Starting phenix.real_space_refine on Wed Apr 8 06:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sy5_55340/04_2026/9sy5_55340_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sy5_55340/04_2026/9sy5_55340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sy5_55340/04_2026/9sy5_55340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sy5_55340/04_2026/9sy5_55340.map" model { file = "/net/cci-nas-00/data/ceres_data/9sy5_55340/04_2026/9sy5_55340_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sy5_55340/04_2026/9sy5_55340_neut.cif" } resolution = 2.61 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= 0.007 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 142 5.16 5 C 21715 2.51 5 N 5843 2.21 5 O 6597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34297 Number of models: 1 Model: "" Number of chains: 10 Chain: "8" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3416 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3405 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 398} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3389 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 396} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 3507 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 424, 3375 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 424, 3369 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 26, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 3311 Chain: "X" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3383 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 396} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "i" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3396 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3394 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 26, 'TRANS': 398} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 3534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 427, 3416 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 400} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 427, 3410 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 400} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 3367 Chain: "v" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3437 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 402} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "w" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3436 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 26, 'TRANS': 403} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N AGLY T 47 " occ=0.49 ... (6 atoms not shown) pdb=" O BGLY T 47 " occ=0.51 residue: pdb=" N AARG T 48 " occ=0.49 ... (14 atoms not shown) pdb=" CB BARG T 48 " occ=0.51 residue: pdb=" N AASN T 49 " occ=0.49 ... (14 atoms not shown) pdb=" ND2BASN T 49 " occ=0.51 residue: pdb=" N ASER T 50 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER T 50 " occ=0.51 residue: pdb=" N AILE T 51 " occ=0.49 ... (14 atoms not shown) pdb=" CD1BILE T 51 " occ=0.51 residue: pdb=" N AARG T 52 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG T 52 " occ=0.51 residue: pdb=" N ATYR T 53 " occ=0.49 ... (22 atoms not shown) pdb=" OH BTYR T 53 " occ=0.51 residue: pdb=" N ASER T 54 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER T 54 " occ=0.51 residue: pdb=" N AGLU T 55 " occ=0.49 ... (16 atoms not shown) pdb=" OE2BGLU T 55 " occ=0.51 residue: pdb=" N ALEU T 56 " occ=0.49 ... (14 atoms not shown) pdb=" CD2BLEU T 56 " occ=0.51 residue: pdb=" N ACYS T 57 " occ=0.49 ... (10 atoms not shown) pdb=" SG BCYS T 57 " occ=0.51 residue: pdb=" N APRO T 58 " occ=0.49 ... (12 atoms not shown) pdb=" CD BPRO T 58 " occ=0.51 ... (remaining 20 not shown) Time building chain proxies: 9.18, per 1000 atoms: 0.27 Number of scatterers: 34297 At special positions: 0 Unit cell: (167.99, 202.23, 129.47, 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 142 16.00 O 6597 8.00 N 5843 7.00 C 21715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG ACYS T 57 " - pdb=" SG ACYS k 57 " distance=2.31 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 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8132 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 70 sheets defined 18.0% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain '8' and resid 71 through 78 removed outlier: 3.855A pdb=" N ALA 8 76 " --> pdb=" O SER 8 72 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER 8 77 " --> pdb=" O ALA 8 73 " (cutoff:3.500A) Processing helix chain '8' and resid 98 through 104 removed outlier: 4.112A pdb=" N THR 8 104 " --> pdb=" O THR 8 100 " (cutoff:3.500A) Processing helix chain '8' and resid 182 through 201 removed outlier: 3.505A pdb=" N ILE 8 194 " --> pdb=" O MET 8 190 " (cutoff:3.500A) Processing helix chain '8' and resid 260 through 266 removed outlier: 3.785A pdb=" N LEU 8 264 " --> pdb=" O ARG 8 260 " (cutoff:3.500A) Processing helix chain '8' and resid 282 through 285 removed outlier: 3.962A pdb=" N GLU 8 285 " --> pdb=" O GLU 8 282 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 282 through 285' Processing helix chain '8' and resid 296 through 303 removed outlier: 3.953A pdb=" N GLU 8 303 " --> pdb=" O GLU 8 299 " (cutoff:3.500A) Processing helix chain '8' and resid 378 through 385 Processing helix chain '8' and resid 390 through 393 Processing helix chain '8' and resid 428 through 432 Processing helix chain 'K' and resid 71 through 78 removed outlier: 3.654A pdb=" N ALA K 76 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 103 Processing helix chain 'K' and resid 182 through 202 removed outlier: 3.629A pdb=" N ALA K 200 " --> pdb=" O ASP K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 206 removed outlier: 3.958A pdb=" N GLY K 206 " --> pdb=" O ARG K 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 203 through 206' Processing helix chain 'K' and resid 208 through 212 Processing helix chain 'K' and resid 260 through 266 removed outlier: 3.856A pdb=" N LEU K 264 " --> pdb=" O ARG K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 285 removed outlier: 4.125A pdb=" N GLU K 285 " --> pdb=" O GLU K 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 282 through 285' Processing helix chain 'K' and resid 294 through 299 Processing helix chain 'K' and resid 378 through 385 Processing helix chain 'K' and resid 390 through 393 Processing helix chain 'K' and resid 428 through 432 Processing helix chain 'K' and resid 450 through 453 Processing helix chain 'R' and resid 71 through 76 removed outlier: 3.771A pdb=" N ALA R 76 " --> pdb=" O SER R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 103 Processing helix chain 'R' and resid 182 through 201 Processing helix chain 'R' and resid 202 through 206 removed outlier: 4.178A pdb=" N GLY R 206 " --> pdb=" O ARG R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 212 removed outlier: 3.656A pdb=" N ILE R 212 " --> pdb=" O GLU R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 266 removed outlier: 3.808A pdb=" N LEU R 264 " --> pdb=" O ARG R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 285 removed outlier: 4.144A pdb=" N GLU R 285 " --> pdb=" O GLU R 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 282 through 285' Processing helix chain 'R' and resid 294 through 300 Processing helix chain 'R' and resid 378 through 385 Processing helix chain 'R' and resid 390 through 393 Processing helix chain 'R' and resid 428 through 432 removed outlier: 3.630A pdb=" N TYR R 432 " --> pdb=" O VAL R 429 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 78 removed outlier: 3.918A pdb=" N ALA T 76 " --> pdb=" O SER T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 105 removed outlier: 4.098A pdb=" N THR T 104 " --> pdb=" O THR T 100 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN T 105 " --> pdb=" O GLU T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 199 removed outlier: 3.539A pdb=" N ILE T 194 " --> pdb=" O MET T 190 " (cutoff:3.500A) Processing helix chain 'T' and resid 208 through 212 Processing helix chain 'T' and resid 260 through 265 removed outlier: 3.763A pdb=" N LEU T 264 " --> pdb=" O ARG T 260 " (cutoff:3.500A) Processing helix chain 'T' and resid 282 through 285 removed outlier: 3.947A pdb=" N GLU T 285 " --> pdb=" O GLU T 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 282 through 285' Processing helix chain 'T' and resid 294 through 303 removed outlier: 3.514A pdb=" N LYS T 300 " --> pdb=" O ASP T 296 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER T 301 " --> pdb=" O ALA T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 378 through 385 Processing helix chain 'T' and resid 390 through 393 Processing helix chain 'T' and resid 428 through 432 removed outlier: 3.633A pdb=" N TYR T 432 " --> pdb=" O VAL T 429 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 78 removed outlier: 3.680A pdb=" N ALA X 76 " --> pdb=" O SER X 72 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER X 77 " --> pdb=" O ALA X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 98 through 104 removed outlier: 4.006A pdb=" N THR X 104 " --> pdb=" O THR X 100 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 201 Processing helix chain 'X' and resid 202 through 205 Processing helix chain 'X' and resid 208 through 212 removed outlier: 3.873A pdb=" N ILE X 212 " --> pdb=" O GLU X 209 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 265 removed outlier: 3.802A pdb=" N LEU X 264 " --> pdb=" O ARG X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 284 No H-bonds generated for 'chain 'X' and resid 282 through 284' Processing helix chain 'X' and resid 294 through 301 Processing helix chain 'X' and resid 378 through 384 Processing helix chain 'X' and resid 390 through 393 Processing helix chain 'X' and resid 428 through 432 Processing helix chain 'i' and resid 71 through 78 removed outlier: 3.827A pdb=" N ALA i 76 " --> pdb=" O SER i 72 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 103 Processing helix chain 'i' and resid 182 through 199 Processing helix chain 'i' and resid 208 through 212 removed outlier: 3.853A pdb=" N ILE i 212 " --> pdb=" O GLU i 209 " (cutoff:3.500A) Processing helix chain 'i' and resid 260 through 265 removed outlier: 3.753A pdb=" N LEU i 264 " --> pdb=" O ARG i 260 " (cutoff:3.500A) Processing helix chain 'i' and resid 282 through 285 removed outlier: 3.725A pdb=" N GLU i 285 " --> pdb=" O GLU i 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 282 through 285' Processing helix chain 'i' and resid 294 through 300 Processing helix chain 'i' and resid 378 through 385 Processing helix chain 'i' and resid 390 through 393 Processing helix chain 'i' and resid 428 through 432 removed outlier: 3.609A pdb=" N TYR i 432 " --> pdb=" O VAL i 429 " (cutoff:3.500A) Processing helix chain 'i' and resid 450 through 453 removed outlier: 3.640A pdb=" N VAL i 453 " --> pdb=" O GLU i 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 450 through 453' Processing helix chain 'j' and resid 71 through 78 removed outlier: 3.820A pdb=" N ALA j 76 " --> pdb=" O SER j 72 " (cutoff:3.500A) Processing helix chain 'j' and resid 98 through 105 removed outlier: 4.165A pdb=" N THR j 104 " --> pdb=" O THR j 100 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) Processing helix chain 'j' and resid 182 through 201 removed outlier: 3.551A pdb=" N ILE j 194 " --> pdb=" O MET j 190 " (cutoff:3.500A) Processing helix chain 'j' and resid 202 through 206 removed outlier: 3.661A pdb=" N GLY j 206 " --> pdb=" O ARG j 203 " (cutoff:3.500A) Processing helix chain 'j' and resid 208 through 212 removed outlier: 3.975A pdb=" N ILE j 212 " --> pdb=" O GLU j 209 " (cutoff:3.500A) Processing helix chain 'j' and resid 260 through 266 removed outlier: 3.774A pdb=" N LEU j 264 " --> pdb=" O ARG j 260 " (cutoff:3.500A) Processing helix chain 'j' and resid 282 through 285 removed outlier: 4.078A pdb=" N GLU j 285 " --> pdb=" O GLU j 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 282 through 285' Processing helix chain 'j' and resid 294 through 302 Processing helix chain 'j' and resid 378 through 385 Processing helix chain 'j' and resid 390 through 393 Processing helix chain 'j' and resid 428 through 432 Processing helix chain 'k' and resid 71 through 78 removed outlier: 4.216A pdb=" N ALA k 76 " --> pdb=" O SER k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 98 through 105 removed outlier: 3.935A pdb=" N THR k 104 " --> pdb=" O THR k 100 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN k 105 " --> pdb=" O GLU k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 182 through 199 Processing helix chain 'k' and resid 208 through 212 removed outlier: 3.804A pdb=" N ILE k 212 " --> pdb=" O GLU k 209 " (cutoff:3.500A) Processing helix chain 'k' and resid 260 through 266 removed outlier: 3.806A pdb=" N LEU k 264 " --> pdb=" O ARG k 260 " (cutoff:3.500A) Processing helix chain 'k' and resid 282 through 285 removed outlier: 4.144A pdb=" N GLU k 285 " --> pdb=" O GLU k 