Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 15:57:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/07_2023/7tfd_25870.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/07_2023/7tfd_25870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/07_2023/7tfd_25870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/07_2023/7tfd_25870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/07_2023/7tfd_25870.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/07_2023/7tfd_25870.pdb" } resolution = 3.16 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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: 5 Type Number sf(0) Gaussians Mg 24 5.21 5 S 228 5.16 5 C 26386 2.51 5 N 7104 2.21 5 O 7666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 41408 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "J" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "K" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "L" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3445 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 14, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 73 Chain: "Q" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "S" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "T" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "W" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "X" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3449 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 25, 'TRANS': 415} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU B 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 248 " occ=0.97 residue: pdb=" N LEU E 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU E 248 " occ=0.97 residue: pdb=" N LEU F 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 248 " occ=0.97 residue: pdb=" N LEU J 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 248 " occ=0.97 residue: pdb=" N LEU K 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU K 248 " occ=0.97 residue: pdb=" N LEU L 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 248 " occ=0.97 residue: pdb=" N LEU Q 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU Q 248 " occ=0.97 residue: pdb=" N LEU R 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU R 248 " occ=0.97 residue: pdb=" N LEU S 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU S 248 " occ=0.97 residue: pdb=" N LEU T 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU T 248 " occ=0.97 residue: pdb=" N LEU W 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU W 248 " occ=0.97 residue: pdb=" N LEU X 248 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU X 248 " occ=0.97 Time building chain proxies: 19.50, per 1000 atoms: 0.47 Number of scatterers: 41408 At special positions: 0 Unit cell: (159.28, 150.48, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 228 16.00 Mg 24 11.99 O 7666 8.00 N 7104 7.00 C 26386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 17.07 Conformation dependent library (CDL) restraints added in 6.5 seconds 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9960 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 28 sheets defined 44.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 40 through 46 Processing helix chain 'B' and resid 53 through 61 removed outlier: 6.580A pdb=" N TYR B 59 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 105 through 119 Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.637A pdb=" N GLU B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 223 Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 279 through 288 removed outlier: 4.517A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.599A pdb=" N ARG B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.701A pdb=" N THR B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'B' and resid 374 through 381 Processing helix chain 'B' and resid 389 through 400 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 408 through 428 removed outlier: 3.505A pdb=" N TYR B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 removed outlier: 3.639A pdb=" N ARG B 435 " --> pdb=" O HIS B 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'E' and resid 53 through 61 removed outlier: 6.622A pdb=" N TYR E 59 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL E 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 105 through 119 Processing helix chain 'E' and resid 165 through 178 Processing helix chain 'E' and resid 202 through 223 Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 279 through 288 removed outlier: 4.355A pdb=" N ALA E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.556A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 328 removed outlier: 3.575A pdb=" N THR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 Processing helix chain 'E' and resid 374 through 381 Processing helix chain 'E' and resid 389 through 400 Processing helix chain 'E' and resid 402 through 408 Processing helix chain 'E' and resid 408 through 428 removed outlier: 3.537A pdb=" N TYR E 414 " --> pdb=" O HIS E 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR E 428 " --> pdb=" O ASP E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 438 removed outlier: 3.623A pdb=" N ARG E 435 " --> pdb=" O HIS E 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 53 through 61 removed outlier: 6.553A pdb=" N TYR F 59 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 61 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 Processing helix chain 'F' and resid 165 through 178 removed outlier: 3.797A pdb=" N GLU F 169 " --> pdb=" O ASN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 223 Processing helix chain 'F' and resid 266 through 279 Processing helix chain 'F' and resid 279 through 288 removed outlier: 4.357A pdb=" N ALA F 285 " --> pdb=" O ARG F 281 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 3.550A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 328 removed outlier: 3.618A pdb=" N THR F 328 " --> pdb=" O GLY F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 Processing helix chain 'F' and resid 374 through 381 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 402 