Starting phenix.real_space_refine on Sat Feb 24 04:40:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/02_2024/7tfd_25870.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/02_2024/7tfd_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_25870/02_2024/7tfd_25870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/02_2024/7tfd_25870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/02_2024/7tfd_25870.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfd_25870/02_2024/7tfd_25870.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 19.97, per 1000 atoms: 0.48 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: 17.83 Conformation dependent library (CDL) restraints added in 7.4 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: 4.14 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: 14.97 Time building geometry restraints manager: 18.77 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 17.690 Check model and map are aligned: 0.560 Set scattering table: 0.390 Process input model: 105.790 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.170 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.400 ------------------------------------------------------------------------------- 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 % Allowed : 0.30 % Favored : 99.14 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 81 HIS 0.005 0.001 HIS W 226 PHE 0.026 0.002 PHE X 134 TYR 0.022 0.002 TYR R 371 ARG 0.007 0.001 ARG R 329 *********************** 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 : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6620 (mp0) REVERT: B 156 ASP cc_start: 0.6106 (m-30) cc_final: 0.5888 (m-30) REVERT: B 204 LYS cc_start: 0.5125 (ttpt) cc_final: 0.4547 (mptt) REVERT: B 242 MET cc_start: 0.7798 (ttm) cc_final: 0.7176 (ttp) REVERT: B 257 TYR cc_start: 0.7560 (t80) cc_final: 0.6900 (t80) REVERT: B 319 ARG cc_start: 0.6523 (ttp80) cc_final: 0.6287 (ttt180) REVERT: E 15 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6596 (mp0) REVERT: E 230 MET cc_start: 0.6812 (ttt) cc_final: 0.6604 (ttt) REVERT: E 242 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6581 (tpp) REVERT: E 319 ARG cc_start: 0.6665 (ttt-90) cc_final: 0.6232 (ttt180) REVERT: E 358 ARG cc_start: 0.6754 (mtp180) cc_final: 0.6498 (mtm180) REVERT: F 15 GLU cc_start: 0.7335 (tp30) cc_final: 0.6752 (tp30) REVERT: F 61 ARG cc_start: 0.3728 (ptm-80) cc_final: 0.3433 (ptm-80) REVERT: F 310 SER cc_start: 0.7167 (t) cc_final: 0.6925 (p) REVERT: F 417 GLU cc_start: 0.6250 (tt0) cc_final: 0.5590 (mm-30) REVERT: F 442 TYR cc_start: 0.5971 (m-80) cc_final: 0.5736 (m-80) REVERT: J 61 ARG cc_start: 0.3793 (ptm-80) cc_final: 0.3544 (ptm-80) REVERT: J 86 ARG cc_start: 0.5667 (ttm110) cc_final: 0.4829 (ttm170) REVERT: J 221 ARG cc_start: 0.5655 (mpt90) cc_final: 0.5423 (mpt90) REVERT: J 257 TYR cc_start: 0.7595 (t80) cc_final: 0.7060 (t80) REVERT: J 319 ARG cc_start: 0.6558 (ttp80) cc_final: 0.6327 (ttt180) REVERT: J 358 ARG cc_start: 0.6709 (mtp180) cc_final: 0.6493 (mtm180) REVERT: J 398 ILE cc_start: 0.6907 (mm) cc_final: 0.6016 (pt) REVERT: J 417 GLU cc_start: 0.6329 (tt0) cc_final: 0.5782 (mm-30) REVERT: K 204 LYS cc_start: 0.4996 (ttpt) cc_final: 0.4432 (mptt) REVERT: L 15 GLU cc_start: 0.7514 (tp30) cc_final: 0.7112 (mm-30) REVERT: L 86 ARG cc_start: 0.6189 (tpp80) cc_final: 0.4848 (ttt90) REVERT: L 169 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7185 (tm-30) REVERT: L 417 GLU cc_start: 0.6282 (tt0) cc_final: 0.5640 (mp0) REVERT: L 439 LEU cc_start: 0.6518 (tp) cc_final: 0.6311 (tp) REVERT: Q 15 GLU cc_start: 0.7449 (tp30) cc_final: 0.7077 (mm-30) REVERT: Q 86 ARG cc_start: 0.6023 (tpp80) cc_final: 0.4779 (ttt90) REVERT: Q 177 MET cc_start: 0.5126 (ttm) cc_final: 0.4536 (ttm) REVERT: Q 204 LYS cc_start: 0.5170 (ttpt) cc_final: 0.4559 (mptt) REVERT: Q 310 SER cc_start: 0.7209 (t) cc_final: 0.7000 (p) REVERT: R 61 ARG cc_start: 0.3752 (ptm-80) cc_final: 0.3500 (ptm-80) REVERT: R 86 ARG cc_start: 0.6043 (tpp80) cc_final: 0.4538 (ttt90) REVERT: R 417 GLU cc_start: 0.6305 (tt0) cc_final: 0.5652 (mp0) REVERT: S 15 GLU cc_start: 0.7479 (tp30) cc_final: 0.7219 (mm-30) REVERT: S 61 ARG cc_start: 0.3748 (ptm-80) cc_final: 0.3441 (ptm-80) REVERT: S 204 LYS cc_start: 0.5329 (ttpt) cc_final: 0.4657 (mptt) REVERT: S 257 TYR cc_start: 0.7538 (t80) cc_final: 0.6904 (t80) REVERT: S 283 MET cc_start: 0.4866 (ptp) cc_final: 0.4579 (ptp) REVERT: S 324 ARG cc_start: 0.5469 (mmt-90) cc_final: 0.4597 (mmm160) REVERT: S 398 ILE cc_start: 0.6875 (mm) cc_final: 0.6016 (pt) REVERT: S 417 GLU cc_start: 0.6357 (tt0) cc_final: 0.5734 (mm-30) REVERT: T 15 GLU cc_start: 0.7401 (tp30) cc_final: 0.7118 (tp30) REVERT: T 177 MET cc_start: 0.4929 (ttm) cc_final: 0.4712 (ttm) REVERT: T 242 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6632 (tpp) REVERT: T 350 ARG cc_start: 0.6257 (tpt-90) cc_final: 0.4983 (tpp-160) REVERT: T 417 GLU cc_start: 0.6253 (tt0) cc_final: 0.5587 (mp0) REVERT: W 257 TYR cc_start: 0.7532 (t80) cc_final: 0.6970 (t80) REVERT: W 319 ARG cc_start: 0.6446 (ttp80) cc_final: 0.5893 (ttt180) REVERT: W 414 TYR cc_start: 0.5975 (m-80) cc_final: 0.5768 (m-80) REVERT: W 417 GLU cc_start: 0.6278 (tt0) cc_final: 0.5980 (mt-10) REVERT: X 15 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6795 (mm-30) REVERT: X 182 GLU cc_start: 0.7304 (tp30) cc_final: 0.7011 (tp30) REVERT: X 204 LYS cc_start: 0.4703 (ttpt) cc_final: 0.4284 (mptt) REVERT: X 242 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6584 (tpp) REVERT: X 319 ARG cc_start: 0.6631 (ttp80) cc_final: 0.6009 (ttt180) REVERT: X 399 ARG cc_start: 0.6413 (mmt90) cc_final: 0.6068 (mtt180) outliers start: 24 outliers final: 5 residues processed: 949 average time/residue: 0.6142 time to fit residues: 910.1196 Evaluate side-chains 669 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 661 time to evaluate : 4.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain J residue 334 ASN Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain S residue 336 ASP Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain X residue 242 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 1.9990 chunk 400 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 213 optimal weight: 7.9990 chunk 413 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 251 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 479 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** 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 S 238 ASN S 429 GLN ** T 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 238 ASN W 238 ASN X 226 HIS ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.1578 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= 0.179 Angle : 0.551 6.619 57523 Z= 0.284 Chirality : 0.041 0.157 6312 Planarity : 0.004 0.044 7523 Dihedral : 4.763 51.985 5863 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.33 % Allowed : 7.24 % Favored : 91.43 % 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: -0.02 (0.12), residues: 5268 helix: 1.02 (0.11), residues: 2124 sheet: -0.80 (0.18), residues: 864 loop : -0.59 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 81 HIS 0.004 0.001 HIS R 185 PHE 0.021 0.002 PHE R 212 TYR 0.019 0.001 TYR R 371 ARG 0.005 0.000 ARG F 86 *********************** 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 820 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 763 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6230 (tp30) REVERT: B 204 LYS cc_start: 0.5110 (ttpt) cc_final: 0.4578 (mptt) REVERT: B 242 MET cc_start: 0.7786 (ttm) cc_final: 0.7399 (ttp) REVERT: B 257 TYR cc_start: 0.7543 (t80) cc_final: 0.7017 (t80) REVERT: B 324 ARG cc_start: 0.6234 (mmp80) cc_final: 0.5907 (mmt180) REVERT: B 417 GLU cc_start: 0.6228 (tt0) cc_final: 0.5718 (mp0) REVERT: E 86 ARG cc_start: 0.5606 (mtp-110) cc_final: 0.5272 (mtp-110) REVERT: E 242 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6319 (tpp) REVERT: E 319 ARG cc_start: 0.6518 (ttt-90) cc_final: 0.5943 (ttt180) REVERT: E 358 ARG cc_start: 0.6813 (mtp180) cc_final: 0.6563 (mtm180) REVERT: F 15 GLU cc_start: 0.7270 (tp30) cc_final: 0.6793 (tp30) REVERT: F 139 ASP cc_start: 0.6239 (p0) cc_final: 0.5029 (p0) REVERT: F 417 GLU cc_start: 0.6416 (tt0) cc_final: 0.5811 (mp0) REVERT: J 15 GLU cc_start: 0.7648 (tp30) cc_final: 0.7127 (tp30) REVERT: J 86 ARG cc_start: 0.5593 (ttm110) cc_final: 0.5005 (ttm170) REVERT: J 125 MET cc_start: 0.6441 (ttp) cc_final: 0.6173 (ttp) REVERT: J 169 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6722 (tp30) REVERT: J 242 MET cc_start: 0.6967 (tmm) cc_final: 0.6260 (tmm) REVERT: J 257 TYR cc_start: 0.7550 (t80) cc_final: 0.7067 (t80) REVERT: J 324 ARG cc_start: 0.6337 (mmt180) cc_final: 0.5726 (mmt180) REVERT: J 358 ARG cc_start: 0.6839 (mtp180) cc_final: 0.6628 (mtm180) REVERT: J 417 GLU cc_start: 0.6360 (tt0) cc_final: 0.5834 (mp0) REVERT: K 15 GLU cc_start: 0.7318 (tp30) cc_final: 0.6710 (tp30) REVERT: K 64 GLU cc_start: 0.6243 (mp0) cc_final: 0.5955 (tt0) REVERT: K 169 GLU cc_start: 0.7111 (tp30) cc_final: 0.5357 (mp0) REVERT: K 204 LYS cc_start: 0.5148 (ttpt) cc_final: 0.4646 (mptt) REVERT: L 86 ARG cc_start: 0.6119 (tpp80) cc_final: 0.4817 (ttt180) REVERT: L 139 ASP cc_start: 0.6198 (p0) cc_final: 0.4961 (p0) REVERT: L 319 ARG cc_start: 0.6515 (ttt-90) cc_final: 0.6234 (ttt180) REVERT: L 417 GLU cc_start: 0.6318 (tt0) cc_final: 0.5914 (mt-10) REVERT: Q 86 ARG cc_start: 0.5935 (tpp80) cc_final: 0.4891 (ttt90) REVERT: Q 112 ARG cc_start: 0.5843 (ptm-80) cc_final: 0.5640 (ptm-80) REVERT: Q 177 MET cc_start: 0.5347 (ttm) cc_final: 0.4896 (ttm) REVERT: Q 204 LYS cc_start: 0.5258 (ttpt) cc_final: 0.4607 (mptt) REVERT: R 15 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6605 (mm-30) REVERT: R 86 ARG cc_start: 0.5629 (tpp80) cc_final: 0.5159 (mmm160) REVERT: R 204 LYS cc_start: 0.5543 (ttpt) cc_final: 0.4784 (mptt) REVERT: R 366 ILE cc_start: 0.5325 (OUTLIER) cc_final: 0.4534 (mm) REVERT: R 417 GLU cc_start: 0.6309 (tt0) cc_final: 0.5955 (mt-10) REVERT: S 125 MET cc_start: 0.6384 (ttp) cc_final: 0.6095 (ttp) REVERT: S 169 GLU cc_start: 0.7033 (tp30) cc_final: 0.5420 (mp0) REVERT: S 198 LYS cc_start: 0.6735 (mtpp) cc_final: 0.6365 (mmmt) REVERT: S 204 LYS cc_start: 0.5279 (ttpt) cc_final: 0.4662 (mptt) REVERT: S 257 TYR cc_start: 0.7566 (t80) cc_final: 0.6959 (t80) REVERT: S 283 MET cc_start: 0.5649 (ptp) cc_final: 0.5391 (ptp) REVERT: S 370 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4840 (tp) REVERT: S 417 GLU cc_start: 0.6304 (tt0) cc_final: 0.5986 (mt-10) REVERT: T 169 GLU cc_start: 0.7183 (tm-30) cc_final: 0.5681 (mt-10) REVERT: T 242 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6374 (tpp) REVERT: T 417 GLU cc_start: 0.6341 (tt0) cc_final: 0.5657 (mp0) REVERT: W 86 ARG cc_start: 0.5524 (tpp80) cc_final: 0.4752 (ttt90) REVERT: W 139 ASP cc_start: 0.6536 (p0) cc_final: 0.5214 (p0) REVERT: W 198 LYS cc_start: 0.6581 (mtpp) cc_final: 0.6255 (mmmt) REVERT: W 257 TYR cc_start: 0.7536 (t80) cc_final: 0.7003 (t80) REVERT: W 317 MET cc_start: 0.6167 (tpt) cc_final: 0.5767 (tpt) REVERT: W 319 ARG cc_start: 0.6380 (ttp80) cc_final: 0.5838 (ttt180) REVERT: W 417 GLU cc_start: 0.6295 (tt0) cc_final: 0.5800 (mp0) REVERT: X 86 ARG cc_start: 0.5747 (mtp-110) cc_final: 0.5494 (mtm110) REVERT: X 204 LYS cc_start: 0.4420 (ttpt) cc_final: 0.3946 (mptt) REVERT: X 242 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6376 (tpp) REVERT: X 257 TYR cc_start: 0.7262 (t80) cc_final: 0.7021 (t80) REVERT: X 319 ARG cc_start: 0.6488 (ttp80) cc_final: 0.5958 (ttt180) REVERT: X 399 ARG cc_start: 0.6196 (mmt90) cc_final: 0.5902 (mtt180) outliers start: 57 outliers final: 33 residues processed: 777 average time/residue: 0.5820 time to fit residues: 711.5218 Evaluate side-chains 704 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 666 time to evaluate : 4.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 334 ASN Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain K residue 175 GLU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 370 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 242 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 399 optimal weight: 4.9990 chunk 326 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 480 optimal weight: 2.9990 chunk 518 optimal weight: 0.9980 chunk 427 optimal weight: 3.9990 chunk 476 optimal weight: 6.9990 chunk 163 optimal weight: 0.0770 chunk 385 optimal weight: 0.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 HIS ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN J 23 GLN K 149 ASN K 193 HIS L 226 HIS Q 23 GLN Q 149 ASN ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN R 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.2032 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= 0.173 Angle : 0.527 6.258 57523 Z= 0.269 Chirality : 0.040 0.141 6312 Planarity : 0.004 0.034 7523 Dihedral : 4.514 48.253 5857 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.75 % Allowed : 10.41 % Favored : 87.84 % 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: 0.03 (0.12), residues: 5268 helix: 1.06 (0.11), residues: 2136 sheet: -0.66 (0.18), residues: 828 loop : -0.63 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 76 HIS 0.006 0.001 HIS K 185 PHE 0.030 0.002 PHE X 212 TYR 0.014 0.001 TYR R 371 ARG 0.006 0.000 ARG J 329 *********************** 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 777 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 702 time to evaluate : 4.797 Fit side-chains revert: symmetry clash REVERT: B 204 LYS cc_start: 0.5056 (ttpt) cc_final: 0.4534 (mptt) REVERT: B 257 TYR cc_start: 0.7566 (t80) cc_final: 0.7052 (t80) REVERT: B 324 ARG cc_start: 0.6063 (mmp80) cc_final: 0.5740 (mmt180) REVERT: E 219 ILE cc_start: 0.6058 (tp) cc_final: 0.5836 (pt) REVERT: E 242 MET cc_start: 0.7272 (tmm) cc_final: 0.6547 (tpp) REVERT: E 319 ARG cc_start: 0.6597 (ttt-90) cc_final: 0.6141 (ttt180) REVERT: E 358 ARG cc_start: 0.6814 (mtp180) cc_final: 0.6550 (mtm180) REVERT: F 15 GLU cc_start: 0.7220 (tp30) cc_final: 0.6673 (tp30) REVERT: F 417 GLU cc_start: 0.6406 (tt0) cc_final: 0.5805 (mp0) REVERT: J 15 GLU cc_start: 0.7621 (tp30) cc_final: 0.6933 (tp30) REVERT: J 86 ARG cc_start: 0.5736 (ttm110) cc_final: 0.5217 (ttm170) REVERT: J 125 MET cc_start: 0.6296 (ttp) cc_final: 0.6053 (ttp) REVERT: J 198 LYS cc_start: 0.6690 (mtpp) cc_final: 0.6256 (mmmt) REVERT: J 204 LYS cc_start: 0.5325 (ttpt) cc_final: 0.4693 (mptt) REVERT: J 257 TYR cc_start: 0.7540 (t80) cc_final: 0.7029 (t80) REVERT: J 306 TYR cc_start: 0.6562 (m-80) cc_final: 0.6335 (m-80) REVERT: J 324 ARG cc_start: 