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 282 through 285' Processing helix chain 'k' and resid 294 through 299 Processing helix chain 'k' and resid 378 through 385 Processing helix chain 'k' and resid 390 through 393 Processing helix chain 'k' and resid 428 through 432 removed outlier: 3.542A pdb=" N TYR k 432 " --> pdb=" O VAL k 429 " (cutoff:3.500A) Processing helix chain 'k' and resid 450 through 455 removed outlier: 3.946A pdb=" N TYR k 454 " --> pdb=" O GLU k 450 " (cutoff:3.500A) Processing helix chain 'v' and resid 71 through 78 removed outlier: 3.565A pdb=" N ALA v 76 " --> pdb=" O SER v 72 " (cutoff:3.500A) Processing helix chain 'v' and resid 98 through 105 removed outlier: 3.954A pdb=" N THR v 104 " --> pdb=" O THR v 100 " (cutoff:3.500A) Processing helix chain 'v' and resid 182 through 199 Processing helix chain 'v' and resid 208 through 212 removed outlier: 3.675A pdb=" N ILE v 212 " --> pdb=" O GLU v 209 " (cutoff:3.500A) Processing helix chain 'v' and resid 260 through 265 removed outlier: 3.825A pdb=" N LEU v 264 " --> pdb=" O ARG v 260 " (cutoff:3.500A) Processing helix chain 'v' and resid 282 through 284 No H-bonds generated for 'chain 'v' and resid 282 through 284' Processing helix chain 'v' and resid 294 through 303 Processing helix chain 'v' and resid 378 through 384 Processing helix chain 'v' and resid 390 through 393 Processing helix chain 'v' and resid 428 through 432 removed outlier: 3.543A pdb=" N TYR v 432 " --> pdb=" O VAL v 429 " (cutoff:3.500A) Processing helix chain 'w' and resid 71 through 78 Processing helix chain 'w' and resid 98 through 103 Processing helix chain 'w' and resid 182 through 199 Processing helix chain 'w' and resid 208 through 212 removed outlier: 4.220A pdb=" N ILE w 212 " --> pdb=" O GLU w 209 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 265 removed outlier: 3.810A pdb=" N LEU w 264 " --> pdb=" O ARG w 260 " (cutoff:3.500A) Processing helix chain 'w' and resid 282 through 284 No H-bonds generated for 'chain 'w' and resid 282 through 284' Processing helix chain 'w' and resid 294 through 303 Processing helix chain 'w' and resid 378 through 384 Processing helix chain 'w' and resid 390 through 393 Processing helix chain 'w' and resid 428 through 432 Processing sheet with id=AA1, first strand: chain '8' and resid 59 through 60 Processing sheet with id=AA2, first strand: chain '8' and resid 65 through 67 removed outlier: 3.543A pdb=" N LYS 8 528 " --> pdb=" O HIS 8 124 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG 8 114 " --> pdb=" O LEU 8 538 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY 8 499 " --> pdb=" O LEU 8 119 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR 8 121 " --> pdb=" O ASP 8 497 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ASP 8 497 " --> pdb=" O THR 8 121 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N MET 8 123 " --> pdb=" O LEU 8 495 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU 8 495 " --> pdb=" O MET 8 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '8' and resid 86 through 90 removed outlier: 3.785A pdb=" N GLY 8 436 " --> pdb=" O TRP 8 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '8' and resid 171 through 175 removed outlier: 3.701A pdb=" N GLY 8 253 " --> pdb=" O ARG 8 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '8' and resid 215 through 217 removed outlier: 5.715A pdb=" N TYR 8 375 " --> pdb=" O ILE 8 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '8' and resid 267 through 269 Processing sheet with id=AA7, first strand: chain '8' and resid 442 through 448 Processing sheet with id=AA8, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'K' and resid 65 through 67 removed outlier: 3.614A pdb=" N LYS K 528 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG K 114 " --> pdb=" O LEU K 538 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TRP K 115 " --> pdb=" O LEU K 503 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY K 499 " --> pdb=" O LEU K 119 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR K 121 " --> pdb=" O ASP K 497 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ASP K 497 " --> pdb=" O THR K 121 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N MET K 123 " --> pdb=" O LEU K 495 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU K 495 " --> pdb=" O MET K 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 86 through 90 removed outlier: 3.605A pdb=" N GLY K 436 " --> pdb=" O TRP K 411 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 166 through 175 removed outlier: 6.924A pdb=" N ILE K 166 " --> pdb=" O ARG K 147 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG K 147 " --> pdb=" O ILE K 166 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU K 168 " --> pdb=" O VAL K 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 215 through 219 removed outlier: 4.641A pdb=" N ARG K 219 " --> pdb=" O HIS K 243 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS K 243 " --> pdb=" O ARG K 219 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE K 289 " --> pdb=" O THR K 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 267 through 269 Processing sheet with id=AB5, first strand: chain 'K' and resid 442 through 448 Processing sheet with id=AB6, first strand: chain 'R' and resid 59 through 60 Processing sheet with id=AB7, first strand: chain 'R' and resid 65 through 67 removed outlier: 6.656A pdb=" N ARG R 114 " --> pdb=" O LEU R 538 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY R 499 " --> pdb=" O LEU R 119 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR R 121 " --> pdb=" O ASP R 497 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP R 497 " --> pdb=" O THR R 121 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N MET R 123 " --> pdb=" O LEU R 495 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU R 495 " --> pdb=" O MET R 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 86 through 90 removed outlier: 3.568A pdb=" N GLY R 436 " --> pdb=" O TRP R 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 166 through 175 removed outlier: 6.366A pdb=" N ILE R 166 " --> pdb=" O ARG R 147 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG R 147 " --> pdb=" O ILE R 166 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU R 168 " --> pdb=" O VAL R 145 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY R 253 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 215 through 219 removed outlier: 4.524A pdb=" N ARG R 219 " --> pdb=" O HIS R 243 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS R 243 " --> pdb=" O ARG R 219 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 267 through 269 Processing sheet with id=AC3, first strand: chain 'R' and resid 442 through 448 Processing sheet with id=AC4, first strand: chain 'T' and resid 56 through 60 removed outlier: 5.292A pdb=" N ACYS T 57 " --> pdb=" O ATYR T 53 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ATYR T 53 " --> pdb=" O ACYS T 57 " (cutoff:3.500A) removed outlier: 15.889A pdb=" N BLEU T 59 " --> pdb=" O BILE T 51 " (cutoff:3.500A) removed outlier: 20.590A pdb=" N BILE T 51 " --> pdb=" O BLEU T 59 " (cutoff:3.500A) removed outlier: 20.688A pdb=" N BARG T 52 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 22.777A pdb=" N ASN T 108 " --> pdb=" O BARG T 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 65 through 67 removed outlier: 3.531A pdb=" N LYS T 528 " --> pdb=" O HIS T 124 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY T 499 " --> pdb=" O LEU T 119 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR T 121 " --> pdb=" O ASP T 497 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP T 497 " --> pdb=" O THR T 121 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET T 123 " --> pdb=" O LEU T 495 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU T 495 " --> pdb=" O MET T 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 86 through 90 removed outlier: 3.564A pdb=" N GLY T 436 " --> pdb=" O TRP T 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 166 through 175 removed outlier: 6.505A pdb=" N ILE T 166 " --> pdb=" O ARG T 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG T 147 " --> pdb=" O ILE T 166 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU T 168 " --> pdb=" O VAL T 145 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY T 253 " --> pdb=" O ARG T 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 214 through 217 removed outlier: 5.623A pdb=" N TYR T 375 " --> pdb=" O ILE T 289 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 267 through 269 Processing sheet with id=AD1, first strand: chain 'T' and resid 442 through 448 Processing sheet with id=AD2, first strand: chain 'X' and resid 59 through 60 Processing sheet with id=AD3, first strand: chain 'X' and resid 65 through 68 removed outlier: 3.573A pdb=" N LYS X 528 " --> pdb=" O HIS X 124 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG X 114 " --> pdb=" O LEU X 538 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TRP X 115 " --> pdb=" O PRO X 502 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY X 117 " --> pdb=" O THR X 500 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR X 500 " --> pdb=" O GLY X 117 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU X 119 " --> pdb=" O HIS X 498 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 86 through 90 removed outlier: 3.933A pdb=" N GLY X 436 " --> pdb=" O TRP X 411 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 166 through 175 removed outlier: 6.189A pdb=" N ILE X 166 " --> pdb=" O ARG X 147 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG X 147 " --> pdb=" O ILE X 166 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU X 168 " --> pdb=" O VAL X 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 214 through 219 removed outlier: 4.621A pdb=" N ARG X 219 " --> pdb=" O HIS X 243 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS X 243 " --> pdb=" O ARG X 219 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR X 375 " --> pdb=" O ILE X 289 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 267 through 269 Processing sheet with id=AD8, first strand: chain 'X' and resid 442 through 448 Processing sheet with id=AD9, first strand: chain 'i' and resid 59 through 60 Processing sheet with id=AE1, first strand: chain 'i' and resid 65 through 67 removed outlier: 3.552A pdb=" N LYS i 528 " --> pdb=" O HIS i 124 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ARG i 114 " --> pdb=" O LEU i 538 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY i 499 " --> pdb=" O LEU i 119 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR i 121 " --> pdb=" O ASP i 497 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP i 497 " --> pdb=" O THR i 121 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N MET i 123 " --> pdb=" O LEU i 495 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU i 495 " --> pdb=" O MET i 123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'i' and resid 86 through 90 removed outlier: 3.660A pdb=" N GLY i 436 " --> pdb=" O TRP i 411 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'i' and resid 166 through 175 removed outlier: 3.614A pdb=" N SER i 146 " --> pdb=" O GLU i 168 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU i 170 " --> pdb=" O MET i 144 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N MET i 144 " --> pdb=" O GLU i 170 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL i 172 " --> pdb=" O ARG i 142 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG i 142 " --> pdb=" O VAL i 172 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE i 174 " --> pdb=" O LYS i 140 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYS i 140 " --> pdb=" O PHE i 174 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY i 253 " --> pdb=" O ARG i 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 215 through 219 removed outlier: 4.615A pdb=" N ARG i 219 " --> pdb=" O HIS i 243 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS i 243 " --> pdb=" O ARG i 219 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR i 375 " --> pdb=" O ILE i 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'i' and resid 267 through 269 Processing sheet with id=AE6, first strand: chain 'i' and resid 442 through 448 Processing sheet with id=AE7, first strand: chain 'j' and resid 59 through 60 Processing sheet with id=AE8, first strand: chain 'j' and resid 65 through 67 removed outlier: 3.605A pdb=" N LYS j 528 " --> pdb=" O HIS j 124 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG j 114 " --> pdb=" O LEU j 538 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TRP j 115 " --> pdb=" O PRO j 502 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY j 117 " --> pdb=" O THR j 500 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N THR j 500 " --> pdb=" O GLY j 117 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU j 119 " --> pdb=" O HIS j 498 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'j' and resid 86 through 