through 408 Processing helix chain 'F' and resid 408 through 428 removed outlier: 3.504A pdb=" N ALA F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR F 414 " --> pdb=" O HIS F 410 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR F 428 " --> pdb=" O ASP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 438 removed outlier: 3.619A pdb=" N ARG F 435 " --> pdb=" O HIS F 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 40 through 46 Processing helix chain 'J' and resid 53 through 61 removed outlier: 6.564A pdb=" N TYR J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL J 60 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG J 61 " --> pdb=" O GLY J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 76 Processing helix chain 'J' and resid 105 through 119 Processing helix chain 'J' and resid 165 through 178 Processing helix chain 'J' and resid 201 through 223 Processing helix chain 'J' and resid 266 through 279 Processing helix chain 'J' and resid 279 through 288 removed outlier: 4.404A pdb=" N ALA J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE J 286 " --> pdb=" O ALA J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.530A pdb=" N ARG J 296 " --> pdb=" O ASN J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 328 removed outlier: 3.546A pdb=" N THR J 328 " --> pdb=" O GLY J 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 359 Processing helix chain 'J' and resid 374 through 381 Processing helix chain 'J' and resid 389 through 400 Processing helix chain 'J' and resid 402 through 408 Processing helix chain 'J' and resid 408 through 428 removed outlier: 3.507A pdb=" N TYR J 414 " --> pdb=" O HIS J 410 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 428 " --> pdb=" O ASP J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 438 removed outlier: 3.633A pdb=" N ARG J 435 " --> pdb=" O HIS J 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 53 through 61 removed outlier: 6.617A pdb=" N TYR K 59 " --> pdb=" O ILE K 56 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 60 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG K 61 " --> pdb=" O GLY K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 76 Processing helix chain 'K' and resid 105 through 119 Processing helix chain 'K' and resid 165 through 177 Processing helix chain 'K' and resid 202 through 223 Processing helix chain 'K' and resid 266 through 279 Processing helix chain 'K' and resid 279 through 288 removed outlier: 4.388A pdb=" N ALA K 285 " --> pdb=" O ARG K 281 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE K 286 " --> pdb=" O ALA K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 297 removed outlier: 3.583A pdb=" N ARG K 296 " --> pdb=" O ASN K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 328 Processing helix chain 'K' and resid 340 through 359 Processing helix chain 'K' and resid 374 through 381 Processing helix chain 'K' and resid 389 through 400 Processing helix chain 'K' and resid 402 through 408 Processing helix chain 'K' and resid 408 through 428 removed outlier: 3.535A pdb=" N TYR K 414 " --> pdb=" O HIS K 410 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR K 428 " --> pdb=" O ASP K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 438 removed outlier: 3.604A pdb=" N ARG K 435 " --> pdb=" O HIS K 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 16 Processing helix chain 'L' and resid 40 through 46 Processing helix chain 'L' and resid 53 through 61 removed outlier: 6.590A pdb=" N TYR L 59 " --> pdb=" O ILE L 56 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL L 60 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG L 61 " --> pdb=" O GLY L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 76 Processing helix chain 'L' and resid 105 through 119 Processing helix chain 'L' and resid 165 through 178 removed outlier: 3.714A pdb=" N GLU L 169 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 223 Processing helix chain 'L' and resid 266 through 279 Processing helix chain 'L' and resid 279 through 288 removed outlier: 4.371A pdb=" N ALA L 285 " --> pdb=" O ARG L 281 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE L 286 " --> pdb=" O ALA L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 297 removed outlier: 3.585A pdb=" N ARG L 296 " --> pdb=" O ASN L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 328 removed outlier: 3.771A pdb=" N THR L 328 " --> pdb=" O GLY L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 359 Processing helix chain 'L' and resid 374 through 381 Processing helix chain 'L' and resid 389 through 400 Processing helix chain 'L' and resid 402 through 408 Processing helix chain 'L' and resid 408 through 428 removed outlier: 3.531A pdb=" N TYR L 414 " --> pdb=" O HIS L 410 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR L 428 " --> pdb=" O ASP L 424 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 438 removed outlier: 3.654A pdb=" N ARG L 435 " --> pdb=" O HIS L 431 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 16 Processing helix chain 'Q' and resid 40 through 46 Processing helix chain 'Q' and resid 53 through 61 removed outlier: 6.585A pdb=" N TYR Q 59 " --> pdb=" O ILE Q 56 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL Q 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG Q 61 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 76 Processing helix chain 'Q' and resid 105 through 119 Processing helix chain 'Q' and resid 165 through 178 Processing helix chain 'Q' and resid 201 through 223 Processing helix chain 'Q' and resid 266 through 279 Processing helix chain 'Q' and resid 279 through 288 removed outlier: 4.370A pdb=" N ALA Q 285 " --> pdb=" O ARG Q 281 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 297 removed outlier: 3.572A pdb=" N ARG Q 296 " --> pdb=" O ASN Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 324 through 328 removed outlier: 3.636A pdb=" N THR Q 328 " --> pdb=" O GLY Q 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 340 through 359 Processing helix chain 'Q' and resid 374 through 381 Processing helix chain 'Q' and resid 389 through 400 Processing helix chain 'Q' and