0.6216 (mmt180) cc_final: 0.5606 (mmt180) REVERT: J 414 TYR cc_start: 0.6045 (m-80) cc_final: 0.5822 (m-10) REVERT: J 417 GLU cc_start: 0.6416 (tt0) cc_final: 0.6054 (mt-10) REVERT: K 366 ILE cc_start: 0.5587 (OUTLIER) cc_final: 0.4729 (mm) REVERT: L 49 MET cc_start: 0.2076 (mmm) cc_final: 0.1870 (mmm) REVERT: L 86 ARG cc_start: 0.6187 (tpp80) cc_final: 0.4919 (ttt180) REVERT: L 319 ARG cc_start: 0.6368 (ttt-90) cc_final: 0.5966 (ttt180) REVERT: L 417 GLU cc_start: 0.6292 (tt0) cc_final: 0.5926 (mt-10) REVERT: Q 86 ARG cc_start: 0.5963 (tpp80) cc_final: 0.4891 (ttt180) REVERT: Q 177 MET cc_start: 0.5440 (ttm) cc_final: 0.4970 (ttm) REVERT: Q 204 LYS cc_start: 0.5184 (ttpt) cc_final: 0.4570 (mptt) REVERT: R 15 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6633 (mm-30) REVERT: R 61 ARG cc_start: 0.3532 (ptm-80) cc_final: 0.3253 (ptm160) REVERT: R 86 ARG cc_start: 0.5817 (tpp80) cc_final: 0.5352 (mmm160) REVERT: R 139 ASP cc_start: 0.6385 (p0) cc_final: 0.5129 (p0) REVERT: R 156 ASP cc_start: 0.6322 (m-30) cc_final: 0.5987 (m-30) REVERT: R 204 LYS cc_start: 0.5422 (ttpt) cc_final: 0.4722 (mptt) REVERT: R 366 ILE cc_start: 0.5354 (OUTLIER) cc_final: 0.4568 (mm) REVERT: R 417 GLU cc_start: 0.6307 (tt0) cc_final: 0.5990 (mt-10) REVERT: S 86 ARG cc_start: 0.6041 (tpp80) cc_final: 0.4612 (ttm170) REVERT: S 125 MET cc_start: 0.6172 (ttp) cc_final: 0.5909 (ttp) REVERT: S 198 LYS cc_start: 0.6866 (mtpp) cc_final: 0.6478 (mmmt) REVERT: S 234 LEU cc_start: 0.8261 (mm) cc_final: 0.8055 (mt) REVERT: S 257 TYR cc_start: 0.7576 (t80) cc_final: 0.7024 (t80) REVERT: S 302 GLU cc_start: 0.4891 (tp30) cc_final: 0.4683 (tp30) REVERT: S 324 ARG cc_start: 0.5796 (mmt180) cc_final: 0.5122 (mmp-170) REVERT: S 417 GLU cc_start: 0.6453 (tt0) cc_final: 0.6033 (mt-10) REVERT: T 15 GLU cc_start: 0.7382 (tp30) cc_final: 0.7145 (tp30) REVERT: T 61 ARG cc_start: 0.3184 (ptm-80) cc_final: 0.2825 (ptm-80) REVERT: T 135 LEU cc_start: 0.7654 (mt) cc_final: 0.7156 (mt) REVERT: T 156 ASP cc_start: 0.6314 (m-30) cc_final: 0.6031 (m-30) REVERT: T 169 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6882 (tm-30) REVERT: T 242 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6616 (tpp) REVERT: W 86 ARG cc_start: 0.5476 (tpp80) cc_final: 0.4703 (ttt90) REVERT: W 198 LYS cc_start: 0.6586 (mtpp) cc_final: 0.6237 (mmmt) REVERT: W 257 TYR cc_start: 0.7527 (t80) cc_final: 0.7023 (t80) REVERT: W 317 MET cc_start: 0.6251 (tpt) cc_final: 0.5811 (tpt) REVERT: W 319 ARG cc_start: 0.6397 (ttp80) cc_final: 0.5825 (ttt180) REVERT: W 324 ARG cc_start: 0.6325 (mmt180) cc_final: 0.5404 (mmp-170) REVERT: W 417 GLU cc_start: 0.6353 (tt0) cc_final: 0.5672 (mp0) REVERT: X 15 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7436 (mp0) REVERT: X 242 MET cc_start: 0.7282 (tmm) cc_final: 0.6575 (tpp) REVERT: X 399 ARG cc_start: 0.6228 (mmt90) cc_final: 0.5949 (mtt180) outliers start: 75 outliers final: 57 residues processed: 720 average time/residue: 0.5982 time to fit residues: 679.6148 Evaluate side-chains 700 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 640 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 155 PHE Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 87 VAL Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 155 PHE Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 155 PHE Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 155 PHE Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 322 optimal weight: 0.9990 chunk 482 optimal weight: 5.9990 chunk 510 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 456 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 226 HIS ** J 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 245 ASN Q 149 ASN ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN R 149 ASN R 238 ASN S 238 ASN T 226 HIS W 223 HIS ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42356 Z= 0.198 Angle : 0.541 6.615 57523 Z= 0.276 Chirality : 0.041 0.148 6312 Planarity : 0.004 0.032 7523 Dihedral : 4.430 46.060 5847 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.10 % Allowed : 12.49 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.12), residues: 5268 helix: 1.07 (0.11), residues: 2136 sheet: -0.69 (0.18), residues: 828 loop : -0.69 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 76 HIS 0.004 0.001 HIS R 243 PHE 0.015 0.002 PHE L 179 TYR 0.022 0.001 TYR L 257 ARG 0.006 0.000 ARG E 86 *********************** 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 760 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 670 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 LYS cc_start: 0.5043 (ttpt) cc_final: 0.4515 (mptt) REVERT: B 257 TYR cc_start: 0.7568 (t80) cc_final: 0.6970 (t80) REVERT: B 324 ARG cc_start: 0.5972 (mmp80) cc_final: 0.5651 (mmt180) REVERT: B 417 GLU cc_start: 0.6400 (tt0) cc_final: 0.5758 (mp0) REVERT: E 177 MET cc_start: 0.4862 (tpp) cc_final: 0.4611 (ttm) REVERT: E 219 ILE cc_start: 0.6134 (tp) cc_final: 0.5907 (pt) REVERT: E 242 MET cc_start: 0.7374 (tmm) cc_final: 0.6674 (tpp) REVERT: E 319 ARG cc_start: 0.6476 (ttt-90) cc_final: 0.6158 (ttt180) REVERT: F 15 GLU cc_start: 0.7280 (tp30) cc_final: 0.6680 (tp30) REVERT: F 417 GLU cc_start: 0.6424 (tt0) cc_final: 0.5805 (mp0) REVERT: J 15 GLU cc_start: 0.7568 (tp30) cc_final: 0.6816 (tp30) REVERT: J 86 ARG cc_start: 0.5817 (ttm110) cc_final: 0.5277 (ttm170) REVERT: J 125 MET cc_start: 0.6222 (ttp) cc_final: 0.6012 (ttp) REVERT: J 204 LYS cc_start: 0.5372 (ttpt) cc_final: 0.4724 (mptt) REVERT: J 234 LEU cc_start: 0.8335 (mm) cc_final: 0.8091 (mt) REVERT: J 242 MET cc_start: 0.7134 (tmm) cc_final: 0.6449 (tmm) REVERT: J 257 TYR cc_start: 0.7538 (t80) cc_final: 0.7042 (t80) REVERT: J 306 TYR cc_start: 0.6906 (m-80) cc_final: 0.6700 (m-80) REVERT: J 360 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6482 (mtt) REVERT: J 417 GLU cc_start: 0.6450 (tt0) cc_final: 0.5803 (mp0) REVERT: K 219 ILE cc_start: 0.6151 (tp) cc_final: 0.5871 (pt) REVERT: K 366 ILE cc_start: 0.5625 (OUTLIER) cc_final: 0.4758 (mm) REVERT: L 64 GLU cc_start: 0.7174 (mp0) cc_final: 0.6967 (mp0) REVERT: L 86 ARG cc_start: 0.6274 (tpp80) cc_final: 0.5020 (ttt180) REVERT: L 134 PHE cc_start: 0.7640 (m-80) cc_final: 0.7380 (m-80) REVERT: L 204 LYS cc_start: 0.5411 (ttpt) cc_final: 0.4723 (mptt) REVERT: L 319 ARG cc_start: 0.6367 (ttt-90) cc_final: 0.6009 (ttt180) REVERT: L 417 GLU cc_start: 0.6314 (tt0) cc_final: 0.5675 (mp0) REVERT: Q 86 ARG cc_start: 0.6147 (tpp80) cc_final: 0.4993 (ttt90) REVERT: Q 177 MET cc_start: 0.5528 (ttm) cc_final: 0.5036 (ttm) REVERT: Q 204 LYS cc_start: 0.5207 (ttpt) cc_final: 0.4579 (mptt) REVERT: R 15 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6613 (mm-30) REVERT: R 61 ARG cc_start: 0.3590 (ptm-80) cc_final: 0.3248 (ptm160) REVERT: R 86 ARG cc_start: 0.5804 (tpp80) cc_final: 0.5327 (mmm160) REVERT: R 156 ASP cc_start: 0.6387 (m-30) cc_final: 0.6026 (m-30) REVERT: R 157 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5964 (tt) REVERT: R 204 LYS cc_start: 0.5454 (ttpt) cc_final: 0.4759 (mptt) REVERT: R 257 TYR cc_start: 0.6633 (t80) cc_final: 0.6390 (t80) REVERT: R 366 ILE cc_start: 0.5435 (OUTLIER) cc_final: 0.4640 (mm) REVERT: R 417 GLU cc_start: 0.6342 (tt0) cc_final: 0.5752 (mp0) REVERT: S 86 ARG cc_start: 0.6053 (tpp80) cc_final: 0.4799 (ttt90) REVERT: S 125 MET cc_start: 0.5936 (ttp) cc_final: 0.5652 (ttp) REVERT: S 198 LYS cc_start: 0.6855 (mtpp) cc_final: 0.6520 (mmmt) REVERT: S 257 TYR cc_start: 0.7588 (t80) cc_final: 0.7041 (t80) REVERT: S 324 ARG cc_start: 0.5844 (mmt180) cc_final: 0.5055 (mmp-170) REVERT: S 417 GLU cc_start: 0.6474 (tt0) cc_final: 0.5995 (mt-10) REVERT: T 15 GLU cc_start: 0.7257 (tp30) cc_final: 0.6942 (tp30) REVERT: T 135 LEU cc_start: 0.7664 (mt) cc_final: 0.7169 (mt) REVERT: T 139 ASP cc_start: 0.6166 (p0) cc_final: 0.4958 (p0) REVERT: T 143 ASP cc_start: 0.6367 (m-30) cc_final: 0.6138 (p0) REVERT: T 156 ASP cc_start: 0.6336 (m-30) cc_final: 0.5985 (m-30) REVERT: T 169 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6946 (tm-30) REVERT: T 242 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6616 (tpp) REVERT: W 86 ARG cc_start: 0.5596 (tpp80) cc_final: 0.4788 (ttt90) REVERT: W 198 LYS cc_start: 0.6443 (mtpp) cc_final: 0.6213 (tptp) REVERT: W 257 TYR cc_start: 0.7546 (t80) cc_final: 0.7050 (t80) REVERT: W 319 ARG cc_start: 0.6438 (ttp80) cc_final: 0.5879 (ttt180) REVERT: W 417 GLU cc_start: 0.6387 (tt0) cc_final: 0.5802 (mp0) REVERT: X 15 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7400 (mp0) REVERT: X 242 MET cc_start: 0.7308 (tmm) cc_final: 0.6652 (tpp) REVERT: X 399 ARG cc_start: 0.6233 (mmt90) cc_final: 0.6033 (mtt90) outliers start: 90 outliers final: 63 residues processed: 698 average time/residue: 0.5518 time to fit residues: 616.0299 Evaluate side-chains 693 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 625 time to evaluate : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 360 MET Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 216 VAL Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 155 PHE Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 380 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 435 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 0.0670 chunk 458 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- 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 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 334 ASN K 149 ASN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 313 ASN Q 149 ASN ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN R 313 ASN S 245 ASN ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 313 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42356 Z= 0.284 Angle : 0.620 8.040 57523 Z= 0.315 Chirality : 0.044 0.169 