90 removed outlier: 3.539A pdb=" N GLY j 436 " --> pdb=" O TRP j 411 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'j' and resid 166 through 175 removed outlier: 3.908A pdb=" N SER j 146 " --> pdb=" O GLU j 168 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU j 170 " --> pdb=" O MET j 144 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N MET j 144 " --> pdb=" O GLU j 170 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL j 172 " --> pdb=" O ARG j 142 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG j 142 " --> pdb=" O VAL j 172 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE j 174 " --> pdb=" O LYS j 140 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS j 140 " --> pdb=" O PHE j 174 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'j' and resid 215 through 219 removed outlier: 4.630A pdb=" N ARG j 219 " --> pdb=" O HIS j 243 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS j 243 " --> pdb=" O ARG j 219 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR j 375 " --> pdb=" O ILE j 289 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'j' and resid 267 through 269 Processing sheet with id=AF4, first strand: chain 'j' and resid 442 through 448 Processing sheet with id=AF5, first strand: chain 'k' and resid 59 through 60 removed outlier: 14.070A pdb=" N BLEU k 59 " --> pdb=" O BILE k 51 " (cutoff:3.500A) removed outlier: 17.434A pdb=" N BILE k 51 " --> pdb=" O BLEU k 59 " (cutoff:3.500A) removed outlier: 20.733A pdb=" N BARG k 52 " --> pdb=" O ASN k 108 " (cutoff:3.500A) removed outlier: 22.732A pdb=" N ASN k 108 " --> pdb=" O BARG k 52 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'k' and resid 65 through 67 removed outlier: 3.567A pdb=" N LYS k 528 " --> pdb=" O HIS k 124 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG k 114 " --> pdb=" O LEU k 538 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N TRP k 115 " --> pdb=" O PRO k 502 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY k 117 " --> pdb=" O THR k 500 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR k 500 " --> pdb=" O GLY k 117 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU k 119 " --> pdb=" O HIS k 498 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'k' and resid 86 through 90 removed outlier: 3.903A pdb=" N GLY k 436 " --> pdb=" O TRP k 411 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'k' and resid 166 through 175 removed outlier: 6.615A pdb=" N ILE k 166 " --> pdb=" O ARG k 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG k 147 " --> pdb=" O ILE k 166 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU k 168 " --> pdb=" O VAL k 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'k' and resid 214 through 217 removed outlier: 4.741A pdb=" N ILE k 289 " --> pdb=" O THR k 373 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'k' and resid 267 through 269 Processing sheet with id=AG2, first strand: chain 'k' and resid 442 through 448 Processing sheet with id=AG3, first strand: chain 'v' and resid 59 through 60 Processing sheet with id=AG4, first strand: chain 'v' and resid 65 through 67 removed outlier: 5.596A pdb=" N ALA v 529 " --> pdb=" O HIS v 124 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS v 124 " --> pdb=" O ALA v 529 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLY v 531 " --> pdb=" O ILE v 122 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE v 122 " --> pdb=" O GLY v 531 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL v 533 " --> pdb=" O LYS v 120 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS v 120 " --> pdb=" O VAL v 533 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN v 118 " --> pdb=" O PRO v 535 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL v 537 " --> pdb=" O GLY v 116 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLY v 116 " --> pdb=" O VAL v 537 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TRP v 115 " --> pdb=" O PRO v 502 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLY v 117 " --> pdb=" O THR v 500 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR v 500 " --> pdb=" O GLY v 117 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU v 119 " --> pdb=" O HIS v 498 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'v' and resid 86 through 90 Processing sheet with id=AG6, first strand: chain 'v' and resid 166 through 175 removed outlier: 6.268A pdb=" N ILE v 166 " --> pdb=" O ARG v 147 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG v 147 " --> pdb=" O ILE v 166 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU v 168 " --> pdb=" O VAL v 145 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'v' and resid 214 through 219 removed outlier: 4.548A pdb=" N ARG v 219 " --> pdb=" O HIS v 243 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS v 243 " --> pdb=" O ARG v 219 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TYR v 375 " --> pdb=" O ILE v 289 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'v' and resid 267 through 269 Processing sheet with id=AG9, first strand: chain 'v' and resid 442 through 448 Processing sheet with id=AH1, first strand: chain 'w' and resid 59 through 60 Processing sheet with id=AH2, first strand: chain 'w' and resid 65 through 67 removed outlier: 3.576A pdb=" N LYS w 528 " --> pdb=" O HIS w 124 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG w 114 " --> pdb=" O LEU w 538 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY w 499 " --> pdb=" O LEU w 119 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR w 121 " --> pdb=" O ASP w 497 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ASP w 497 " --> pdb=" O THR w 121 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N MET w 123 " --> pdb=" O LEU w 495 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU w 495 " --> pdb=" O MET w 123 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'w' and resid 86 through 90 removed outlier: 3.665A pdb=" N GLY w 436 " --> pdb=" O TRP w 411 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'w' and resid 166 through 175 removed outlier: 3.648A pdb=" N SER w 146 " --> pdb=" O GLU w 168 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU w 170 " --> pdb=" O MET w 144 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET w 144 " --> pdb=" O GLU w 170 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL w 172 " --> pdb=" O ARG w 142 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG w 142 " --> pdb=" O VAL w 172 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE w 174 " --> pdb=" O LYS w 140 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS w 140 " --> pdb=" O PHE w 174 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'w' and resid 214 through 217 removed outlier: 5.392A pdb=" N TYR w 375 " --> pdb=" O ILE w 289 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'w' and resid 267 through 269 Processing sheet with id=AH7, first strand: chain 'w' and resid 442 through 448 924 hydrogen bonds defined for protein. 2523 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: 7.87 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10526 1.33 - 1.45: 5602 1.45 - 1.57: 18706 1.57 - 1.69: 1 1.69 - 1.81: 242 Bond restraints: 35077 Sorted by residual: bond pdb=" N VAL w 478 " pdb=" CA VAL w 478 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.06e+01 bond pdb=" N VAL w 355 " pdb=" CA VAL w 355 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.10e-02 8.26e+03 1.05e+01 bond pdb=" N VAL v 92 " pdb=" CA VAL v 92 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N ASN k 431 " pdb=" CA ASN k 431 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.00e-02 1.00e+04 1.01e+01 bond pdb=" N VAL j 510 " pdb=" CA VAL j 510 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.80e+00 ... (remaining 35072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 46904 2.35 - 4.69: 820 4.69 - 7.04: 44 7.04 - 9.39: 6 9.39 - 11.73: 3 Bond angle restraints: 47777 Sorted by residual: angle pdb=" N ALEU k 59 " pdb=" CA ALEU k 59 " pdb=" C ALEU k 59 " ideal model delta sigma weight residual 110.50 100.40 10.10 1.41e+00 5.03e-01 5.13e+01 angle pdb=" N ATYR k 60 " pdb=" CA ATYR k 60 " pdb=" C ATYR k 60 " ideal model delta sigma weight residual 109.40 119.59 -10.19 1.63e+00 3.76e-01 3.91e+01 angle pdb=" CA ASP w 61 " pdb=" C ASP w 61 " pdb=" N THR w 62 " ideal model delta sigma weight residual 119.63 115.87 3.76 8.10e-01 1.52e+00 2.15e+01 angle pdb=" CA PRO X 58 " pdb=" N PRO X 58 " pdb=" CD PRO X 58 " ideal model delta sigma weight residual 112.00 105.53 6.47 1.40e+00 5.10e-01 2.14e+01 angle pdb=" N PRO X 58 " pdb=" CD PRO X 58 " pdb=" CG PRO X 58 " ideal model delta sigma weight residual 103.20 96.37 6.83 1.50e+00 4.44e-01 2.08e+01 ... (remaining 47772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 20380 35.90 - 71.80: 655 71.80 - 107.69: 48 107.69 - 143.59: 0 143.59 - 179.49: 1 Dihedral angle restraints: 21084 sinusoidal: 8496 harmonic: 12588 Sorted by residual: dihedral pdb=" CB ACYS T 57 " pdb=" SG ACYS T 57 " pdb=" SG ACYS k 57 " pdb=" CB ACYS k 57 " ideal model delta sinusoidal sigma weight residual 93.00 175.17 -82.17 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB BGLU k 55 " pdb=" CG BGLU k 55 " pdb=" CD BGLU k 55 " pdb=" OE1BGLU k 55 " ideal model delta sinusoidal sigma weight residual 0.00 179.49 -179.49 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA ILE 8 212 " pdb=" C ILE 8 212 " pdb=" N GLY 8 213 " pdb=" CA GLY 8 213 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 21081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4323 0.060 - 0.121: 886 0.121 - 0.181: 126 0.181 - 0.241: 21 0.241 - 0.301: 3 Chirality restraints: 5359 Sorted by residual: chirality pdb=" CA ILE i 107 " pdb=" N ILE i 107 " pdb=" C ILE i 107 " pdb=" CB ILE i 107 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE X 51 " pdb=" N ILE X 51 " pdb=" C ILE X 51 " pdb=" CB ILE X 51 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ATYR k 60 " pdb=" N ATYR k 60 " pdb=" C ATYR k 60 " pdb=" CB ATYR k 60 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 5356 not shown) Planarity restraints: 6233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 367 " 0.057 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO K 368 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO K 368 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO K 368 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG i 64 " -0.267 9.50e-02 1.11e+02 1.20e-01 8.81e+00 pdb=" NE ARG i 64 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG i 64 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG i 64 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG i 64 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG w 362 " -0.246 9.50e-02 1.11e+02 1.10e-01 7.46e+00 pdb=" NE ARG w 362 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG w 362 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG w 362 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG w 362 " -0.008 2.00e-02 2.50e+03 ... (remaining 6230 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1165 2.71 - 3.26: 32812 3.26 - 3.80: 56639 3.80 - 4.35: 77814 4.35 - 4.90: 123906 Nonbonded interactions: 292336 Sorted by model distance: nonbonded pdb=" OG SER 8 210 " pdb=" OD1 ASP 8 211 " model vdw 2.162 3.040 nonbonded pdb=" O VAL X 391 " pdb=" OG1 THR X 395 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR K 53 " pdb=" OE1 GLN K 105 " model vdw 2.220 3.040 nonbonded pdb=" O VAL 8 92 " pdb=" OG1 THR X 422 " model vdw 2.221 3.040 nonbonded pdb=" O THR 8 542 " pdb=" OG1 THR 8 542 " model vdw 2.221 3.040 ... (remaining 292331 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 '8' and (resid 64 through 298 or (resid 299 through 301 and (name N or na \ me CA or name C or name O or name CB )) or resid 351 through 426 or (resid 427 a \ nd (name N or name CA or name C or name O or name CB )) or resid 428 through 450 \ or resid 466 through 507 or (resid 508 and (name N or name CA or name C or name \ O or name CB )) or resid 509 through 518 or (resid 519 and (name N or name CA o \ r name C or name O or name CB )) or resid 520 through 542)) selection = (chain 'K' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 298 or (resid 299 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 426 \ or (resid 427 and (name N or name CA or name C or name O or name CB )) or resid \ 428 through 450 or resid 466 through 507 or (resid 508 and (name N or name CA o \ r name C or name O or name CB )) or resid 509 through 518 or (resid 519 and (nam \ e N or name CA or name C or name O or name CB )) or resid 520 through 542)) selection = (chain 'R' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 298 or (resid 299 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 426 \ or (resid 427 and (name N or name CA or name C or name O or name CB )) or resid \ 428 through 450 or resid 466 through 507 or (resid 508 and (name N or name CA o \ r name C or name O or name CB )) or resid 509 through 518 or (resid 519 and (nam \ e N or name CA or name C or name O or name CB )) or resid 520 through 542)) selection = (chain 'T' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 301 or resid 351 through 426 or \ (resid 427 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 8 through 450 or resid 466 through 518 or (resid 519 and (name N or name CA or n \ ame C or name O or name CB )) or resid 520 through 542)) selection = (chain 'X' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 298 or (resid 299 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 426 \ or (resid 427 and (name N or name CA or name C or name O or name CB )) or resid \ 428 through 450 or resid 466 through 518 or (resid 519 and (name N or name CA o \ r name C or name O or name CB )) or resid 520 through 542)) selection = (chain 'i' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 298 or (resid 299 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 426 \ or (resid 427 and (name N or name CA or name C or name O or name CB )) or resid \ 428 through 450 or resid 466 through 518 or (resid 519 and (name N or name CA o \ r name C or name O or name CB )) or resid 520 through 540 or (resid 541 and (nam \ e N or name CA or name C or name O or name CB )) or resid 542)) selection = (chain 'j' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 298 or (resid 299 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 426 \ or (resid 427 and (name N or name CA or name C or name O or name CB )) or resid \ 428 through 450 or resid 466 through 518 or (resid 519 and (name N or name CA o \ r name C or name O or name CB )) or resid 520 through 540 or (resid 541 and (nam \ e N or name CA or name C or name O or name CB )) or resid 542)) selection = (chain 'k' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 298 or (resid 299 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 450 \ or resid 466 through 507 or (resid 508 and (name N or name CA or name C or name \ O or name CB )) or resid 509 through 518 or (resid 519 and (name N or name CA o \ r name C or name O or name CB )) or resid 520 through 542)) selection = (chain 'v' and (resid 64 through 298 or (resid 299 through 301 and (name N or na \ me CA or name C or name O or name CB )) or resid 351 through 426 or (resid 427 a \ nd (name N or name CA or name C or name O or name CB )) or resid 428 through 450 \ or resid 466 through 518 or (resid 519 and (name N or name CA or name C or name \ O or name CB )) or resid 520 through 540 or (resid 541 and (name N or name CA o \ r name C or name O or name CB )) or resid 542)) selection = (chain 'w' and (resid 64 through 150 or (resid 164 and (name N or name CA or nam \ e C or name O or name CB )) or resid 165 through 298 or (resid 299 through 301 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 426 \ or (resid 427 and (name N or name CA or name C or name O or name CB )) or resid \ 428 through 450 or resid 466 through 507 or (resid 508 and (name N or name CA o \ r name C or name O or name CB )) or resid 509 through 542)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=0.99 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: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 33.460 Find NCS groups from input model: 0.900 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: 0.010 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.282 35078 Z= 0.300 Angle : 0.698 26.575 47779 Z= 0.430 Chirality : 0.051 0.301 5359 Planarity : 0.005 0.120 6233 Dihedral : 16.512 179.490 12949 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 2.93 % Allowed : 19.09 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4208 helix: -0.37 (0.22), residues: 504 sheet: 0.68 (0.16), residues: 979 loop : -0.63 (0.11), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 8 147 TYR 0.015 0.001 TYR k 80 PHE 0.010 0.001 PHE k 221 TRP 0.028 0.001 TRP w 225 HIS 0.003 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00430 (35077) covalent geometry : angle 0.68159 (47777) SS BOND : bond 0.28154 ( 1) SS BOND : angle 23.47070 ( 2) hydrogen bonds : bond 0.20962 ( 924) hydrogen bonds : angle 8.76801 ( 2523) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 590 time to evaluate : 1.320 Fit side-chains REVERT: 8 245 ASP cc_start: 0.6161 (t0) cc_final: 0.5955 (t0) REVERT: 8 356 GLU cc_start: 0.4775 (mp0) cc_final: 0.4534 (mp0) REVERT: 8 418 GLN cc_start: 0.7677 (mt0) cc_final: 0.7424 (mt0) REVERT: 8 427 ARG cc_start: 0.5550 (tpp80) cc_final: 0.5252 (mtt180) REVERT: K 104 THR cc_start: 0.7945 (p) cc_final: 0.7672 (t) REVERT: K 173 GLU cc_start: 0.7020 (tt0) cc_final: 0.6679 (tm-30) REVERT: K 451 GLN cc_start: 0.5040 (mt0) cc_final: 0.4729 (mt0) REVERT: R 104 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6734 (t) REVERT: R 166 ILE cc_start: 0.6357 (mm) cc_final: 0.5879 (mp) REVERT: T 353 GLN cc_start: 0.5491 (pt0) cc_final: 0.4991 (pm20) REVERT: X 59 LEU cc_start: 0.7242 (mp) cc_final: 0.7040 (mm) REVERT: i 61 ASP cc_start: 0.6633 (m-30) cc_final: 0.6197 (m-30) REVERT: i 144 MET cc_start: 0.7004 (ttp) cc_final: 0.5944 (ttt) REVERT: i 369 ASP cc_start: 0.5694 (p0) cc_final: 0.5394 (t0) REVERT: i 517 ASP cc_start: 0.7745 (p0) cc_final: 0.7300 (p0) REVERT: j 166 ILE cc_start: 0.6089 (mt) cc_final: 0.5812 (pt) REVERT: k 351 VAL cc_start: 0.6215 (p) cc_final: 0.5965 (m) REVERT: v 75 ILE cc_start: 0.7433 (mt) cc_final: 0.7181 (mm) REVERT: v 365 ASN cc_start: 0.7491 (m-40) cc_final: 0.7281 (m110) REVERT: v 517 ASP cc_start: 0.7518 (p0) cc_final: 0.7307 (p0) REVERT: w 275 GLU cc_start: 0.6357 (pt0) cc_final: 0.5542 (tt0) REVERT: w 296 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5568 (p0) REVERT: w 360 LYS cc_start: 0.6570 (mtpt) cc_final: 0.6356 (mttm) REVERT: w 389 LYS cc_start: 0.6969 (mppt) cc_final: 0.6485 (mttt) REVERT: w 406 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7381 (m) REVERT: w 450 GLU cc_start: 0.4781 (mt-10) cc_final: 0.4144 (tp30) outliers start: 100 outliers final: 24 residues processed: 666 average time/residue: 0.7197 time to fit residues: 572.0803 Evaluate side-chains 364 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 337 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 63 THR Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 467 VAL Chi-restraints excluded: chain 8 residue 505 SER Chi-restraints excluded: chain K residue 59 LEU Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 505 SER Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain X residue 178 GLU Chi-restraints excluded: chain X residue 542 THR Chi-restraints excluded: chain j residue 406 VAL Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 522 THR Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 453 VAL Chi-restraints excluded: chain v residue 228 VAL Chi-restraints excluded: chain v residue 238 THR Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 296 ASP Chi-restraints excluded: chain w residue 406 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 81 GLN K 239 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 ASN ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN T 105 GLN X 93 GLN i 118 GLN i 469 ASN j 95 ASN j 475 GLN k 81 GLN k 220 ASN w 94 ASN w 95 ASN w 124 HIS ** w 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.109605 restraints weight = 142521.775| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.33 r_work: 0.3090 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 35078 Z= 0.289 Angle : 0.803 10.353 47779 Z= 0.426 Chirality : 0.055 0.308 5359 Planarity : 0.007 0.061 6233 Dihedral : 6.451 98.320 4757 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.48 % Favored : 95.50 % Rotamer: Outliers : 5.21 % Allowed : 18.68 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.12), residues: 4208 helix: -0.18 (0.22), residues: 527 sheet: 0.57 (0.16), residues: 992 loop : -0.84 (0.11), residues: 2689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG w 219 TYR 0.019 0.003 TYR T 443 PHE 0.023 0.003 PHE w 221 TRP 0.022 0.003 TRP w 225 HIS 0.008 0.002 HIS v 498 Details of bonding type rmsd covalent geometry : bond 0.00660 (35077) covalent geometry : angle 0.80199 (47777) SS BOND : bond 0.00722 ( 1) SS BOND : angle 5.17815 ( 2) hydrogen bonds : bond 0.06031 ( 924) hydrogen bonds : angle 6.97917 ( 2523) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 316 time to evaluate : 1.409 Fit side-chains REVERT: 8 103 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8157 (t) REVERT: 8 123 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8208 (ttm) REVERT: 8 134 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8126 (tpt) REVERT: 8 142 ARG cc_start: 0.7609 (ttp-170) cc_final: 0.7165 (ttt90) REVERT: 8 217 ASP cc_start: 0.7788 (t0) cc_final: 0.7528 (t70) REVERT: 8 230 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: 8 240 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: 8 353 GLN cc_start: 0.6604 (tp40) cc_final: 0.5660 (pt0) REVERT: 8 427 ARG cc_start: 0.5846 (tpp80) cc_final: 0.5181 (mtt180) REVERT: K 229 THR cc_start: 0.7718 (p) cc_final: 0.7471 (m) REVERT: K 240 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: K 451 GLN cc_start: 0.5111 (mt0) cc_final: 0.4792 (mt0) REVERT: R 61 ASP cc_start: 0.7306 (m-30) cc_final: 0.7000 (m-30) REVERT: R 111 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7239 (mp0) REVERT: R 127 MET cc_start: 0.8733 (ttm) cc_final: 0.8509 (ttp) REVERT: R 166 ILE cc_start: 0.7057 (mm) cc_final: 0.6497 (mp) REVERT: R 190 MET cc_start: 0.9052 (mtp) cc_final: 0.8223 (mtm) REVERT: R 486 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8698 (p) REVERT: T 134 MET cc_start: 0.8565 (mmm) cc_final: 0.8341 (mmm) REVERT: T 199 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7929 (pp) REVERT: X 132 GLU cc_start: 0.8477 (tt0) cc_final: 0.8170 (tm-30) REVERT: X 134 MET cc_start: 0.8274 (mmt) cc_final: 0.8035 (tpt) REVERT: X 356 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6923 (mt-10) REVERT: X 389 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6879 (mppt) REVERT: i 401 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7440 (t70) REVERT: j 52 ARG cc_start: 0.7792 (mtt-85) cc_final: 0.7566 (mpp80) REVERT: j 166 ILE cc_start: 0.6399 (mt) cc_final: 0.5789 (pt) REVERT: j 188 ASP cc_start: 0.7822 (m-30) cc_final: 0.7521 (m-30) REVERT: j 208 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7124 (mt) REVERT: j 282 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: k 81 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6962 (pm20) REVERT: k 470 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7511 (mtp85) REVERT: v 105 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.6573 (mm-40) REVERT: v 112 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7292 (mtm110) REVERT: v 185 MET cc_start: 0.8873 (tpp) cc_final: 0.8514 (tpp) REVERT: w 106 THR cc_start: 0.8320 (p) cc_final: 0.8099 (t) REVERT: w 389 LYS cc_start: 0.8222 (mppt) cc_final: 0.7872 (mttt) REVERT: w 427 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.4872 (mtm180) REVERT: w 429 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7593 (m) REVERT: w 486 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8368 (t) outliers start: 187 outliers final: 60 residues processed: 467 average time/residue: 0.8112 time to fit residues: 444.1137 Evaluate side-chains 344 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 266 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 123 MET Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 214 VAL Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 238 THR Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 505 SER Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 240 GLU Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 489 SER Chi-restraints excluded: chain K residue 522 THR Chi-restraints excluded: chain R residue 57 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 275 GLU Chi-restraints excluded: chain R residue 358 ASP Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 505 SER Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 178 GLU Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 540 SER Chi-restraints excluded: chain X residue 542 THR Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 295 VAL Chi-restraints excluded: chain i residue 351 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 412 SER Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain j residue 208 LEU Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 377 SER Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 453 VAL Chi-restraints excluded: chain k residue 500 THR Chi-restraints excluded: chain v residue 59 LEU Chi-restraints excluded: chain v residue 105 GLN Chi-restraints excluded: chain v residue 112 ARG Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 445 LYS Chi-restraints excluded: chain v residue 451 GLN Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 406 VAL Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 429 VAL Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 320 optimal weight: 9.9990 