resid 402 through 408 Processing helix chain 'Q' and resid 408 through 428 removed outlier: 3.512A pdb=" N TYR Q 414 " --> pdb=" O HIS Q 410 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR Q 428 " --> pdb=" O ASP Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 431 through 438 removed outlier: 3.611A pdb=" N ARG Q 435 " --> pdb=" O HIS Q 431 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 40 through 46 Processing helix chain 'R' and resid 53 through 61 removed outlier: 6.621A pdb=" N TYR R 59 " --> pdb=" O ILE R 56 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL R 60 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG R 61 " --> pdb=" O GLY R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 76 Processing helix chain 'R' and resid 105 through 119 Processing helix chain 'R' and resid 165 through 178 Processing helix chain 'R' and resid 202 through 223 Processing helix chain 'R' and resid 266 through 279 Processing helix chain 'R' and resid 279 through 288 removed outlier: 4.390A pdb=" N ALA R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 297 removed outlier: 3.573A pdb=" N ARG R 296 " --> pdb=" O ASN R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 328 removed outlier: 3.622A pdb=" N THR R 328 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 359 Processing helix chain 'R' and resid 374 through 381 Processing helix chain 'R' and resid 389 through 400 Processing helix chain 'R' and resid 402 through 408 Processing helix chain 'R' and resid 408 through 428 removed outlier: 3.526A pdb=" N TYR R 414 " --> pdb=" O HIS R 410 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR R 428 " --> pdb=" O ASP R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 438 removed outlier: 3.624A pdb=" N ARG R 435 " --> pdb=" O HIS R 431 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 16 Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 53 through 61 removed outlier: 6.575A pdb=" N TYR S 59 " --> pdb=" O ILE S 56 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL S 60 " --> pdb=" O GLU S 57 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG S 61 " --> pdb=" O GLY S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 76 Processing helix chain 'S' and resid 105 through 119 Processing helix chain 'S' and resid 165 through 178 Processing helix chain 'S' and resid 202 through 223 Processing helix chain 'S' and resid 266 through 279 Processing helix chain 'S' and resid 279 through 288 removed outlier: 4.450A pdb=" N ALA S 285 " --> pdb=" O ARG S 281 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE S 286 " --> pdb=" O ALA S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 292 through 297 removed outlier: 3.566A pdb=" N ARG S 296 " --> pdb=" O ASN S 292 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU S 297 " --> pdb=" O SER S 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 292 through 297' Processing helix chain 'S' and resid 324 through 328 removed outlier: 3.623A pdb=" N THR S 328 " --> pdb=" O GLY S 325 " (cutoff:3.500A) Processing helix chain 'S' and resid 340 through 359 Processing helix chain 'S' and resid 374 through 381 Processing helix chain 'S' and resid 389 through 400 Processing helix chain 'S' and resid 402 through 408 Processing helix chain 'S' and resid 408 through 428 removed outlier: 3.529A pdb=" N TYR S 414 " --> pdb=" O HIS S 410 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR S 428 " --> pdb=" O ASP S 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 431 through 438 removed outlier: 3.647A pdb=" N ARG S 435 " --> pdb=" O HIS S 431 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 16 Processing helix chain 'T' and resid 40 through 46 Processing helix chain 'T' and resid 53 through 61 removed outlier: 6.557A pdb=" N TYR T 59 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL T 60 " --> pdb=" O GLU T 57 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG T 61 " --> pdb=" O GLY T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 76 Processing helix chain 'T' and resid 105 through 119 Processing helix chain 'T' and resid 165 through 178 removed outlier: 3.883A pdb=" N GLU T 169 " --> pdb=" O ASN T 165 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 223 Processing helix chain 'T' and resid 266 through 279 removed outlier: 3.502A pdb=" N HIS T 279 " --> pdb=" O GLY T 275 " (cutoff:3.500A) Processing helix chain 'T' and resid 279 through 288 removed outlier: 4.324A pdb=" N ALA T 285 " --> pdb=" O ARG T 281 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE T 286 " --> pdb=" O ALA T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 292 through 297 removed outlier: 3.594A pdb=" N ARG T 296 " --> pdb=" O ASN T 292 " (cutoff:3.500A) Processing helix chain 'T' and resid 324 through 328 removed outlier: 3.742A pdb=" N THR T 328 " --> pdb=" O GLY T 325 " (cutoff:3.500A) Processing helix chain 'T' and resid 340 through 359 Processing helix chain 'T' and resid 374 through 381 Processing helix chain 'T' and resid 389 through 400 Processing helix chain 'T' and resid 402 through 408 Processing helix chain 'T' and resid 408 through 428 removed outlier: 3.502A pdb=" N ALA T 413 " --> pdb=" O ASP T 409 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR T 414 " --> pdb=" O HIS T 410 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR T 428 " --> pdb=" O ASP T 424 " (cutoff:3.500A) Processing helix chain 'T' and resid 431 through 438 removed outlier: 3.629A pdb=" N ARG T 435 " --> pdb=" O HIS T 431 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 15 Processing helix chain 'W' and resid 40 through 46 Processing helix chain 'W' and resid 53 through 61 removed outlier: 6.554A pdb=" N TYR W 59 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL W 60 " --> pdb=" O GLU W 57 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG W 61 " --> pdb=" O GLY W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 76 Processing helix chain 'W' and resid 105 through 119 Processing helix chain 'W' and resid 165 through 178 removed outlier: 3.807A pdb=" N GLU W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 223 Processing helix chain 'W' and