUTLIER) cc_final: 0.0997 (tm) REVERT: G 170 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.4472 (p90) REVERT: G 425 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6661 (mt) REVERT: H 158 LEU cc_start: 0.8958 (mm) cc_final: 0.8739 (mp) REVERT: H 311 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8129 (pt) REVERT: J 151 VAL cc_start: 0.6870 (m) cc_final: 0.6431 (p) REVERT: J 240 TYR cc_start: 0.8270 (t80) cc_final: 0.7940 (t80) REVERT: J 273 TYR cc_start: 0.7673 (p90) cc_final: 0.7352 (p90) REVERT: J 404 LYS cc_start: 0.7827 (ttpm) cc_final: 0.7020 (tppt) REVERT: J 433 MET cc_start: 0.5770 (tpt) cc_final: 0.5386 (tpt) REVERT: K 305 ASP cc_start: 0.8435 (t70) cc_final: 0.8198 (t70) REVERT: K 394 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.6321 (ttm110) REVERT: L 168 MET cc_start: 0.5326 (mtt) cc_final: 0.4650 (mmp) outliers start: 117 outliers final: 63 residues processed: 471 average time/residue: 0.1949 time to fit residues: 152.7014 Evaluate side-chains 417 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 378 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 270 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 275 optimal weight: 0.0980 chunk 94 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 380 optimal weight: 2.9990 chunk 194 optimal weight: 30.0000 chunk 305 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN ** D 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 ASN J 175 HIS J 377 ASN K 363 HIS ** M 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.189124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132736 restraints weight = 38468.438| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.46 r_work: 0.3150 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32569 Z= 0.172 Angle : 0.645 10.107 44396 Z= 0.326 Chirality : 0.047 0.203 5000 Planarity : 0.005 0.065 5671 Dihedral : 5.507 51.080 4592 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.64 % Allowed : 16.88 % Favored : 78.49 % 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 aren not related in a simple way. whole: -2.82 (0.12), residues: 4081 helix: 0.36 (0.26), residues: 410 sheet: -2.04 (0.14), residues: 1236 loop : -2.24 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 134 TYR 0.023 0.001 TYR D 308 PHE 0.020 0.002 PHE G 414 TRP 0.012 0.001 TRP B 279 HIS 0.008 0.001 HIS E 157 Details of bonding type rmsd covalent geometry : bond 0.00432 (32505) covalent geometry : angle 0.63741 (44260) SS BOND : bond 0.00397 ( 56) SS BOND : angle 1.98190 ( 112) hydrogen bonds : bond 0.03861 ( 241) hydrogen bonds : angle 3.84764 ( 723) link_NAG-ASN : bond 0.00389 ( 8) link_NAG-ASN : angle 1.71049 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 354 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8903 (m-10) cc_final: 0.8554 (m-80) REVERT: A 42 THR cc_start: 0.8604 (m) cc_final: 0.8327 (m) REVERT: A 102 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8991 (tt0) REVERT: A 195 MET cc_start: 0.9381 (mpp) cc_final: 0.8313 (mtm) REVERT: A 237 VAL cc_start: 0.9379 (p) cc_final: 0.9142 (t) REVERT: A 288 VAL cc_start: 0.9308 (p) cc_final: 0.9037 (m) REVERT: A 386 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.8271 (p-80) REVERT: B 217 MET cc_start: 0.7646 (mmp) cc_final: 0.6858 (mmt) REVERT: B 225 GLN cc_start: 0.7870 (mt0) cc_final: 0.7573 (mt0) REVERT: B 327 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: D 62 CYS cc_start: 0.7940 (m) cc_final: 0.7664 (m) REVERT: D 97 ASP cc_start: 0.6908 (m-30) cc_final: 0.6274 (p0) REVERT: D 170 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.5935 (p90) REVERT: D 207 SER cc_start: 0.9054 (p) cc_final: 0.8837 (p) REVERT: D 284 ASP cc_start: 0.8337 (m-30) cc_final: 0.8041 (m-30) REVERT: D 321 LYS cc_start: 0.8219 (pptt) cc_final: 0.7964 (mmtm) REVERT: D 328 CYS cc_start: 0.7484 (m) cc_final: 0.7079 (m) REVERT: D 346 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8131 (m) REVERT: E 20 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7723 (ptm160) REVERT: E 131 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6166 (ptp-110) REVERT: E 217 MET cc_start: 0.6570 (ptp) cc_final: 0.5624 (ppp) REVERT: E 285 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8311 (pt) REVERT: E 295 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8344 (tt) REVERT: E 311 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8758 (pt) REVERT: E 412 LEU cc_start: 0.1077 (OUTLIER) cc_final: 0.0760 (tm) REVERT: G 170 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5046 (p90) REVERT: G 278 ILE cc_start: 0.8671 (mt) cc_final: 0.8352 (mt) REVERT: G 425 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6659 (mt) REVERT: H 65 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8403 (mtp180) REVERT: H 158 LEU cc_start: 0.8949 (mm) cc_final: 0.8676 (mp) REVERT: H 311 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8289 (pt) REVERT: J 151 VAL cc_start: 0.7036 (m) cc_final: 0.6527 (p) REVERT: J 273 TYR cc_start: 0.7742 (p90) cc_final: 0.7442 (p90) REVERT: J 404 LYS cc_start: 0.7725 (ttpm) cc_final: 0.6832 (tppt) REVERT: K 305 ASP cc_start: 0.8503 (t70) cc_final: 0.8112 (t70) REVERT: L 168 MET cc_start: 0.5881 (mtt) cc_final: 0.4810 (mmp) REVERT: M 65 ASP cc_start: 0.7732 (t70) cc_final: 0.7337 (t0) outliers start: 161 outliers final: 114 residues processed: 481 average time/residue: 0.1961 time to fit residues: 156.9074 Evaluate side-chains 460 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 332 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 160 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 202 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 374 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 360 optimal weight: 0.0060 chunk 79 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN F 136 HIS H 174 HIS ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 HIS J 377 ASN K 363 HIS M 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.190304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.134273 restraints weight = 38298.043| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.43 r_work: 0.3185 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32569 Z= 0.131 Angle : 0.598 9.369 44396 Z= 0.302 Chirality : 0.045 0.241 5000 Planarity : 0.005 0.065 5671 Dihedral : 5.273 43.552 4592 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.23 % Allowed : 18.00 % Favored : 77.76 % 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 aren not related in a simple way. whole: -2.61 (0.13), residues: 4081 helix: 0.55 (0.26), residues: 410 sheet: -1.89 (0.14), residues: 1224 loop : -2.12 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 21 TYR 0.020 0.001 TYR D 308 PHE 0.017 0.001 PHE K 100 TRP 0.017 0.001 TRP A 409 HIS 0.007 0.001 HIS J 345 Details of bonding type rmsd covalent geometry : bond 0.00322 (32505) covalent geometry : angle 0.59137 (44260) SS BOND : bond 0.00313 ( 56) SS BOND : angle 1.55559 ( 112) hydrogen bonds : bond 0.03569 ( 241) hydrogen bonds : angle 3.78203 ( 723) link_NAG-ASN : bond 0.00694 ( 8) link_NAG-ASN : angle 2.18276 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 363 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8870 (m-10) cc_final: 0.8513 (m-80) REVERT: A 42 THR cc_start: 0.8424 (m) cc_final: 0.8197 (m) REVERT: A 102 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9017 (tt0) REVERT: A 195 MET cc_start: 0.9358 (mpp) cc_final: 0.8482 (mtm) REVERT: A 237 VAL cc_start: 0.9353 (p) cc_final: 0.9117 (t) REVERT: A 288 VAL cc_start: 0.9278 (p) cc_final: 0.9016 (m) REVERT: A 386 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.8050 (p-80) REVERT: B 217 MET cc_start: 0.7522 (mmp) cc_final: 0.6694 (mmt) REVERT: B 225 GLN cc_start: 0.7880 (mt0) cc_final: 0.7622 (mt0) REVERT: B 327 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: C 176 THR cc_start: 0.7682 (t) cc_final: 0.7211 (p) REVERT: D 89 TRP cc_start: 0.8820 (t-100) cc_final: 0.8444 (t-100) REVERT: D 97 ASP cc_start: 0.7106 (m-30) cc_final: 0.6475 (p0) REVERT: D 125 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.6747 (p90) REVERT: D 170 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.5939 (p90) REVERT: D 284 ASP cc_start: 0.8186 (m-30) cc_final: 0.7915 (m-30) REVERT: D 321 LYS cc_start: 0.8204 (pptt) cc_final: 0.7993 (mmtm) REVERT: D 328 CYS cc_start: 0.7414 (m) cc_final: 0.6987 (m) REVERT: E 20 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7650 (ptm160) REVERT: E 131 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.5694 (ptp-110) REVERT: E 217 MET cc_start: 0.6476 (ptp) cc_final: 0.5606 (ppp) REVERT: E 285 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8209 (pt) REVERT: E 295 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8312 (tt) REVERT: E 412 LEU cc_start: 0.2028 (OUTLIER) cc_final: 0.1672 (tm) REVERT: G 170 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6344 (p90) REVERT: G 278 ILE cc_start: 0.8715 (mt) cc_final: 0.8438 (mt) REVERT: G 362 GLN cc_start: 0.7744 (pt0) cc_final: 0.7423 (pt0) REVERT: G 425 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6682 (mt) REVERT: H 158 LEU cc_start: 0.8972 (mm) cc_final: 0.8670 (mp) REVERT: H 311 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8138 (pt) REVERT: H 412 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.3936 (tp) REVERT: J 109 GLU cc_start: 0.8457 (pt0) cc_final: 0.8157 (pm20) REVERT: J 240 TYR cc_start: 0.8296 (t80) cc_final: 0.7978 (t80) REVERT: J 246 ASN cc_start: 0.8520 (m-40) cc_final: 0.8214 (m110) REVERT: J 273 TYR cc_start: 0.7605 (p90) cc_final: 0.7385 (p90) REVERT: J 404 LYS cc_start: 0.7741 (ttpm) cc_final: 0.6882 (tppt) REVERT: K 151 LYS cc_start: 0.7533 (mtpm) cc_final: 0.7107 (mttp) REVERT: K 305 ASP cc_start: 0.8481 (t70) cc_final: 0.8103 (t70) REVERT: L 168 MET cc_start: 0.5697 (mtt) cc_final: 0.4774 (mmp) REVERT: M 65 ASP cc_start: 0.7675 (t70) cc_final: 0.7222 (t0) outliers start: 147 outliers final: 106 residues processed: 476 average time/residue: 0.1963 time to fit residues: 154.9048 Evaluate side-chains 456 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 337 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 CYS Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 276 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 357 ILE Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 160 GLU Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 50 optimal weight: 6.9990 chunk 162 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 384 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 345 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS D 246 ASN G 377 ASN ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 HIS J 377 ASN K 50 GLN K 363 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.188476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.131617 restraints weight = 38498.824| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.42 r_work: 0.3135 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32569 Z= 0.178 Angle : 0.638 8.872 44396 Z= 0.322 Chirality : 0.047 0.200 5000 Planarity : 0.005 0.065 5671 Dihedral : 5.290 37.432 4592 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.10 % Allowed : 17.77 % Favored : 77.13 % 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 aren not related in a simple way. whole: -2.52 (0.13), residues: 4081 helix: 0.52 (0.26), residues: 412 sheet: -1.80 (0.14), residues: 1218 loop : -2.05 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 134 TYR 0.022 0.001 TYR G 308 PHE 0.019 0.002 PHE K 100 TRP 0.012 0.001 TRP K 351 HIS 0.007 0.001 HIS E 157 Details of bonding type rmsd covalent geometry : bond 0.00448 (32505) covalent geometry : angle 0.63185 (44260) SS BOND : bond 0.00345 ( 56) SS BOND : angle 1.65946 ( 112) hydrogen bonds : bond 0.03789 ( 241) hydrogen