6312 Planarity : 0.004 0.043 7523 Dihedral : 4.924 41.668 5847 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.66 % Allowed : 13.73 % Favored : 83.61 % 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: -0.34 (0.12), residues: 5268 helix: 0.83 (0.11), residues: 2136 sheet: -0.89 (0.19), residues: 792 loop : -0.90 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 81 HIS 0.006 0.001 HIS Q 410 PHE 0.020 0.002 PHE K 136 TYR 0.016 0.002 TYR T 257 ARG 0.005 0.000 ARG L 61 *********************** 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 749 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 635 time to evaluate : 4.716 Fit side-chains revert: symmetry clash REVERT: B 204 LYS cc_start: 0.5124 (ttpt) cc_final: 0.4572 (mptt) REVERT: B 234 LEU cc_start: 0.8159 (mm) cc_final: 0.7854 (mt) REVERT: B 257 TYR cc_start: 0.7604 (t80) cc_final: 0.7009 (t80) REVERT: B 324 ARG cc_start: 0.6109 (mmp80) cc_final: 0.5782 (mmt180) REVERT: B 392 GLU cc_start: 0.6365 (mp0) cc_final: 0.5746 (tt0) REVERT: B 417 GLU cc_start: 0.6520 (tt0) cc_final: 0.5929 (mp0) REVERT: E 143 ASP cc_start: 0.6078 (m-30) cc_final: 0.5686 (p0) REVERT: E 219 ILE cc_start: 0.6137 (tp) cc_final: 0.5896 (pt) REVERT: E 242 MET cc_start: 0.7384 (tmm) cc_final: 0.6675 (tpp) REVERT: E 392 GLU cc_start: 0.6715 (mp0) cc_final: 0.5846 (tt0) REVERT: F 15 GLU cc_start: 0.7368 (tp30) cc_final: 0.7134 (tp30) REVERT: F 61 ARG cc_start: 0.4215 (ptt90) cc_final: 0.3747 (ptt90) REVERT: F 125 MET cc_start: 0.6051 (ttp) cc_final: 0.5785 (ttp) REVERT: F 204 LYS cc_start: 0.5442 (ttpt) cc_final: 0.4740 (mptt) REVERT: F 234 LEU cc_start: 0.8251 (mm) cc_final: 0.7905 (mt) REVERT: F 273 MET cc_start: 0.6221 (mmp) cc_final: 0.5900 (mmp) REVERT: F 360 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6496 (mtt) REVERT: F 417 GLU cc_start: 0.6509 (tt0) cc_final: 0.5723 (mp0) REVERT: J 86 ARG cc_start: 0.5739 (ttm110) cc_final: 0.5077 (ttt180) REVERT: J 125 MET cc_start: 0.6210 (ttp) cc_final: 0.5926 (ttp) REVERT: J 139 ASP cc_start: 0.6236 (p0) cc_final: 0.6025 (p0) REVERT: J 204 LYS cc_start: 0.5381 (ttpt) cc_final: 0.4762 (mptt) REVERT: J 234 LEU cc_start: 0.8295 (mm) cc_final: 0.8042 (mt) REVERT: J 242 MET cc_start: 0.7204 (tmm) cc_final: 0.6735 (tpp) REVERT: J 257 TYR cc_start: 0.7567 (t80) cc_final: 0.7008 (t80) REVERT: J 417 GLU cc_start: 0.6559 (tt0) cc_final: 0.5894 (mp0) REVERT: K 366 ILE cc_start: 0.5640 (OUTLIER) cc_final: 0.4820 (mm) REVERT: L 86 ARG cc_start: 0.6196 (tpp80) cc_final: 0.4954 (ttt180) REVERT: L 204 LYS cc_start: 0.5498 (ttpt) cc_final: 0.4868 (mptt) REVERT: L 242 MET cc_start: 0.7420 (tmm) cc_final: 0.6012 (tmm) REVERT: L 319 ARG cc_start: 0.6507 (ttt-90) cc_final: 0.6183 (ttt180) REVERT: L 417 GLU cc_start: 0.6440 (tt0) cc_final: 0.5686 (mp0) REVERT: Q 61 ARG cc_start: 0.3791 (OUTLIER) cc_final: 0.2555 (ptt180) REVERT: Q 64 GLU cc_start: 0.7161 (mp0) cc_final: 0.6746 (mp0) REVERT: Q 86 ARG cc_start: 0.6086 (tpp80) cc_final: 0.4851 (ttt90) REVERT: Q 177 MET cc_start: 0.5540 (ttm) cc_final: 0.5062 (ttm) REVERT: Q 204 LYS cc_start: 0.5385 (ttpt) cc_final: 0.4739 (mptt) REVERT: R 86 ARG cc_start: 0.5840 (tpp80) cc_final: 0.4861 (ttt90) REVERT: R 157 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6354 (tt) REVERT: R 204 LYS cc_start: 0.5612 (ttpt) cc_final: 0.4904 (mptt) REVERT: R 366 ILE cc_start: 0.5683 (OUTLIER) cc_final: 0.4839 (mm) REVERT: R 417 GLU cc_start: 0.6424 (tt0) cc_final: 0.5745 (mp0) REVERT: S 86 ARG cc_start: 0.6093 (tpp80) cc_final: 0.4956 (ttt90) REVERT: S 125 MET cc_start: 0.6056 (ttp) cc_final: 0.5756 (ttp) REVERT: S 139 ASP cc_start: 0.6452 (p0) cc_final: 0.6180 (m-30) REVERT: S 148 LEU cc_start: 0.7272 (mm) cc_final: 0.7071 (mt) REVERT: S 204 LYS cc_start: 0.5459 (ttpt) cc_final: 0.4852 (mptt) REVERT: S 257 TYR cc_start: 0.7642 (t80) cc_final: 0.7050 (t80) REVERT: S 417 GLU cc_start: 0.6600 (tt0) cc_final: 0.6005 (mt-10) REVERT: T 15 GLU cc_start: 0.7371 (tp30) cc_final: 0.7017 (tp30) REVERT: T 139 ASP cc_start: 0.6114 (p0) cc_final: 0.4919 (p0) REVERT: T 169 GLU cc_start: 0.7353 (tm-30) cc_final: 0.6972 (tm-30) REVERT: T 242 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6785 (tpp) REVERT: T 366 ILE cc_start: 0.5588 (OUTLIER) cc_final: 0.4802 (mm) REVERT: T 392 GLU cc_start: 0.6462 (mp0) cc_final: 0.5523 (tt0) REVERT: T 417 GLU cc_start: 0.6422 (tt0) cc_final: 0.5672 (mp0) REVERT: W 86 ARG cc_start: 0.5637 (tpp80) cc_final: 0.4742 (ttt90) REVERT: W 125 MET cc_start: 0.6144 (ttp) cc_final: 0.5898 (ttp) REVERT: W 174 LEU cc_start: 0.3520 (OUTLIER) cc_final: 0.3254 (mm) REVERT: W 257 TYR cc_start: 0.7550 (t80) cc_final: 0.7000 (t80) REVERT: W 302 GLU cc_start: 0.5342 (tp30) cc_final: 0.5061 (tp30) REVERT: W 317 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5477 (tpt) REVERT: W 319 ARG cc_start: 0.6474 (ttp80) cc_final: 0.5952 (ttt180) REVERT: W 417 GLU cc_start: 0.6547 (tt0) cc_final: 0.5892 (mp0) REVERT: X 15 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7360 (mp0) REVERT: X 148 LEU cc_start: 0.7167 (mm) cc_final: 0.6896 (mt) REVERT: X 242 MET cc_start: 0.7208 (tmm) cc_final: 0.6532 (tpp) outliers start: 114 outliers final: 74 residues processed: 682 average time/residue: 0.5832 time to fit residues: 636.5994 Evaluate side-chains 676 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 593 time to evaluate : 4.