resid 266 through 279 Processing helix chain 'W' and resid 279 through 288 removed outlier: 4.441A pdb=" N ALA W 285 " --> pdb=" O ARG W 281 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE W 286 " --> pdb=" O ALA W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 292 through 297 removed outlier: 3.593A pdb=" N ARG W 296 " --> pdb=" O ASN W 292 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU W 297 " --> pdb=" O SER W 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 292 through 297' Processing helix chain 'W' and resid 324 through 328 Processing helix chain 'W' and resid 340 through 359 Processing helix chain 'W' and resid 374 through 381 Processing helix chain 'W' and resid 389 through 400 Processing helix chain 'W' and resid 402 through 408 Processing helix chain 'W' and resid 408 through 428 removed outlier: 3.516A pdb=" N TYR W 414 " --> pdb=" O HIS W 410 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR W 428 " --> pdb=" O ASP W 424 " (cutoff:3.500A) Processing helix chain 'W' and resid 431 through 438 removed outlier: 3.630A pdb=" N ARG W 435 " --> pdb=" O HIS W 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 16 Processing helix chain 'X' and resid 40 through 46 Processing helix chain 'X' and resid 53 through 61 removed outlier: 6.614A pdb=" N TYR X 59 " --> pdb=" O ILE X 56 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL X 60 " --> pdb=" O GLU X 57 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG X 61 " --> pdb=" O GLY X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 76 Processing helix chain 'X' and resid 105 through 119 Processing helix chain 'X' and resid 165 through 177 removed outlier: 3.842A pdb=" N GLU X 169 " --> pdb=" O ASN X 165 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 223 Processing helix chain 'X' and resid 266 through 279 Processing helix chain 'X' and resid 279 through 288 removed outlier: 4.375A pdb=" N ALA X 285 " --> pdb=" O ARG X 281 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE X 286 " --> pdb=" O ALA X 282 " (cutoff:3.500A) Processing helix chain 'X' and resid 292 through 297 removed outlier: 3.568A pdb=" N ARG X 296 " --> pdb=" O ASN X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 324 through 328 Processing helix chain 'X' and resid 340 through 359 Processing helix chain 'X' and resid 374 through 381 Processing helix chain 'X' and resid 389 through 400 Processing helix chain 'X' and resid 402 through 408 Processing helix chain 'X' and resid 408 through 428 removed outlier: 3.533A pdb=" N TYR X 414 " --> pdb=" O HIS X 410 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR X 428 " --> pdb=" O ASP X 424 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 438 removed outlier: 3.621A pdb=" N ARG X 435 " --> pdb=" O HIS X 431 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 31 through 37 current: chain 'B' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 67 through 71 current: chain 'B' and resid 86 through 95 Processing sheet with id=AA2, first strand: chain 'B' and resid 124 through 138 removed outlier: 7.509A pdb=" N LEU B 135 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 137 " --> pdb=" O THR B 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 144 through 148 current: chain 'B' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 192 through 197 current: chain 'B' and resid 318 through 319 Processing sheet with id=AA3, first strand: chain 'E' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 31 through 37 current: chain 'E' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 67 through 71 current: chain 'E' and resid 86 through 95 Processing sheet with id=AA4, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'E' and resid 132 through 138 removed outlier: 7.523A pdb=" N LEU E 135 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLU E 147 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LYS E 137 " --> pdb=" O THR E 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 148 current: chain 'E' and resid 192 through 197 Processing sheet with id=AA6, first strand: chain 'F' and resid 31 through 37 removed outlier: 4.955A pdb=" N VAL F 17 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA F 88 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE F 19 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 90 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG F 21 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N CYS F 92 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN F 23 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE F 94 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N THR F 25 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE F 91 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR F 75 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N ASP F 93 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 10.351A pdb=" N LEU F 73 " --> pdb=" O ASP F 93 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N TYR F 95 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 200 through 201 removed outlier: 4.034A pdb=" N HIS F 243 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 132 through 138 removed outlier: 7.605A pdb=" N LEU F 135 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLU F 147 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS F 137 " --> pdb=" O THR F 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 144 through 148 current: chain 'F' and resid 192 through 197 Processing sheet with id=AA9, first strand: chain 'J' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 31 through 37 current: chain 'J' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 67 through 71 current: chain 'J' and resid 86 through 95 Processing sheet with id=AB1, first strand: chain 'J' and resid 124 through 138 removed outlier: 7.537A pdb=" N LEU J 135 " --> pdb=" O GLU J 147 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU J 147 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS J 137 " --> pdb=" O THR J 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 144 through 148 current: chain 'J' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 192 