chunk 410 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 412 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 363 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 431 ASN ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 431 ASN j 81 GLN j 474 ASN k 431 ASN v 466 HIS w 95 ASN w 451 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.109237 restraints weight = 132283.840| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.31 r_work: 0.3091 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35078 Z= 0.154 Angle : 0.613 9.585 47779 Z= 0.322 Chirality : 0.049 0.196 5359 Planarity : 0.005 0.062 6233 Dihedral : 5.878 92.755 4742 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 3.81 % Allowed : 19.66 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4208 helix: 0.30 (0.22), residues: 529 sheet: 0.55 (0.16), residues: 1032 loop : -0.76 (0.11), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 8 147 TYR 0.013 0.002 TYR w 60 PHE 0.016 0.002 PHE w 221 TRP 0.019 0.002 TRP w 225 HIS 0.004 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00349 (35077) covalent geometry : angle 0.61303 (47777) SS BOND : bond 0.00134 ( 1) SS BOND : angle 3.65178 ( 2) hydrogen bonds : bond 0.04789 ( 924) hydrogen bonds : angle 6.51930 ( 2523) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 298 time to evaluate : 1.207 Fit side-chains REVERT: 8 111 GLU cc_start: 0.7609 (mp0) cc_final: 0.7322 (mt-10) REVERT: 8 134 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8135 (tpt) REVERT: 8 230 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: 8 240 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: 8 353 GLN cc_start: 0.6627 (tp40) cc_final: 0.5634 (pt0) REVERT: 8 427 ARG cc_start: 0.6266 (tpp80) cc_final: 0.5236 (mtt180) REVERT: K 240 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: K 451 GLN cc_start: 0.5205 (mt0) cc_final: 0.4943 (mt0) REVERT: R 111 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: R 127 MET cc_start: 0.8803 (ttm) cc_final: 0.8556 (ttp) REVERT: R 166 ILE cc_start: 0.6959 (mm) cc_final: 0.6382 (mp) REVERT: R 190 MET cc_start: 0.9007 (mtp) cc_final: 0.8291 (mtm) REVERT: R 486 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8767 (p) REVERT: T 134 MET cc_start: 0.8556 (mmm) cc_final: 0.8280 (mmm) REVERT: X 132 GLU cc_start: 0.8491 (tt0) cc_final: 0.8162 (tm-30) REVERT: X 170 GLU cc_start: 0.7170 (tt0) cc_final: 0.6961 (tt0) REVERT: X 280 MET cc_start: 0.8292 (mmt) cc_final: 0.8059 (mmt) REVERT: X 356 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: X 389 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6957 (mppt) REVERT: i 196 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: i 359 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7257 (p) REVERT: i 401 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7447 (t70) REVERT: j 52 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.7543 (mpp80) REVERT: j 208 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7060 (mt) REVERT: j 495 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8502 (mt) REVERT: v 105 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6550 (mt0) REVERT: w 106 THR cc_start: 0.8408 (p) cc_final: 0.8155 (t) REVERT: w 427 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.5694 (mtm180) REVERT: w 429 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7543 (m) REVERT: w 486 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8266 (t) outliers start: 136 outliers final: 66 residues processed: 408 average time/residue: 0.8083 time to fit residues: 385.9017 Evaluate side-chains 346 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 263 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 92 VAL Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 214 VAL Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 238 THR Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 351 VAL Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 240 GLU Chi-restraints excluded: chain K residue 275 GLU Chi-restraints excluded: chain K residue 350 ILE Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 358 ASP Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain R residue 505 SER Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 178 GLU Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 540 SER Chi-restraints excluded: chain X residue 542 THR Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 132 GLU Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 146 SER Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 208 LEU Chi-restraints excluded: chain j residue 406 VAL Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 453 VAL Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 105 GLN Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 285 GLU Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 429 VAL Chi-restraints excluded: chain w residue 486 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 116 optimal weight: 9.9990 chunk 388 optimal weight: 0.0040 chunk 405 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 354 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** T 105 GLN X 431 ASN i 118 GLN j 197 ASN k 431 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110153 restraints weight = 117283.730| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.07 r_work: 0.3116 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35078 Z= 0.126 Angle : 0.569 9.483 47779 Z= 0.297 Chirality : 0.047 0.180 5359 Planarity : 0.005 0.063 6233 Dihedral : 5.567 86.092 4739 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.41 % Rotamer: Outliers : 3.99 % Allowed : 19.35 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.13), residues: 4208 helix: 0.59 (0.23), residues: 529 sheet: 0.59 (0.16), residues: 1033 loop : -0.64 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 8 147 TYR 0.012 0.001 TYR 8 53 PHE 0.013 0.001 PHE w 221 TRP 0.023 0.001 TRP w 225 HIS 0.004 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00285 (35077) covalent geometry : angle 0.56884 (47777) SS BOND : bond 0.00312 ( 1) SS BOND : angle 2.62323 ( 2) hydrogen bonds : bond 0.04042 ( 924) hydrogen bonds : angle 6.17516 ( 2523) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 296 time to evaluate : 0.966 Fit side-chains REVERT: 8 103 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8083 (t) REVERT: 8 134 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8076 (tpt) REVERT: 8 209 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5912 (pp20) REVERT: 8 230 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: 8 353 GLN cc_start: 0.6693 (tp40) cc_final: 0.5728 (pt0) REVERT: 8 427 ARG cc_start: 0.6259 (tpp80) cc_final: 0.5238 (mtt180) REVERT: K 240 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7632 (mm-30) REVERT: K 451 GLN cc_start: 0.5303 (mt0) cc_final: 0.4940 (mt0) REVERT: R 111 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: R 127 MET cc_start: 0.8806 (ttm) cc_final: 0.8600 (ttp) REVERT: R 166 ILE cc_start: 0.7004 (mm) cc_final: 0.6417 (mp) REVERT: R 190 MET cc_start: 0.8919 (mtp) cc_final: 0.8186 (mtm) REVERT: R 407 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: R 486 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8776 (p) REVERT: T 134 MET cc_start: 0.8487 (mmm) cc_final: 0.8137 (mmm) REVERT: T 165 ASP cc_start: 0.6405 (m-30) cc_final: 0.6124 (m-30) REVERT: X 132 GLU cc_start: 0.8468 (tt0) cc_final: 0.8140 (tm-30) REVERT: X 280 MET cc_start: 0.8214 (mmt) cc_final: 0.7877 (mmt) REVERT: X 356 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6836 (mt-10) REVERT: X 389 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6947 (mppt) REVERT: X 530 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7994 (tm) REVERT: i 196 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: i 359 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.7325 (p) REVERT: i 401 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7356 (t70) REVERT: j 52 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7487 (mpp80) REVERT: j 208 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7106 (mt) REVERT: j 282 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: j 427 ARG cc_start: 0.7945 (mmm-85) cc_final: 0.7530 (mmm160) REVERT: j 495 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8429 (mt) REVERT: k 140 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7521 (mppt) REVERT: v 105 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.6622 (mt0) REVERT: w 106 THR cc_start: 0.8406 (p) cc_final: 0.8176 (t) REVERT: w 299 GLU cc_start: 0.6376 (mm-30) cc_final: 0.5703 (tp30) REVERT: w 427 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5756 (mtm180) REVERT: w 450 GLU cc_start: 0.6054 (mt-10) cc_final: 0.5749 (mt-10) REVERT: w 486 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8265 (t) outliers start: 142 outliers final: 64 residues processed: 405 average time/residue: 0.8325 time to fit residues: 393.5435 Evaluate side-chains 361 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 276 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 196 ASP Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 209 GLU Chi-restraints excluded: chain 8 residue 228 VAL Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 240 GLU Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 407 GLU Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain R residue 505 SER Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 178 GLU Chi-restraints excluded: chain X residue 203 ARG Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 430 SER Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 132 GLU Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 351 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 484 THR Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 134 MET Chi-restraints excluded: chain j residue 208 LEU Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain k residue 140 LYS Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 453 VAL Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 105 GLN Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 233 MET Chi-restraints excluded: chain v residue 359 SER Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 431 ASN Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 75 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 396 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 326 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 360 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** X 431 ASN j 86 ASN j 197 ASN j 205 ASN k 431 ASN v 108 ASN v 431 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108534 restraints weight = 129346.581| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.37 r_work: 0.3089 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35078 Z= 0.183 Angle : 0.648 11.296 47779 Z= 0.339 Chirality : 0.050 0.219 5359 Planarity : 0.006 0.059 6233 Dihedral : 5.865 84.694 4736 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 4.40 % Allowed : 19.38 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.12), residues: 4208 helix: 0.51 (0.23), residues: 528 sheet: 0.53 (0.16), residues: 1021 loop : -0.70 (0.11), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 8 147 TYR 0.016 0.002 TYR R 443 PHE 0.019 0.002 PHE w 221 TRP 0.030 0.002 TRP w 225 HIS 0.007 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00423 (35077) covalent geometry : angle 0.64806 (47777) SS BOND : bond 0.00441 ( 1) SS BOND : angle 2.08987 ( 2) hydrogen bonds : bond 0.04610 ( 924) hydrogen bonds : angle 6.38749 ( 2523) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 282 time to evaluate : 1.369 Fit side-chains REVERT: 8 103 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8066 (t) REVERT: 8 134 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8075 (tpt) REVERT: 8 142 ARG cc_start: 0.7514 (ttp-170) cc_final: 0.7293 (ttt90) REVERT: 8 209 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.5956 (pp20) REVERT: 8 230 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: 8 240 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: 8 427 ARG cc_start: 0.6237 (tpp80) cc_final: 0.5268 (mtt180) REVERT: 8 495 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8294 (mt) REVERT: K 93 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6311 (mp10) REVERT: K 118 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: K 240 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: R 111 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: R 127 MET cc_start: 0.8815 (ttm) cc_final: 0.8582 (ttp) REVERT: R 190 MET cc_start: 0.8992 (mtp) cc_final: 0.8219 (mtm) REVERT: R 360 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7034 (mmmt) REVERT: R 407 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: R 486 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8773 (p) REVERT: T 134 MET cc_start: 0.8399 (mmm) cc_final: 0.8150 (mmm) REVERT: T 173 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6796 (tp30) REVERT: T 222 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7661 (ttt-90) REVERT: X 132 GLU cc_start: 0.8511 (tt0) cc_final: 0.8164 (tm-30) REVERT: X 230 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: X 280 MET cc_start: 0.8398 (mmt) cc_final: 0.8160 (mmt) REVERT: X 356 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7045 (mt-10) REVERT: X 389 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7070 (mppt) REVERT: X 503 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8052 (tp) REVERT: X 530 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8012 (tm) REVERT: i 48 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6389 (mtm-85) REVERT: i 196 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: i 300 LYS cc_start: 0.5782 (tttt) cc_final: 0.5292 (ttpp) REVERT: i 359 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7348 (p) REVERT: i 401 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7411 (t70) REVERT: j 52 ARG cc_start: 0.7801 (mtt-85) cc_final: 0.7586 (mpp80) REVERT: j 282 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: j 495 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8492 (mt) REVERT: w 258 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: w 299 GLU cc_start: 0.6430 (mm-30) cc_final: 0.6081 (tp30) REVERT: w 427 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5783 (mtm180) REVERT: w 486 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8185 (t) outliers start: 158 outliers final: 85 residues processed: 414 average time/residue: 0.8180 time to fit residues: 396.7870 Evaluate side-chains 383 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 269 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 92 VAL Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 196 ASP Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 209 GLU Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 238 THR Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 351 VAL Chi-restraints excluded: chain 8 residue 360 LYS Chi-restraints excluded: chain 8 residue 453 VAL Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 495 LEU Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 240 GLU Chi-restraints excluded: chain K residue 294 ASP Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 358 ASP Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 407 GLU Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain R residue 505 SER Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 173 GLU Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 178 GLU Chi-restraints excluded: chain X residue 230 GLU Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 425 SER Chi-restraints excluded: chain X residue 430 SER Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain i residue 48 ARG Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 360 LYS Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 484 THR Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 134 MET Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 356 GLU Chi-restraints excluded: chain j residue 406 VAL Chi-restraints excluded: chain j residue 416 MET Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain j residue 507 ILE Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 453 VAL Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain k residue 500 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 233 MET Chi-restraints excluded: chain v residue 359 SER Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 164 GLN Chi-restraints excluded: chain w residue 258 GLU Chi-restraints excluded: chain w residue 285 GLU Chi-restraints excluded: chain w residue 357 LYS Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 142 optimal weight: 0.5980 chunk 223 optimal weight: 6.9990 chunk 192 optimal weight: 0.0570 chunk 285 optimal weight: 9.9990 chunk 228 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 358 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 395 optimal weight: 0.0060 chunk 312 optimal weight: 7.9990 overall best weight: 2.1318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** j 197 ASN j 205 ASN k 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109349 restraints weight = 119742.853| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.05 r_work: 0.3108 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35078 Z= 0.133 Angle : 0.584 10.779 47779 Z= 0.304 Chirality : 0.048 0.207 5359 Planarity : 0.005 0.060 6233 Dihedral : 5.618 80.601 4736 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 4.07 % Allowed : 19.66 % 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 are not related in a simple way. whole: -0.24 (0.13), residues: 4208 helix: 0.69 (0.23), residues: 528 sheet: 0.52 (0.16), residues: 1033 loop : -0.61 (0.12), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 8 147 TYR 0.012 0.001 TYR 8 53 PHE 0.014 0.001 PHE w 221 TRP 0.032 0.001 TRP w 225 HIS 0.003 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00303 (35077) covalent geometry : angle 0.58347 (47777) SS BOND : bond 0.00371 ( 1) SS BOND : angle 1.94840 ( 2) hydrogen bonds : bond 0.04059 ( 924) hydrogen bonds : angle 6.15979 ( 2523) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 280 time to evaluate : 1.322 Fit side-chains REVERT: 8 103 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.8058 (t) REVERT: 8 134 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8076 (tpt) REVERT: 8 209 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5947 (pp20) REVERT: 8 230 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: 8 353 GLN cc_start: 0.6632 (tp40) cc_final: 0.5729 (pt0) REVERT: 8 427 ARG cc_start: 0.6256 (tpp80) cc_final: 0.5267 (mtt180) REVERT: K 93 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: K 258 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: K 451 GLN cc_start: 0.5292 (mt0) cc_final: 0.4958 (mt0) REVERT: R 111 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: R 127 MET cc_start: 0.8799 (ttm) cc_final: 0.8526 (ttp) REVERT: R 164 GLN cc_start: 0.5156 (mm-40) cc_final: 0.4816 (tp40) REVERT: R 190 MET cc_start: 0.8933 (mtp) cc_final: 0.8174 (mtm) REVERT: R 407 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: R 486 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8796 (p) REVERT: T 134 MET cc_start: 0.8383 (mmm) cc_final: 0.8073 (mmm) REVERT: T 222 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7653 (ttt-90) REVERT: X 132 GLU cc_start: 0.8458 (tt0) cc_final: 0.8136 (tm-30) REVERT: X 230 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: X 280 MET cc_start: 0.8261 (mmt) cc_final: 0.7984 (mmt) REVERT: X 356 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: X 389 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6901 (mppt) REVERT: X 530 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7973 (tm) REVERT: i 48 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6320 (mtm-85) REVERT: i 196 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: i 359 SER cc_start: 0.7765 (OUTLIER) cc_final: 0.7338 (p) REVERT: i 401 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7367 (t70) REVERT: j 52 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7534 (mpp80) REVERT: j 282 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: j 416 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8283 (ttm) REVERT: j 427 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7530 (mmm160) REVERT: j 495 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8427 (mt) REVERT: k 140 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7475 (mppt) REVERT: v 55 GLU cc_start: 0.6781 (mp0) cc_final: 0.6143 (mp0) REVERT: v 105 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6798 (mt0) REVERT: v 519 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7548 (pmm-80) REVERT: w 299 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6092 (tp30) REVERT: w 427 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5940 (mtm180) REVERT: w 451 GLN cc_start: 0.5583 (pp30) cc_final: 0.4493 (mm-40) REVERT: w 486 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8184 (t) outliers start: 145 outliers final: 80 residues processed: 399 average time/residue: 0.8467 time to fit residues: 394.6051 Evaluate side-chains 375 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 270 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 92 VAL Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 196 ASP Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 209 GLU Chi-restraints excluded: chain 8 residue 228 VAL Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 453 VAL Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain 8 residue 542 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 294 ASP Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain R residue 57 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 358 ASP Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 407 GLU Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain R residue 505 SER Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 203 ARG Chi-restraints excluded: chain X residue 230 GLU Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 425 SER Chi-restraints excluded: chain X residue 430 SER Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain i residue 48 ARG Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 484 THR Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 134 MET Chi-restraints excluded: chain j residue 247 VAL Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 356 GLU Chi-restraints excluded: chain j residue 416 MET Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain j residue 507 ILE Chi-restraints excluded: chain k residue 140 LYS Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 105 GLN Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 359 SER Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 164 GLN Chi-restraints excluded: chain w residue 357 LYS Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 20.0000 chunk 327 optimal weight: 1.9990 chunk 336 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 367 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 325 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** j 81 GLN j 197 ASN j 205 ASN k 431 ASN w 431 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108245 restraints weight = 131124.934| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.34 r_work: 0.3080 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35078 Z= 0.169 Angle : 0.627 11.337 47779 Z= 0.327 Chirality : 0.049 0.229 5359 Planarity : 0.005 0.059 6233 Dihedral : 5.578 52.900 4732 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 4.07 % Allowed : 19.97 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 4208 helix: 0.61 (0.23), residues: 528 sheet: 0.48 (0.16), residues: 1019 loop : -0.66 (0.12), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 8 147 TYR 0.015 0.002 TYR R 443 PHE 0.018 0.002 PHE w 221 TRP 0.036 0.002 TRP w 225 HIS 0.005 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00391 (35077) covalent geometry : angle 0.62724 (47777) SS BOND : bond 0.00408 ( 1) SS BOND : angle 1.80195 ( 2) hydrogen bonds : bond 0.04366 ( 924) hydrogen bonds : angle 6.25657 ( 2523) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 273 time to evaluate : 1.404 Fit side-chains REVERT: 8 103 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8072 (t) REVERT: 8 134 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8084 (tpt) REVERT: 8 209 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6036 (pp20) REVERT: 8 230 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: 8 240 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: 8 427 ARG cc_start: 0.6404 (tpp80) cc_final: 0.5377 (mtt180) REVERT: K 93 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6298 (mp10) REVERT: K 118 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: K 258 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6724 (mp0) REVERT: K 451 GLN cc_start: 0.5202 (mt0) cc_final: 0.4892 (mt0) REVERT: R 111 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: R 127 MET cc_start: 0.8834 (ttm) cc_final: 0.8561 (ttp) REVERT: R 164 GLN cc_start: 0.5110 (mm-40) cc_final: 0.4783 (tp40) REVERT: R 190 MET cc_start: 0.8983 (mtp) cc_final: 0.8261 (mtm) REVERT: R 407 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: R 486 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8804 (p) REVERT: T 134 MET cc_start: 0.8368 (mmm) cc_final: 0.8041 (mmm) REVERT: T 173 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6770 (tp30) REVERT: T 222 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7694 (ttt-90) REVERT: X 132 GLU cc_start: 0.8542 (tt0) cc_final: 0.8172 (tm-30) REVERT: X 230 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: X 280 MET cc_start: 0.8412 (mmt) cc_final: 0.8193 (mmt) REVERT: X 356 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: X 389 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6908 (mppt) REVERT: X 503 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8048 (tp) REVERT: X 530 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7991 (tm) REVERT: i 48 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6440 (mtm-85) REVERT: i 196 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: i 359 SER cc_start: 0.7757 (OUTLIER) cc_final: 0.7315 (p) REVERT: i 401 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7432 (t70) REVERT: j 52 ARG cc_start: 0.7786 (mtt-85) cc_final: 0.7504 (mpp80) REVERT: j 282 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: j 416 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8186 (ttm) REVERT: j 495 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8487 (mt) REVERT: k 140 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7504 (mppt) REVERT: v 105 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6839 (mt0) REVERT: w 299 GLU cc_start: 0.6426 (mm-30) cc_final: 0.6069 (tp30) REVERT: w 358 ASP cc_start: 0.6627 (t0) cc_final: 0.6344 (t0) REVERT: w 427 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5859 (mtm180) REVERT: w 451 GLN cc_start: 0.5594 (pp30) cc_final: 0.4555 (mm-40) REVERT: w 486 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8214 (t) outliers start: 145 outliers final: 88 residues processed: 392 average time/residue: 0.8462 time to fit residues: 387.9583 Evaluate side-chains 385 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 268 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 92 VAL Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 196 ASP Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 209 GLU Chi-restraints excluded: chain 8 residue 228 VAL Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 238 THR Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 351 VAL Chi-restraints excluded: chain 8 residue 360 LYS Chi-restraints excluded: chain 8 residue 388 GLU Chi-restraints excluded: chain 8 residue 453 VAL Chi-restraints excluded: chain 8 residue 473 GLU Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain 8 residue 542 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 294 ASP Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain R residue 57 CYS Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 358 ASP Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 407 GLU Chi-restraints excluded: chain R residue 426 THR Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain R residue 505 SER Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 173 GLU Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 203 ARG Chi-restraints excluded: chain X residue 230 GLU Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 430 SER Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain i residue 48 ARG Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 484 THR Chi-restraints excluded: chain i residue 486 THR Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain i residue 492 VAL Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 134 MET Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 356 GLU Chi-restraints excluded: chain j residue 406 VAL Chi-restraints excluded: chain j residue 416 MET Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain j residue 507 ILE Chi-restraints excluded: chain k residue 140 LYS Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain k residue 500 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 105 GLN Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 359 SER Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 164 GLN Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 73 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 293 optimal weight: 0.7980 chunk 242 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 235 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** j 86 ASN j 197 ASN j 205 ASN k 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109063 restraints weight = 125557.486| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.35 r_work: 0.3095 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35078 Z= 0.125 Angle : 0.576 11.303 47779 Z= 0.299 Chirality : 0.047 0.232 5359 Planarity : 0.005 0.057 6233 Dihedral : 5.357 52.242 4732 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 3.68 % Allowed : 20.44 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 4208 helix: 0.81 (0.23), residues: 529 sheet: 0.53 (0.16), residues: 1016 loop : -0.59 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 8 147 TYR 0.012 0.001 TYR 8 53 PHE 0.013 0.001 PHE w 221 TRP 0.040 0.001 TRP w 225 HIS 0.003 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00285 (35077) covalent geometry : angle 0.57557 (47777) SS BOND : bond 0.00336 ( 1) SS BOND : angle 1.81853 ( 2) hydrogen bonds : bond 0.03926 ( 924) hydrogen bonds : angle 6.06147 ( 2523) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 278 time to evaluate : 1.420 Fit side-chains REVERT: 8 103 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8038 (t) REVERT: 8 134 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8066 (tpt) REVERT: 8 209 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5803 (pp20) REVERT: 8 230 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: 8 240 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7800 (mm-30) REVERT: 8 353 GLN cc_start: 0.6675 (tp40) cc_final: 0.5747 (pt0) REVERT: 8 427 ARG cc_start: 0.6339 (tpp80) cc_final: 0.5310 (mtt180) REVERT: K 93 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: K 118 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: K 258 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: K 451 GLN cc_start: 0.5228 (mt0) cc_final: 0.4899 (mt0) REVERT: R 111 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: R 127 MET cc_start: 0.8813 (ttm) cc_final: 0.8550 (ttp) REVERT: R 164 GLN cc_start: 0.5068 (mm-40) cc_final: 0.4755 (tp40) REVERT: R 190 MET cc_start: 0.8932 (mtp) cc_final: 0.8208 (mtm) REVERT: R 293 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7121 (tp) REVERT: R 407 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: R 486 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8799 (p) REVERT: T 112 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6531 (ttp-110) REVERT: T 134 MET cc_start: 0.8232 (mmm) cc_final: 0.7899 (mmm) REVERT: T 222 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7661 (ttt-90) REVERT: X 132 GLU cc_start: 0.8505 (tt0) cc_final: 0.8180 (tm-30) REVERT: X 280 MET cc_start: 0.8266 (mmt) cc_final: 0.8029 (mmt) REVERT: X 389 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6946 (mppt) REVERT: X 503 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8055 (tp) REVERT: X 530 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7932 (tm) REVERT: i 196 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: i 359 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.7317 (p) REVERT: i 401 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7391 (t70) REVERT: j 52 ARG cc_start: 0.7803 (mtt-85) cc_final: 0.7509 (mpp80) REVERT: j 282 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: j 427 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7516 (mmm160) REVERT: j 495 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8414 (mt) REVERT: k 140 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7507 (mppt) REVERT: k 258 GLU cc_start: 0.7790 (tt0) cc_final: 0.7273 (tm-30) REVERT: v 519 ARG cc_start: 0.7937 (ptp-170) cc_final: 0.7510 (pmm-80) REVERT: w 299 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6009 (tp30) REVERT: w 358 ASP cc_start: 0.6536 (t0) cc_final: 0.6143 (t0) REVERT: w 427 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5962 (mtm180) REVERT: w 451 GLN cc_start: 0.5424 (pp30) cc_final: 0.4491 (mm-40) REVERT: w 486 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8186 (t) outliers start: 130 outliers final: 81 residues processed: 387 average time/residue: 0.8241 time to fit residues: 372.5639 Evaluate side-chains 377 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 271 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 92 VAL Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 196 ASP Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 209 GLU Chi-restraints excluded: chain 8 residue 228 VAL Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 453 VAL Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain 8 residue 542 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 294 ASP Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 293 LEU Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 407 GLU Chi-restraints excluded: chain R residue 426 THR Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 203 ARG Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 425 SER Chi-restraints excluded: chain X residue 430 SER Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 412 SER Chi-restraints excluded: chain i residue 484 THR Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain i residue 492 VAL Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 134 MET Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 356 GLU Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain j residue 507 ILE Chi-restraints excluded: chain k residue 140 LYS Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 295 VAL Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 359 SER Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 406 VAL Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 349 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 411 optimal weight: 0.0040 chunk 101 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** j 197 ASN j 205 ASN k 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.108592 restraints weight = 120967.946| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.11 r_work: 0.3096 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35078 Z= 0.156 Angle : 0.612 11.922 47779 Z= 0.318 Chirality : 0.049 0.249 5359 Planarity : 0.005 0.058 6233 Dihedral : 5.463 50.805 4731 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 3.81 % Allowed : 20.28 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4208 helix: 0.73 (0.23), residues: 529 sheet: 0.47 (0.16), residues: 1029 loop : -0.62 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 8 147 TYR 0.016 0.002 TYR R 443 PHE 0.016 0.002 PHE w 221 TRP 0.045 0.002 TRP w 225 HIS 0.005 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00360 (35077) covalent geometry : angle 0.61151 (47777) SS BOND : bond 0.00378 ( 1) SS BOND : angle 1.74721 ( 2) hydrogen bonds : bond 0.04197 ( 924) hydrogen bonds : angle 6.15913 ( 2523) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 271 time to evaluate : 1.358 Fit side-chains REVERT: 8 103 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8024 (t) REVERT: 8 134 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8044 (tpt) REVERT: 8 209 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5810 (pp20) REVERT: 8 230 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: 8 353 GLN cc_start: 0.6674 (tp40) cc_final: 0.5759 (pt0) REVERT: 8 427 ARG cc_start: 0.6354 (tpp80) cc_final: 0.5354 (mtt180) REVERT: K 93 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6281 (mp10) REVERT: K 118 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8269 (tt0) REVERT: K 258 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: K 451 GLN cc_start: 0.5224 (mt0) cc_final: 0.4896 (mt0) REVERT: R 111 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: R 127 MET cc_start: 0.8824 (ttm) cc_final: 0.8597 (ttp) REVERT: R 190 MET cc_start: 0.8953 (mtp) cc_final: 0.8146 (mtm) REVERT: R 407 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: R 486 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8791 (p) REVERT: T 112 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.6579 (ttp-110) REVERT: T 134 MET cc_start: 0.8105 (mmm) cc_final: 0.7734 (mmm) REVERT: T 173 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6697 (tp30) REVERT: T 222 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7686 (ttt-90) REVERT: X 132 GLU cc_start: 0.8528 (tt0) cc_final: 0.8169 (tm-30) REVERT: X 280 MET cc_start: 0.8314 (mmt) cc_final: 0.8013 (mmt) REVERT: X 389 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6906 (mppt) REVERT: X 503 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8053 (tp) REVERT: X 530 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7968 (tm) REVERT: i 196 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: i 359 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7358 (p) REVERT: i 401 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7383 (t70) REVERT: j 52 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7518 (mpp80) REVERT: j 282 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: j 427 ARG cc_start: 0.7884 (mmm-85) cc_final: 0.7484 (mmm160) REVERT: j 495 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8465 (mt) REVERT: k 81 GLN cc_start: 0.7773 (mp10) cc_final: 0.7523 (mt0) REVERT: k 140 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7456 (mppt) REVERT: v 519 ARG cc_start: 0.7905 (ptp-170) cc_final: 0.7469 (pmm-80) REVERT: w 258 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: w 