bonds : angle 3.75807 ( 723) link_NAG-ASN : bond 0.00393 ( 8) link_NAG-ASN : angle 1.68611 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 348 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8816 (m-10) cc_final: 0.8443 (m-80) REVERT: A 42 THR cc_start: 0.8603 (m) cc_final: 0.8387 (m) REVERT: A 102 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: A 159 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8146 (pt) REVERT: A 195 MET cc_start: 0.9247 (mpp) cc_final: 0.8404 (mtm) REVERT: A 237 VAL cc_start: 0.9312 (p) cc_final: 0.9051 (t) REVERT: A 288 VAL cc_start: 0.9270 (p) cc_final: 0.9003 (m) REVERT: A 362 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8208 (mm-40) REVERT: A 386 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8054 (p-80) REVERT: B 217 MET cc_start: 0.7419 (mmp) cc_final: 0.6672 (mmt) REVERT: B 225 GLN cc_start: 0.7797 (mt0) cc_final: 0.7539 (mt0) REVERT: C 176 THR cc_start: 0.7735 (t) cc_final: 0.7255 (p) REVERT: D 89 TRP cc_start: 0.8691 (t-100) cc_final: 0.8247 (t-100) REVERT: D 97 ASP cc_start: 0.7038 (m-30) cc_final: 0.6440 (p0) REVERT: D 125 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.6408 (p90) REVERT: D 170 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6489 (p90) REVERT: D 212 ASP cc_start: 0.7434 (p0) cc_final: 0.7147 (p0) REVERT: D 284 ASP cc_start: 0.8149 (m-30) cc_final: 0.7880 (m-30) REVERT: D 321 LYS cc_start: 0.8207 (pptt) cc_final: 0.7951 (mmtm) REVERT: E 20 ARG cc_start: 0.8013 (ptm160) cc_final: 0.7565 (ptm160) REVERT: E 113 VAL cc_start: 0.9040 (p) cc_final: 0.8798 (t) REVERT: E 217 MET cc_start: 0.6376 (ptp) cc_final: 0.5406 (ppp) REVERT: E 285 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8309 (pt) REVERT: E 295 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8319 (tt) REVERT: E 412 LEU cc_start: 0.2319 (OUTLIER) cc_final: 0.1979 (tm) REVERT: G 278 ILE cc_start: 0.8682 (mt) cc_final: 0.8464 (mt) REVERT: G 362 GLN cc_start: 0.7728 (pt0) cc_final: 0.7311 (pt0) REVERT: G 425 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6698 (mt) REVERT: H 65 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8244 (mtp180) REVERT: H 311 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8225 (pt) REVERT: H 412 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4241 (tp) REVERT: J 246 ASN cc_start: 0.8394 (m-40) cc_final: 0.8069 (m110) REVERT: J 404 LYS cc_start: 0.7605 (ttpm) cc_final: 0.6665 (tppt) REVERT: K 151 LYS cc_start: 0.7180 (mtpm) cc_final: 0.6913 (mttp) REVERT: K 305 ASP cc_start: 0.8389 (t70) cc_final: 0.7982 (t70) REVERT: L 168 MET cc_start: 0.5685 (mtt) cc_final: 0.4935 (mmp) REVERT: M 65 ASP cc_start: 0.7650 (t70) cc_final: 0.7210 (t0) outliers start: 177 outliers final: 130 residues processed: 491 average time/residue: 0.1951 time to fit residues: 159.3274 Evaluate side-chains 478 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 336 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 70 ASP Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 285 LEU Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 211 THR Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 160 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 262 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 116 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 395 optimal weight: 0.0770 chunk 376 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 374 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 272 optimal weight: 0.0370 chunk 144 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 175 HIS J 345 HIS J 377 ASN K 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.193761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138702 restraints weight = 38604.354| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.44 r_work: 0.3210 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 32569 Z= 0.096 Angle : 0.561 8.917 44396 Z= 0.283 Chirality : 0.044 0.191 5000 Planarity : 0.005 0.062 5671 Dihedral : 4.714 33.091 4592 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.02 % Allowed : 20.16 % Favored : 76.81 % 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 aren not related in a simple way. whole: -2.18 (0.13), residues: 4081 helix: 0.84 (0.27), residues: 408 sheet: -1.55 (0.15), residues: 1212 loop : -1.84 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.022 0.001 TYR J 273 PHE 0.015 0.001 PHE K 142 TRP 0.012 0.001 TRP E 310 HIS 0.007 0.001 HIS J 345 Details of bonding type rmsd covalent geometry : bond 0.00216 (32505) covalent geometry : angle 0.55713 (44260) SS BOND : bond 0.00257 ( 56) SS BOND : angle 1.20369 ( 112) hydrogen bonds : bond 0.03162 ( 241) hydrogen bonds : angle 3.70185 ( 723) link_NAG-ASN : bond 0.00365 ( 8) link_NAG-ASN : angle 1.47004 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 384 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8784 (m-10) cc_final: 0.8406 (m-80) REVERT: A 42 THR cc_start: 0.8284 (m) cc_final: 0.8063 (m) REVERT: A 159 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7833 (pt) REVERT: A 195 MET cc_start: 0.9159 (mpp) cc_final: 0.8585 (mtm) REVERT: A 237 VAL cc_start: 0.9291 (p) cc_final: 0.9047 (t) REVERT: A 288 VAL cc_start: 0.9229 (p) cc_final: 0.8982 (m) REVERT: B 217 MET cc_start: 0.7381 (mmp) cc_final: 0.6772 (mmt) REVERT: B 225 GLN cc_start: 0.7683 (mt0) cc_final: 0.7477 (mt0) REVERT: C 176 THR cc_start: 0.7667 (t) cc_final: 0.7194 (p) REVERT: D 50 LYS cc_start: 0.8415 (tttm) cc_final: 0.8063 (ttpt) REVERT: D 89 TRP cc_start: 0.8611 (t-100) cc_final: 0.8258 (t-100) REVERT: D 97 ASP cc_start: 0.7084 (m-30) cc_final: 0.6418 (p0) REVERT: D 117 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: D 212 ASP cc_start: 0.7515 (p0) cc_final: 0.7233 (p0) REVERT: D 260 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8675 (mtpp) REVERT: D 284 ASP cc_start: 0.8183 (m-30) cc_final: 0.7863 (m-30) REVERT: D 321 LYS cc_start: 0.8219 (pptt) cc_final: 0.7936 (mmtm) REVERT: E 20 ARG cc_start: 0.7944 (ptm160) cc_final: 0.7496 (ptm160) REVERT: E 217 MET cc_start: 0.6189 (ptp) cc_final: 0.5169 (ppp) REVERT: E 285 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7872 (pt) REVERT: E 412 LEU cc_start: 0.1981 (OUTLIER) cc_final: 0.1645 (tm) REVERT: G 38 LEU cc_start: 0.9041 (tp) cc_final: 0.8837 (tt) REVERT: G 278 ILE cc_start: 0.8627 (mt) cc_final: 0.8384 (mt) REVERT: G 362 GLN cc_start: 0.7674 (pt0) cc_final: 0.7235 (pt0) REVERT: G 409 TRP cc_start: 0.7769 (m100) cc_final: 0.7299 (m-10) REVERT: G 425 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6661 (mt) REVERT: H 87 THR cc_start: 0.8822 (m) cc_final: 0.8605 (m) REVERT: H 412 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.4044 (tp) REVERT: I 132 MET cc_start: 0.7359 (tpt) cc_final: 0.6938 (tpt) REVERT: I 156 MET cc_start: 0.7447 (ttm) cc_final: 0.7211 (ttp) REVERT: J 240 TYR cc_start: 0.8172 (t80) cc_final: 0.7874 (t80) REVERT: J 246 ASN cc_start: 0.8389 (m-40) cc_final: 0.8083 (m110) REVERT: J 298 GLU cc_start: 0.7646 (pm20) cc_final: 0.7173 (pm20) REVERT: J 404 LYS cc_start: 0.7713 (ttpm) cc_final: 0.6772 (tppt) REVERT: K 6 PHE cc_start: 0.7339 (m-80) cc_final: 0.7131 (m-80) REVERT: K 151 LYS cc_start: 0.7271 (mtpm) cc_final: 0.6828 (mttp) REVERT: K 305 ASP cc_start: 0.8313 (t70) cc_final: 0.7934 (t70) REVERT: K 394 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.6072 (ttm110) REVERT: L 168 MET cc_start: 0.5572 (mtt) cc_final: 0.4898 (mmp) REVERT: M 65 ASP cc_start: 0.7604 (t70) cc_final: 0.7165 (t0) outliers start: 105 outliers final: 75 residues processed: 462 average time/residue: 0.2039 time to fit residues: 154.7428 Evaluate side-chains 436 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 74 optimal weight: 0.5980 chunk 400 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 194 optimal weight: 40.0000 chunk 115 optimal weight: 9.9990 chunk 381 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN E 252 GLN ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 HIS J 345 HIS J 377 ASN K 363 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.189493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.133269 restraints weight = 38475.336| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.31 r_work: 0.3130 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32569 Z= 0.169 Angle : 0.634 10.991 44396 Z= 0.319 Chirality : 0.047 0.202 5000 Planarity : 0.005 0.109 5671 Dihedral : 5.024 35.271 4592 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.95 % Allowed : 19.59 % Favored : 76.47 % 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 aren not related in a simple way. whole: -2.18 (0.13), residues: 4081 helix: 0.73 (0.27), residues: 412 sheet: -1.45 (0.15), residues: 1204 loop : -1.88 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 131 TYR 0.022 0.001 TYR G 308 PHE 0.017 0.002 PHE K 100 TRP 0.012 0.001 TRP K 351 HIS 0.008 0.001 HIS J 345 Details of bonding type rmsd covalent geometry : bond 0.00427 (32505) covalent geometry : angle 0.62770 (44260) SS BOND : bond 0.00333 ( 56) SS BOND : angle 1.79820 ( 112) hydrogen bonds : bond 0.03596 ( 241) hydrogen bonds : angle 3.64693 ( 723) link_NAG-ASN : bond 0.00159 ( 8) link_NAG-ASN : angle 1.58209 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 352 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8798 (m-10) cc_final: 0.8438 (m-80) REVERT: A 42 THR cc_start: 0.8573 (m) cc_final: 0.8369 (m) REVERT: A 159 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8098 (pt) REVERT: A 178 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8790 (t) REVERT: A 195 MET cc_start: 0.9244 (mpp) cc_final: 0.8474 (mtm) REVERT: A 237 VAL cc_start: 0.9313 (p) cc_final: 0.9051 (t) REVERT: A 288 VAL cc_start: 0.9214 (p) cc_final: 0.8970 (m) REVERT: B 400 TYR cc_start: 0.4652 (OUTLIER) cc_final: 0.4062 (p90) REVERT: C 176 THR cc_start: 0.7801 (t) cc_final: 0.7282 (p) REVERT: D 97 ASP cc_start: 0.7281 (m-30) cc_final: 0.6662 (p0) REVERT: D 204 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: D 260 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8635 (mtpp) REVERT: D 284 ASP cc_start: 0.8208 (m-30) cc_final: 0.7887 (m-30) REVERT: D 321 LYS cc_start: 0.8268 (pptt) cc_final: 0.7980 (mmtm) REVERT: E 20 ARG cc_start: 0.7975 (ptm160) cc_final: 0.7533 (ptm160) REVERT: E 285 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8320 (pt) REVERT: E 295 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8210 (tt) REVERT: E 412 LEU cc_start: 0.2300 (OUTLIER) cc_final: 0.1964 (tm) REVERT: G 252 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8693 (mm-40) REVERT: G 278 ILE cc_start: 0.8622 (mt) cc_final: 0.8400 (mt) REVERT: G 356 PHE cc_start: 0.8270 (p90) cc_final: 0.7951 (p90) REVERT: G 362 GLN cc_start: 0.7750 (pt0) cc_final: 0.7347 (pt0) REVERT: G 409 TRP cc_start: 0.7835 (m100) cc_final: 0.7323 (m-10) REVERT: H 311 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7908 (pt) REVERT: H 412 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4245 (tp) REVERT: I 132 MET cc_start: 0.7106 (tpt) cc_final: 0.6742 (tpt) REVERT: I 135 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4488 (mm) REVERT: I 156 MET cc_start: 0.7351 (ttm) cc_final: 0.7136 (ttp) REVERT: J 99 GLU cc_start: 0.6415 (pp20) cc_final: 0.5591 (pt0) REVERT: J 246 ASN cc_start: 0.8398 (m-40) cc_final: 0.8073 (m110) REVERT: J 404 LYS cc_start: 0.7671 (ttpm) cc_final: 0.6668 (tppt) REVERT: K 6 PHE cc_start: 0.7502 (m-80) cc_final: 0.7211 (m-80) REVERT: K 151 LYS cc_start: 0.7429 (mtpm) cc_final: 0.7081 (mttp) REVERT: K 285 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8802 (mm) REVERT: K 305 ASP cc_start: 0.8364 (t70) cc_final: 0.7964 (t70) REVERT: K 394 ARG cc_start: 0.6980 (ttm-80) cc_final: 0.6025 (ttm110) REVERT: L 168 MET cc_start: 0.5809 (mtt) cc_final: 0.4996 (mmp) REVERT: M 65 ASP cc_start: 0.7560 (t70) cc_final: 0.7117 (t0) outliers start: 137 outliers final: 105 residues processed: 458 average time/residue: 0.1933 time to fit residues: 147.8055 Evaluate side-chains 455 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 337 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain J residue 270 ASN Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 116 optimal weight: 0.8980 chunk 295 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 281 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 393 optimal weight: 30.0000 chunk 403 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 328 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** D 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 HIS J 345 HIS J 377 ASN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 363 HIS M 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.186231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.130673 restraints weight = 38453.779| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.45 r_work: 0.3111 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 32569 Z= 0.259 Angle : 0.733 11.093 44396 Z= 0.371 Chirality : 0.051 0.216 5000 Planarity : 0.006 0.110 5671 Dihedral : 5.434 39.503 4592 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.35 % Allowed : 19.38 % Favored : 76.27 % 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 aren not related in a simple way. whole: -2.32 (0.13), residues: 4081 helix: 0.55 (0.26), residues: 412 sheet: -1.59 (0.15), residues: 1194 loop : -1.93 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 267 TYR 0.025 0.002 TYR G 308 PHE 0.024 0.002 PHE K 100 TRP 0.015 0.002 TRP K 351 HIS 0.009 0.002 HIS E 157 Details of bonding type rmsd covalent geometry : bond 0.00662 (32505) covalent geometry : angle 0.72628 (44260) SS BOND : bond 0.00423 ( 56) SS BOND : angle 1.94903 ( 112) hydrogen bonds : bond 0.04061 ( 241) hydrogen bonds : angle 3.74293 ( 723) link_NAG-ASN : bond 0.00184 ( 8) link_NAG-ASN : angle 1.85405 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8162 Ramachandran restraints generated. 4081 Oldfield, 0 Emsley, 4081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 350 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8813 (m-10) cc_final: 0.8444 (m-80) REVERT: A 102 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8949 (pt0) REVERT: A 159 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8200 (pt) REVERT: A 195 MET cc_start: 0.9256 (mpp) cc_final: 0.8372 (mtm) REVERT: A 216 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8380 (ttm170) REVERT: A 237 VAL cc_start: 0.9310 (p) cc_final: 0.9069 (t) REVERT: A 288 VAL cc_start: 0.9233 (p) cc_final: 0.8982 (m) REVERT: A 386 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8122 (p-80) REVERT: B 225 GLN cc_start: 0.7726 (mt0) cc_final: 0.7496 (mt0) REVERT: B 400 TYR cc_start: 0.4777 (OUTLIER) cc_final: 0.4203 (p90) REVERT: D 97 ASP cc_start: 0.7430 (m-30) cc_final: 0.6931 (p0) REVERT: D 170 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7112 (p90) REVERT: D 204 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: D 284 ASP cc_start: 0.8188 (m-30) cc_final: 0.7850 (m-30) REVERT: E 20 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7592 (ptm160) REVERT: E 295 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8291 (tt) REVERT: E 412 LEU cc_start: 0.2402 (OUTLIER) cc_final: 0.2051 (tm) REVERT: G 252 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.7641 (mp10) REVERT: G 278 ILE cc_start: 0.8732 (mt) cc_final: 0.8498 (mt) REVERT: G 362 GLN cc_start: 0.7684 (pt0) cc_final: 0.7299 (pt0) REVERT: G 409 TRP cc_start: 0.7929 (m100) cc_final: 0.7359 (m-10) REVERT: H 311 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7985 (mt) REVERT: H 412 LEU cc_start: 0.4311 (OUTLIER) cc_final: 0.3824 (tp) REVERT: I 132 MET cc_start: 0.7351 (tpt) cc_final: 0.6950 (tpt) REVERT: I 135 LEU cc_start: 0.4949 (OUTLIER) cc_final: 0.4570 (mm) REVERT: I 156 MET cc_start: 0.7405 (ttm) cc_final: 0.7189 (ttp) REVERT: I 168 MET cc_start: 0.6100 (mpt) cc_final: 0.5296 (mpt) REVERT: J 99 GLU cc_start: 0.6458 (pp20) cc_final: 0.5614 (pt0) REVERT: J 143 HIS cc_start: 0.7966 (m90) cc_final: 0.7622 (m90) REVERT: J 246 ASN cc_start: 0.8469 (m-40) cc_final: 0.8207 (m110) REVERT: J 404 LYS cc_start: 0.7814 (ttpm) cc_final: 0.6728 (tppt) REVERT: K 151 LYS cc_start: 0.7456 (mtpm) cc_final: 0.7043 (mttp) REVERT: K 305 ASP cc_start: 0.8525 (t70) cc_final: 0.8096 (t70) REVERT: K 394 ARG cc_start: 0.7023 (ttm-80) cc_final: 0.6134 (ttm110) REVERT: L 168 MET cc_start: 0.5816 (mtt) cc_final: 0.5077 (mmp) REVERT: M 65 ASP cc_start: 0.7668 (t70) cc_final: 0.7240 (t0) REVERT: M 112 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.7125 (t) outliers start: 151 outliers final: 117 residues processed: 469 average time/residue: 0.1696 time to fit residues: 132.0348 Evaluate side-chains 469 residues out of total 3472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 338 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 165 TYR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 400 TYR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 170 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 407 TRP Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 347 ASP Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 102 GLN Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 170 PHE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 335 THR Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 311 ILE Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 321 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 412 LEU Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 135 LEU Chi-restraints excluded: chain I residue 173 LEU Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 96 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 253 GLU Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 407 TRP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 433 MET Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 113 VAL Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 250 SER Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain K residue 369 ILE Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 215 LEU Chi-restraints excluded: chain M residue 54 GLN Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 281 optimal weight: 0.0000 chunk 271 optimal weight: 3.9990 chunk 364 optimal weight: 9.9990 chunk 314 optimal weight: 0.0000 chunk 108 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 HIS J 345 HIS J 377 ASN K 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.191682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.135660 restraints weight = 38626.830| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.41 r_work: 0.3143 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 32569 Z= 0.104 Angle : 0.591 11.464 44396 Z= 0.299 Chirality : 0.045 0.195 5000 Planarity : 0.005 0.094 5671 Dihedral : 4.862 34.575 4592 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.43 % Allowed : 20.19 % Favored : 76.38 % 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 aren not related in a simple way. whole: -2.04 (0.13), residues: 4081 helix: 0.91 (0.27), residues: 406 sheet: -1.41 (0.15), residues: 1200 loop : -1.77 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 134 TYR 0.021 0.001 TYR J 273 PHE 0.018 0.001 PHE K 100 TRP 0.013 0.001 TRP B 279 HIS 0.009 0.001 HIS J 345 Details of bonding type rmsd covalent geometry : bond 0.00243 (32505) covalent geometry : angle 0.58686 (44260) SS BOND : bond 0.00288 ( 56) SS BOND : angle 1.40622 ( 112) hydrogen bonds : bond 0.03230 ( 241) hydrogen bonds : angle 3.63075 ( 723) link_NAG-ASN : bond 0.00238 ( 8) link_NAG-ASN : angle 1.61047 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9766.68 seconds wall clock time: 167 minutes 43.86 seconds (10063.86 seconds total)