through 197 current: chain 'J' and resid 318 through 319 Processing sheet with id=AB2, first strand: chain 'K' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 31 through 37 current: chain 'K' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 67 through 71 current: chain 'K' and resid 86 through 95 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 138 removed outlier: 5.189A pdb=" N GLU K 147 " --> pdb=" O LYS K 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 144 through 148 current: chain 'K' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 192 through 197 current: chain 'K' and resid 318 through 319 Processing sheet with id=AB4, first strand: chain 'L' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 31 through 37 current: chain 'L' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 67 through 71 current: chain 'L' and resid 86 through 95 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 138 removed outlier: 5.128A pdb=" N GLU L 147 " --> pdb=" O LYS L 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 144 through 148 current: chain 'L' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 192 through 197 current: chain 'L' and resid 318 through 319 Processing sheet with id=AB6, first strand: chain 'Q' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 31 through 37 current: chain 'Q' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 67 through 71 current: chain 'Q' and resid 86 through 95 Processing sheet with id=AB7, first strand: chain 'Q' and resid 124 through 138 removed outlier: 5.125A pdb=" N GLU Q 147 " --> pdb=" O LYS Q 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 144 through 148 current: chain 'Q' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 192 through 197 current: chain 'Q' and resid 318 through 319 Processing sheet with id=AB8, first strand: chain 'R' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 31 through 37 current: chain 'R' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 67 through 71 current: chain 'R' and resid 86 through 95 Processing sheet with id=AB9, first strand: chain 'R' and resid 124 through 138 removed outlier: 5.026A pdb=" N GLU R 147 " --> pdb=" O LYS R 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 144 through 148 current: chain 'R' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 192 through 197 current: chain 'R' and resid 253 through 254 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 253 through 254 current: chain 'R' and resid 318 through 319 Processing sheet with id=AC1, first strand: chain 'S' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 31 through 37 current: chain 'S' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 67 through 71 current: chain 'S' and resid 86 through 95 Processing sheet with id=AC2, first strand: chain 'S' and resid 124 through 138 removed outlier: 7.464A pdb=" N LEU S 135 " --> pdb=" O GLU S 147 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU S 147 " --> pdb=" O LEU S 135 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS S 137 " --> pdb=" O THR S 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 144 through 148 current: chain 'S' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 192 through 197 current: chain 'S' and resid 318 through 319 Processing sheet with id=AC3, first strand: chain 'T' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 31 through 37 current: chain 'T' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 67 through 71 current: chain 'T' and resid 86 through 95 Processing sheet with id=AC4, first strand: chain 'T' and resid 200 through 201 Processing sheet with id=AC5, first strand: chain 'T' and resid 132 through 138 removed outlier: 5.395A pdb=" N GLU T 147 " --> pdb=" O LYS T 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 144 through 148 current: chain 'T' and resid 192 through 197 Processing sheet with id=AC6, first strand: chain 'W' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 31 through 37 current: chain 'W' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 67 through 71 current: chain 'W' and resid 86 through 95 Processing sheet with id=AC7, first strand: chain 'W' and resid 124 through 138 removed outlier: 7.504A pdb=" N LEU W 135 " --> pdb=" O GLU W 147 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU W 147 " --> pdb=" O LEU W 135 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS W 137 " --> pdb=" O THR W 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 144 through 148 current: chain 'W' and resid 192 through 197 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 192 through 197 current: chain 'W' and resid 318 through 319 Processing sheet with id=AC8, first strand: chain 'X' and resid 17 through 25 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 31 through 37 current: chain 'X' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 67 through 71 current: chain 'X' and resid 86 through 95 Processing sheet with id=AC9, first strand: chain 'X' and resid 200 through 201 Processing sheet with id=AD1, first strand: chain 'X' and resid 132 through 138 removed outlier: 7.536A pdb=" N LEU X 135 " --> pdb=" O GLU X 147 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU X 147 " --> pdb=" O LEU X 135 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS X 137 " --> pdb=" O THR X 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 144 through 148 current: chain 'X' and resid 192 through 197 1594 hydrogen bonds defined for protein. 