299 GLU cc_start: 0.6405 (mm-30) cc_final: 0.6098 (tp30) REVERT: w 358 ASP cc_start: 0.6515 (t0) cc_final: 0.6083 (t0) REVERT: w 427 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5927 (mtm180) REVERT: w 451 GLN cc_start: 0.5552 (pp30) cc_final: 0.5347 (pp30) REVERT: w 486 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8191 (t) REVERT: w 495 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8313 (mt) outliers start: 135 outliers final: 94 residues processed: 383 average time/residue: 0.8264 time to fit residues: 370.9565 Evaluate side-chains 389 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 269 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 92 VAL Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 196 ASP Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 209 GLU Chi-restraints excluded: chain 8 residue 228 VAL Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 238 THR Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 351 VAL Chi-restraints excluded: chain 8 residue 360 LYS Chi-restraints excluded: chain 8 residue 388 GLU Chi-restraints excluded: chain 8 residue 453 VAL Chi-restraints excluded: chain 8 residue 473 GLU Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain 8 residue 542 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 294 ASP Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 407 GLU Chi-restraints excluded: chain R residue 426 THR Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 489 SER Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 173 GLU Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 203 ARG Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 425 SER Chi-restraints excluded: chain X residue 430 SER Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 412 SER Chi-restraints excluded: chain i residue 484 THR Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain i residue 492 VAL Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 134 MET Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 356 GLU Chi-restraints excluded: chain j residue 406 VAL Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain j residue 507 ILE Chi-restraints excluded: chain k residue 140 LYS Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 295 VAL Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain k residue 495 LEU Chi-restraints excluded: chain k residue 500 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 359 SER Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 465 THR Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 258 GLU Chi-restraints excluded: chain w residue 406 VAL Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 495 LEU Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 220 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** i 288 ASN j 197 ASN j 205 ASN k 431 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107669 restraints weight = 138077.979| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.20 r_work: 0.3054 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 35078 Z= 0.248 Angle : 0.719 12.062 47779 Z= 0.376 Chirality : 0.053 0.276 5359 Planarity : 0.006 0.064 6233 Dihedral : 5.880 47.627 4731 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.68 % Allowed : 20.28 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 4208 helix: 0.43 (0.22), residues: 532 sheet: 0.42 (0.16), residues: 1001 loop : -0.78 (0.11), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 8 147 TYR 0.023 0.002 TYR R 443 PHE 0.018 0.002 PHE w 221 TRP 0.047 0.002 TRP w 225 HIS 0.007 0.002 HIS w 124 Details of bonding type rmsd covalent geometry : bond 0.00584 (35077) covalent geometry : angle 0.71872 (47777) SS BOND : bond 0.00524 ( 1) SS BOND : angle 1.86731 ( 2) hydrogen bonds : bond 0.04934 ( 924) hydrogen bonds : angle 6.48706 ( 2523) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8416 Ramachandran restraints generated. 4208 Oldfield, 0 Emsley, 4208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 272 time to evaluate : 1.362 Fit side-chains REVERT: 8 103 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8093 (t) REVERT: 8 134 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8150 (tpt) REVERT: 8 165 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.6004 (t0) REVERT: 8 209 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5897 (pp20) REVERT: 8 230 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: 8 240 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: 8 427 ARG cc_start: 0.6448 (tpp80) cc_final: 0.5423 (mtt180) REVERT: K 93 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6282 (mp10) REVERT: K 258 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: K 451 GLN cc_start: 0.5206 (mt0) cc_final: 0.4914 (mt0) REVERT: R 111 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: R 127 MET cc_start: 0.8845 (ttm) cc_final: 0.8596 (ttp) REVERT: R 164 GLN cc_start: 0.5020 (mm-40) cc_final: 0.4705 (tp40) REVERT: R 407 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: R 486 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8788 (p) REVERT: T 112 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6536 (ttp-110) REVERT: T 134 MET cc_start: 0.8223 (mmm) cc_final: 0.7867 (mmm) REVERT: T 173 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: T 222 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7679 (ttt-90) REVERT: X 132 GLU cc_start: 0.8547 (tt0) cc_final: 0.8201 (tm-30) REVERT: X 280 MET cc_start: 0.8455 (mmt) cc_final: 0.8206 (mmt) REVERT: X 356 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: X 389 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6963 (mppt) REVERT: X 503 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8039 (tp) REVERT: X 530 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8090 (tm) REVERT: i 196 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: i 401 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7454 (t70) REVERT: j 282 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: j 495 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8479 (mt) REVERT: k 140 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7525 (mppt) REVERT: w 258 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7219 (mm-30) REVERT: w 427 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5994 (mtm180) REVERT: w 486 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8157 (t) REVERT: w 495 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8387 (mt) outliers start: 130 outliers final: 93 residues processed: 384 average time/residue: 0.8412 time to fit residues: 377.8914 Evaluate side-chains 389 residues out of total 3827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 269 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 62 THR Chi-restraints excluded: chain 8 residue 92 VAL Chi-restraints excluded: chain 8 residue 103 SER Chi-restraints excluded: chain 8 residue 134 MET Chi-restraints excluded: chain 8 residue 140 LYS Chi-restraints excluded: chain 8 residue 165 ASP Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 196 ASP Chi-restraints excluded: chain 8 residue 201 VAL Chi-restraints excluded: chain 8 residue 209 GLU Chi-restraints excluded: chain 8 residue 230 GLU Chi-restraints excluded: chain 8 residue 238 THR Chi-restraints excluded: chain 8 residue 240 GLU Chi-restraints excluded: chain 8 residue 351 VAL Chi-restraints excluded: chain 8 residue 360 LYS Chi-restraints excluded: chain 8 residue 388 GLU Chi-restraints excluded: chain 8 residue 453 VAL Chi-restraints excluded: chain 8 residue 473 GLU Chi-restraints excluded: chain 8 residue 486 THR Chi-restraints excluded: chain 8 residue 506 SER Chi-restraints excluded: chain 8 residue 522 THR Chi-restraints excluded: chain 8 residue 542 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 93 GLN Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 196 ASP Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 294 ASP Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 426 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 377 SER Chi-restraints excluded: chain R residue 407 GLU Chi-restraints excluded: chain R residue 426 THR Chi-restraints excluded: chain R residue 473 GLU Chi-restraints excluded: chain R residue 486 THR Chi-restraints excluded: chain R residue 489 SER Chi-restraints excluded: chain R residue 495 LEU Chi-restraints excluded: chain T residue 67 LEU Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain T residue 112 ARG Chi-restraints excluded: chain T residue 173 GLU Chi-restraints excluded: chain T residue 222 ARG Chi-restraints excluded: chain T residue 406 VAL Chi-restraints excluded: chain T residue 484 THR Chi-restraints excluded: chain T residue 486 THR Chi-restraints excluded: chain X residue 62 THR Chi-restraints excluded: chain X residue 106 THR Chi-restraints excluded: chain X residue 146 SER Chi-restraints excluded: chain X residue 149 THR Chi-restraints excluded: chain X residue 203 ARG Chi-restraints excluded: chain X residue 355 VAL Chi-restraints excluded: chain X residue 356 GLU Chi-restraints excluded: chain X residue 359 SER Chi-restraints excluded: chain X residue 389 LYS Chi-restraints excluded: chain X residue 425 SER Chi-restraints excluded: chain X residue 430 SER Chi-restraints excluded: chain X residue 503 LEU Chi-restraints excluded: chain X residue 530 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 90 THR Chi-restraints excluded: chain i residue 134 MET Chi-restraints excluded: chain i residue 196 ASP Chi-restraints excluded: chain i residue 229 THR Chi-restraints excluded: chain i residue 236 VAL Chi-restraints excluded: chain i residue 359 SER Chi-restraints excluded: chain i residue 367 LEU Chi-restraints excluded: chain i residue 401 ASP Chi-restraints excluded: chain i residue 412 SER Chi-restraints excluded: chain i residue 484 THR Chi-restraints excluded: chain i residue 489 SER Chi-restraints excluded: chain i residue 492 VAL Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 134 MET Chi-restraints excluded: chain j residue 282 GLU Chi-restraints excluded: chain j residue 356 GLU Chi-restraints excluded: chain j residue 406 VAL Chi-restraints excluded: chain j residue 419 ASP Chi-restraints excluded: chain j residue 465 THR Chi-restraints excluded: chain j residue 495 LEU Chi-restraints excluded: chain j residue 507 ILE Chi-restraints excluded: chain k residue 140 LYS Chi-restraints excluded: chain k residue 228 VAL Chi-restraints excluded: chain k residue 231 LEU Chi-restraints excluded: chain k residue 295 VAL Chi-restraints excluded: chain k residue 359 SER Chi-restraints excluded: chain k residue 419 ASP Chi-restraints excluded: chain k residue 486 THR Chi-restraints excluded: chain k residue 495 LEU Chi-restraints excluded: chain k residue 500 THR Chi-restraints excluded: chain v residue 62 THR Chi-restraints excluded: chain v residue 104 THR Chi-restraints excluded: chain v residue 184 THR Chi-restraints excluded: chain v residue 359 SER Chi-restraints excluded: chain v residue 371 ILE Chi-restraints excluded: chain v residue 425 SER Chi-restraints excluded: chain v residue 465 THR Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain w residue 59 LEU Chi-restraints excluded: chain w residue 72 SER Chi-restraints excluded: chain w residue 100 THR Chi-restraints excluded: chain w residue 149 THR Chi-restraints excluded: chain w residue 258 GLU Chi-restraints excluded: chain w residue 357 LYS Chi-restraints excluded: chain w residue 406 VAL Chi-restraints excluded: chain w residue 427 ARG Chi-restraints excluded: chain w residue 486 THR Chi-restraints excluded: chain w residue 495 LEU Chi-restraints excluded: chain w residue 540 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 84 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 389 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** j 197 ASN j 205 ASN k 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107130 restraints weight = 140846.537| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.40 r_work: 0.3054 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 35078 Z= 0.223 Angle : 0.694 12.117 47779 Z= 0.363 Chirality : 0.052 0.331 5359 Planarity : 0.006 0.066 6233 Dihedral : 5.847 47.863 4731 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.31 % Favored : 95.67 % Rotamer: Outliers : 3.78 % Allowed : 20.21 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4208 helix: 0.45 (0.22), residues: 526 sheet: 0.41 (0.16), residues: 1000 loop : -0.81 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 8 147 TYR 0.020 0.002 TYR R 443 PHE 0.019 0.002 PHE w 221 TRP 0.045 0.002 TRP w 225 HIS 0.006 0.002 HIS w 124 Details of bonding type rmsd covalent geometry : bond 0.00522 (35077) covalent geometry : angle 0.69390 (47777) SS BOND : bond 0.00551 ( 1) SS BOND : angle 1.96405 ( 2) hydrogen bonds : bond 0.04749 ( 924) hydrogen bonds : angle 6.43952 ( 2523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15068.22 seconds wall clock time: 256 minutes 40.73 seconds (15400.73 seconds total)