4548 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: 15.71 Time building geometry restraints manager: 18.40 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: 10766 1.33 - 1.45: 7714 1.45 - 1.57: 23468 1.57 - 1.69: 0 1.69 - 1.81: 408 Bond restraints: 42356 Sorted by residual: bond pdb=" N ASN S 334 " pdb=" CA ASN S 334 " ideal model delta sigma weight residual 1.461 1.494 -0.032 9.20e-03 1.18e+04 1.24e+01 bond pdb=" C ALA S 303 " pdb=" N PRO S 304 " ideal model delta sigma weight residual 1.333 1.367 -0.033 1.01e-02 9.80e+03 1.10e+01 bond pdb=" N ILE T 370 " pdb=" CA ILE T 370 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.31e+00 bond pdb=" N ASP S 336 " pdb=" CA ASP S 336 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.18e-02 7.18e+03 8.87e+00 bond pdb=" N VAL S 332 " pdb=" CA VAL S 332 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.49e+00 ... (remaining 42351 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.57: 1081 105.57 - 112.75: 22094 112.75 - 119.92: 14776 119.92 - 127.09: 19052 127.09 - 134.27: 520 Bond angle restraints: 57523 Sorted by residual: angle pdb=" C GLY S 142 " pdb=" N ASP S 143 " pdb=" CA ASP S 143 " ideal model delta sigma weight residual 121.83 127.99 -6.16 1.56e+00 4.11e-01 1.56e+01 angle pdb=" N VAL W 307 " pdb=" CA VAL W 307 " pdb=" C VAL W 307 " ideal model delta sigma weight residual 106.32 112.57 -6.25 1.61e+00 3.86e-01 1.51e+01 angle pdb=" N GLY R 178 " pdb=" CA GLY R 178 " pdb=" C GLY R 178 " ideal model delta sigma weight residual 115.27 109.98 5.29 1.41e+00 5.03e-01 1.41e+01 angle pdb=" C ASN K 334 " pdb=" CA ASN K 334 " pdb=" CB ASN K 334 " ideal model delta sigma weight residual 112.76 105.89 6.87 1.86e+00 2.89e-01 1.36e+01 angle pdb=" CA MET E 242 " pdb=" C MET E 242 " pdb=" O MET E 242 " ideal model delta sigma weight residual 121.89 117.35 4.54 1.29e+00 6.01e-01 1.24e+01 ... (remaining 57518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 23276 17.98 - 35.96: 1817 35.96 - 53.94: 384 53.94 - 71.92: 65 71.92 - 89.90: 39 Dihedral angle restraints: 25581 sinusoidal: 10101 harmonic: 15480 Sorted by residual: dihedral pdb=" CA ILE R 370 " pdb=" C ILE R 370 " pdb=" N TYR R 371 " pdb=" CA TYR R 371 " ideal model delta harmonic sigma weight residual 180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU E 22 " pdb=" C LEU E 22 " pdb=" N GLN E 23 " pdb=" CA GLN E 23 " ideal model delta harmonic sigma weight residual -180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ILE F 370 " pdb=" C ILE F 370 " pdb=" N TYR F 371 " pdb=" CA TYR F 371 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 25578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4644 0.043 - 0.086: 1235 0.086 - 0.129: 387 0.129 - 0.172: 38 0.172 - 0.215: 8 Chirality restraints: 6312 Sorted by residual: chirality pdb=" CG LEU Q 157 " pdb=" CB LEU Q 157 " pdb=" CD1 LEU Q 157 " pdb=" CD2 LEU Q 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE S 370 " pdb=" CA ILE S 370 " pdb=" CG1 ILE S 370 " pdb=" CG2 ILE S 370 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL T 372 " pdb=" N VAL T 372 " pdb=" C VAL T 372 " pdb=" CB VAL T 372 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.91e-01 ... (remaining 6309 not shown) Planarity restraints: 7523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN S 369 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ASN S 369 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN S 369 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE S 370 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 336 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ASP T 336 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP T 336 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO T 337 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET Q 242 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C MET Q 242 " -0.034 2.00e-02 2.50e+03 pdb=" O MET Q 242 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS Q 243 " 0.011 2.00e-02 2.50e+03 ... (remaining 7520 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 497 2.60 - 3.17: 36993 3.17 - 3.75: 67352 3.75 - 4.32: 91948 4.32 - 4.90: 153501 Nonbonded interactions: 350291 Sorted by model distance: nonbonded pdb=" OE2 GLU T 331 " pdb="MG MG T 502 " model vdw 2.024 2.170 nonbonded pdb=" OE2 GLU T 132 " pdb="MG MG T 501 " model vdw 2.031 2.170 nonbonded pdb=" OE2 GLU E 132 " pdb="MG MG E 501 " model vdw 2.033 2.170 nonbonded pdb=" OE2 GLU K 132 " pdb="MG MG K 501 " model vdw 2.034 2.170 nonbonded pdb=" OE2 GLU Q 132 " pdb="MG MG Q 501 " model vdw 2.034 2.170 ... (remaining 350286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'E' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'F' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'J' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'K' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = chain 'L' selection = (chain 'Q' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'R' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'S' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'T' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'W' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) selection = (chain 'X' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 442 or resid 501 through 502)) } 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=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.040 Extract box with map and model: 17.200 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 101.740 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.210 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 42356 Z= 0.283 Angle : 0.707 10.159 57523 Z= 0.403 Chirality : 0.043 0.215 6312 Planarity : 0.004 0.041 7523 Dihedral : 13.899 89.896 15621 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 5268 helix: 1.03 (0.11), residues: 2016 sheet: -0.81 (0.18), residues: 768 loop : -0.58 (0.13), residues: 2484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 940 time to evaluate : 4.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 949 average time/residue: 0.6198 time to fit residues: 918.5576 Evaluate side-chains 643 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 638 time to evaluate : 4.571 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3578 time to fit residues: 9.7595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 0.6980 chunk 400 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 269 optimal weight: 0.3980 chunk 213 optimal weight: 7.9990 chunk 413 optimal weight: 0.9980 chunk 160 optimal weight: 0.3980 chunk 251 optimal weight: 6.9990 chunk 308 optimal weight: 10.0000 chunk 479 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS E 226 HIS F 149 ASN F 193 HIS F 223 HIS F 238 ASN J 23 GLN J 223 HIS J 238 ASN K 149 ASN K 193 HIS K 223 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 ASN L 223 HIS ** L 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 238 ASN Q 149 ASN Q 223 HIS Q 226 HIS R 149 ASN R 223 HIS ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 223 HIS ** S 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 238 ASN S 429 GLN T 223 HIS ** T 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 238 ASN W 238 ASN X 223 HIS X 226 HIS ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 42356 Z= 0.184 Angle : 0.560 6.660 57523 Z= 0.288 Chirality : 0.041 0.161 6312 Planarity : 0.004 0.055 7523 Dihedral : 4.459 18.518 5844 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 5268 helix: 0.99 (0.11), residues: 2124 sheet: -0.82 (0.18), residues: 864 loop : -0.59 (0.14), residues: 2280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 743 time to evaluate : 4.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 32 residues processed: 755 average time/residue: 0.6109 time to fit residues: 734.0726 Evaluate side-chains 671 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 639 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4140 time to fit residues: 30.1171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 399 optimal weight: 0.7980 chunk 326 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 480 optimal weight: 5.9990 chunk 518 optimal weight: 0.9980 chunk 427 optimal weight: 2.9990 chunk 476 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 385 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN K 193 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 HIS Q 149 ASN ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 226 HIS ** T 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 245 ASN ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 42356 Z= 0.280 Angle : 0.621 8.211 57523 Z= 0.317 Chirality : 0.044 0.161 6312 Planarity : 0.005 0.044 7523 Dihedral : 4.866 20.749 5844 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 5268 helix: 0.82 (0.11), residues: 2124 sheet: -0.99 (0.18), residues: 852 loop : -0.76 (0.13), residues: 2292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 656 time to evaluate : 5.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 38 residues processed: 679 average time/residue: 0.5895 time to fit residues: 633.6971 Evaluate side-chains 632 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 594 time to evaluate : 4.470 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.3783 time to fit residues: 32.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 0.8980 chunk 361 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 chunk 482 optimal weight: 4.9990 chunk 510 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 456 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS K 149 ASN K 193 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 313 ASN Q 313 ASN Q 429 GLN R 23 GLN ** R 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 226 HIS R 313 ASN ** S 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 ASN ** T 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 313 ASN ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 42356 Z= 0.400 Angle : 0.716 9.688 57523 Z= 0.364 Chirality : 0.047 0.210 6312 Planarity : 0.005 0.059 7523 Dihedral : 5.451 25.708 5844 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5268 helix: 0.39 (0.11), residues: 2124 sheet: -1.10 (0.18), residues: 792 loop : -1.16 (0.13), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 628 time to evaluate : 5.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 48 residues processed: 671 average time/residue: 0.6249 time to fit residues: 672.4754 Evaluate side-chains 623 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 575 time to evaluate : 4.732 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4145 time to fit residues: 44.2657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 380 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 435 optimal weight: 0.6980 chunk 352 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 458 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 193 HIS ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 GLN K 193 HIS K 223 HIS ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN R 238 ASN S 126 ASN S 149 ASN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 226 HIS X 149 ASN ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 42356 Z= 0.172 Angle : 0.542 7.221 57523 Z= 0.279 Chirality : 0.041 0.214 6312 Planarity : 0.004 0.040 7523 Dihedral : 4.569 30.985 5844 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 5268 helix: 0.72 (0.11), residues: 2136 sheet: -0.87 (0.19), residues: 792 loop : -0.93 (0.13), residues: 2340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 657 time to evaluate : 4.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 15 residues processed: 675 average time/residue: 0.5582 time to fit residues: 605.7154 Evaluate side-chains 604 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 589 time to evaluate : 5.342 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4119 time to fit residues: 18.6297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.9980 chunk 459 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 299 optimal weight: 0.0060 chunk 125 optimal weight: 5.9990 chunk 510 optimal weight: 9.9990 chunk 424 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN R 243 HIS S 149 ASN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 149 ASN ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 42356 Z= 0.232 Angle : 0.584 8.359 57523 Z= 0.298 Chirality : 0.042 0.208 6312 Planarity : 0.004 0.040 7523 Dihedral : 4.684 28.132 5844 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 5268 helix: 0.71 (0.11), residues: 2136 sheet: -0.87 (0.19), residues: 792 loop : -0.99 (0.13), residues: 2340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 588 time to evaluate : 4.860 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 43 residues processed: 625 average time/residue: 0.5736 time to fit residues: 575.5410 Evaluate side-chains 592 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 549 time to evaluate : 4.941 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3593 time to fit residues: 36.2581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 291 optimal weight: 0.9990 chunk 373 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 430 optimal weight: 4.9990 chunk 285 optimal weight: 3.9990 chunk 508 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 310 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 210 GLN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 149 ASN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 126 ASN W 193 HIS ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 42356 Z= 0.191 Angle : 0.553 7.884 57523 Z= 0.283 Chirality : 0.041 0.209 6312 Planarity : 0.004 0.037 7523 Dihedral : 4.521 29.576 5844 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 5268 helix: 0.78 (0.11), residues: 2136 sheet: -0.79 (0.19), residues: 792 loop : -0.92 (0.13), residues: 2340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 605 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 628 average time/residue: 0.5987 time to fit residues: 604.6710 Evaluate side-chains 589 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 570 time to evaluate : 4.602 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3951 time to fit residues: 20.5951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 303 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 chunk 346 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 400 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 ASN K 210 GLN K 313 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 313 ASN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 313 ASN ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 42356 Z= 0.289 Angle : 0.637 11.696 57523 Z= 0.323 Chirality : 0.044 0.206 6312 Planarity : 0.004 0.041 7523 Dihedral : 4.947 27.346 5844 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.12), residues: 5268 helix: 0.61 (0.11), residues: 2136 sheet: -0.86 (0.20), residues: 792 loop : -1.13 (0.13), residues: 2340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 572 time to evaluate : 5.156 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 35 residues processed: 592 average time/residue: 0.5965 time to fit residues: 564.6755 Evaluate side-chains 577 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 542 time to evaluate : 4.692 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3678 time to fit residues: 30.8820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 6.9990 chunk 487 optimal weight: 4.9990 chunk 444 optimal weight: 0.6980 chunk 474 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 372 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 428 optimal weight: 5.9990 chunk 448 optimal weight: 6.9990 chunk 472 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 223 HIS ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 223 HIS ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 42356 Z= 0.192 Angle : 0.572 10.709 57523 Z= 0.293 Chirality : 0.042 0.211 6312 Planarity : 0.004 0.040 7523 Dihedral : 4.634 30.555 5844 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 5268 helix: 0.72 (0.11), residues: 2136 sheet: -0.80 (0.20), residues: 792 loop : -1.00 (0.13), residues: 2340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 573 time to evaluate : 5.191 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 586 average time/residue: 0.5948 time to fit residues: 559.0939 Evaluate side-chains 558 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 543 time to evaluate : 4.779 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3863 time to fit residues: 17.7648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 3.9990 chunk 501 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 348 optimal weight: 0.0980 chunk 526 optimal weight: 2.9990 chunk 484 optimal weight: 10.0000 chunk 418 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 256 optimal weight: 0.0020 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 ASN S 149 ASN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 42356 Z= 0.219 Angle : 0.591 9.955 57523 Z= 0.302 Chirality : 0.042 0.209 6312 Planarity : 0.004 0.042 7523 Dihedral : 4.682 29.140 5844 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 5268 helix: 0.69 (0.11), residues: 2136 sheet: -0.73 (0.20), residues: 792 loop : -1.04 (0.13), residues: 2340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 555 time to evaluate : 4.679 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 563 average time/residue: 0.5943 time to fit residues: 535.4056 Evaluate side-chains 544 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 533 time to evaluate : 4.786 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3672 time to fit residues: 13.8931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 6.9990 chunk 446 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 386 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 419 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 430 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 77 optimal weight: 0.8980 overall best weight: 1.1078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 334 ASN ** W 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.233696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.216744 restraints weight = 50666.629| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 1.80 r_work: 0.4371 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4254 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4247 r_free = 0.4247 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4246 r_free = 0.4246 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 42356 Z= 0.195 Angle : 0.571 9.909 57523 Z= 0.292 Chirality : 0.041 0.210 6312 Planarity : 0.004 0.040 7523 Dihedral : 4.581 30.165 5844 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 5268 helix: 0.74 (0.11), residues: 2136 sheet: -0.70 (0.20), residues: 792 loop : -0.99 (0.13), residues: 2340 =============================================================================== Job complete usr+sys time: 10987.50 seconds wall clock time: 197 minutes 46.57 seconds (11866.57 seconds total)