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain Q residue 50 MET Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 155 PHE Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 155 PHE Chi-restraints excluded: chain W residue 174 LEU Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 317 MET Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 155 PHE Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.8980 chunk 459 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 299 optimal weight: 0.1980 chunk 125 optimal weight: 3.9990 chunk 510 optimal weight: 10.0000 chunk 424 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 42 optimal weight: 0.0770 chunk 168 optimal weight: 7.9990 chunk 268 optimal weight: 0.2980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 ASN E 149 ASN E 193 HIS ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 ASN ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN ** S 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 23 GLN ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 126 ASN X 149 ASN ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.2767 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= 0.171 Angle : 0.532 6.465 57523 Z= 0.272 Chirality : 0.040 0.146 6312 Planarity : 0.004 0.034 7523 Dihedral : 4.462 41.812 5847 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.47 % Allowed : 15.29 % Favored : 82.23 % 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: -0.16 (0.12), residues: 5268 helix: 0.97 (0.11), residues: 2136 sheet: -0.81 (0.18), residues: 828 loop : -0.79 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 76 HIS 0.003 0.001 HIS L 185 PHE 0.017 0.001 PHE W 134 TYR 0.018 0.001 TYR X 257 ARG 0.007 0.000 ARG E 86 *********************** 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 742 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 636 time to evaluate : 4.934 Fit side-chains revert: symmetry clash REVERT: B 134 PHE cc_start: 0.7835 (m-80) cc_final: 0.7608 (m-80) REVERT: B 204 LYS cc_start: 0.5033 (ttpt) cc_final: 0.4503 (mptt) REVERT: B 234 LEU cc_start: 0.8242 (mm) cc_final: 0.8017 (mt) REVERT: B 257 TYR cc_start: 0.7514 (t80) cc_final: 0.6976 (t80) REVERT: B 324 ARG cc_start: 0.5917 (mmp80) cc_final: 0.5288 (mmm160) REVERT: B 417 GLU cc_start: 0.6417 (tt0) cc_final: 0.5847 (mp0) REVERT: B 439 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5999 (tp) REVERT: E 139 ASP cc_start: 0.5437 (m-30) cc_final: 0.4111 (p0) REVERT: E 148 LEU cc_start: 0.7119 (mm) cc_final: 0.6917 (mt) REVERT: E 242 MET cc_start: 0.7384 (tmm) cc_final: 0.6535 (tpp) REVERT: F 15 GLU cc_start: 0.7360 (tp30) cc_final: 0.7117 (tp30) REVERT: F 61 ARG cc_start: 0.4230 (ptt90) cc_final: 0.3679 (ptm-80) REVERT: F 64 GLU cc_start: 0.7264 (mp0) cc_final: 0.7020 (mp0) REVERT: F 125 MET cc_start: 0.5966 (ttp) cc_final: 0.5690 (ttp) REVERT: F 156 ASP cc_start: 0.6446 (m-30) cc_final: 0.6071 (m-30) REVERT: F 234 LEU cc_start: 0.8281 (mm) cc_final: 0.8026 (mt) REVERT: F 242 MET cc_start: 0.7220 (tmm) cc_final: 0.6000 (tmm) REVERT: F 273 MET cc_start: 0.6222 (mmp) cc_final: 0.5859 (mmp) REVERT: F 329 ARG cc_start: 0.4885 (ptp-110) cc_final: 0.4558 (mtp85) REVERT: F 417 GLU cc_start: 0.6419 (tt0) cc_final: 0.5757 (mp0) REVERT: J 125 MET cc_start: 0.5977 (ttp) cc_final: 0.5710 (ttp) REVERT: J 134 PHE cc_start: 0.7973 (m-80) cc_final: 0.7738 (m-80) REVERT: J 148 LEU cc_start: 0.7285 (mm) cc_final: 0.6988 (mt) REVERT: J 204 LYS cc_start: 0.5255 (ttpt) cc_final: 0.4707 (mptt) REVERT: J 242 MET cc_start: 0.7202 (tmm) cc_final: 0.6617 (tpp) REVERT: J 257 TYR cc_start: 0.7509 (t80) cc_final: 0.6984 (t80) REVERT: J 417 GLU cc_start: 0.6462 (tt0) cc_final: 0.5815 (mp0) REVERT: K 366 ILE cc_start: 0.5611 (OUTLIER) cc_final: 0.4709 (mm) REVERT: L 86 ARG cc_start: 0.6317 (tpp80) cc_final: 0.4959 (ttt90) REVERT: L 125 MET cc_start: 0.6128 (ttt) cc_final: 0.5848 (ttp) REVERT: L 156 ASP cc_start: 0.6594 (m-30) cc_final: 0.6234 (m-30) REVERT: L 242 MET cc_start: 0.7327 (tmm) cc_final: 0.6201 (tpp) REVERT: L 319 ARG cc_start: 0.6380 (ttt-90) cc_final: 0.6093 (ttt180) REVERT: L 417 GLU cc_start: 0.6341 (tt0) cc_final: 0.5700 (mp0) REVERT: Q 86 ARG cc_start: 0.6129 (tpp80) cc_final: 0.4970 (ttt90) REVERT: Q 177 MET cc_start: 0.5600 (ttm) cc_final: 0.5152 (ttm) REVERT: Q 204 LYS cc_start: 0.5322 (ttpt) cc_final: 0.4625 (mptt) REVERT: R 15 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6747 (mm-30) REVERT: R 86 ARG cc_start: 0.5832 (tpp80) cc_final: 0.5289 (mmm160) REVERT: R 156 ASP cc_start: 0.6327 (m-30) cc_final: 0.6019 (m-30) REVERT: R 157 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6151 (tt) REVERT: R 366 ILE cc_start: 0.5667 (OUTLIER) cc_final: 0.4836 (mm) REVERT: S 86 ARG cc_start: 0.6286 (tpp80) cc_final: 0.5143 (ttt90) REVERT: S 125 MET cc_start: 0.6057 (ttp) cc_final: 0.5787 (ttp) REVERT: S 126 ASN cc_start: 0.6665 (OUTLIER) cc_final: 0.6115 (t0) REVERT: S 148 LEU cc_start: 0.7285 (mm) cc_final: 0.7020 (mt) REVERT: S 198 LYS cc_start: 0.6696 (mtpp) cc_final: 0.6384 (mmmt) REVERT: S 257 TYR cc_start: 0.7586 (t80) cc_final: 0.7024 (t80) REVERT: T 15 GLU cc_start: 0.7401 (tp30) cc_final: 0.7037 (tp30) REVERT: T 148 LEU cc_start: 0.7130 (mm) cc_final: 0.6875 (mt) REVERT: T 169 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6921 (tm-30) REVERT: T 242 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6556 (tpp) REVERT: T 366 ILE cc_start: 0.5577 (OUTLIER) cc_final: 0.4752 (mm) REVERT: T 439 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6024 (tp) REVERT: W 86 ARG cc_start: 0.5702 (tpp80) cc_final: 0.4745 (ttt90) REVERT: W 125 MET cc_start: 0.6143 (ttp) cc_final: 0.5939 (ttp) REVERT: W 177 MET cc_start: 0.4885 (tpt) cc_final: 0.4200 (mmm) REVERT: W 198 LYS cc_start: 0.6531 (mtpp) cc_final: 0.6156 (mmmt) REVERT: W 257 TYR cc_start: 0.7526 (t80) cc_final: 0.6980 (t80) REVERT: W 317 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5506 (tpt) REVERT: W 319 ARG cc_start: 0.6402 (ttp80) cc_final: 0.5907 (ttt180) REVERT: W 417 GLU cc_start: 0.6440 (tt0) cc_final: 0.5827 (mp0) REVERT: X 242 MET cc_start: 0.7409 (tmm) cc_final: 0.6635 (tpp) outliers start: 106 outliers final: 75 residues processed: 681 average time/residue: 0.5671 time to fit residues: 620.5643 Evaluate side-chains 669 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 585 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 155 PHE Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 366 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 36 ILE Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 399 ARG Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 155 PHE Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 439 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 155 PHE Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 317 MET Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 373 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 chunk 285 optimal weight: 4.9990 chunk 508 optimal weight: 8.9990 chunk 318 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 234 optimal weight: 0.0980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN K 210 GLN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 ASN ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 ASN ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 223 HIS ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 313 ASN W 313 ASN X 149 ASN ** X 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42356 Z= 0.192 Angle : 0.545 6.867 57523 Z= 0.278 Chirality : 0.041 0.148 6312 Planarity : 0.004 0.037 7523 Dihedral : 4.459 42.327 5847 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.69 % Allowed : 15.55 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.17 (0.12), residues: 5268 helix: 0.95 (0.11), residues: 2136 sheet: -0.78 (0.19), residues: 828 loop : -0.80 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 76 HIS 0.004 0.001 HIS J 226 PHE 0.015 0.001 PHE L 179 TYR 0.015 0.001 TYR R 257 ARG 0.006 0.000 ARG E 86 *********************** 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 714 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 599 time to evaluate : 4.609 Fit side-chains revert: symmetry clash REVERT: B 61 ARG cc_start: 0.4065 (ptt90) cc_final: 0.3693 (ptm-80) REVERT: B 134 PHE cc_start: 0.7994 (m-80) cc_final: 0.7752 (m-80) REVERT: B 257 TYR cc_start: 0.7561 (t80) cc_final: 0.7026 (t80) REVERT: B 324 ARG cc_start: 0.5865 (mmp80) cc_final: 0.5271 (mmm160) REVERT: B 417 GLU cc_start: 0.6431 (tt0) cc_final: 0.5848 (mp0) REVERT: B 439 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.6051 (tp) REVERT: E 139 ASP cc_start: 0.5616 (m-30) cc_final: 0.4253 (p0) REVERT: E 148 LEU cc_start: 0.7125 (mm) cc_final: 0.6846 (mt) REVERT: E 242 MET cc_start: 0.7383 (tmm) cc_final: 0.6582 (tpp) REVERT: F 15 GLU cc_start: 0.7309 (tp30) cc_final: 0.7071 (tp30) REVERT: F 61 ARG cc_start: 0.4031 (ptt90) cc_final: 0.3410 (ptt90) REVERT: F 234 LEU cc_start: 0.8294 (mm) cc_final: 0.8054 (mt) REVERT: F 273 MET cc_start: 0.6203 (mmp) cc_final: 0.5890 (mmp) REVERT: F 329 ARG cc_start: 0.4809 (ptp-110) cc_final: 0.4508 (mtp85) REVERT: F 360 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6574 (mtt) REVERT: F 417 GLU cc_start: 0.6436 (tt0) cc_final: 0.5758 (mp0) REVERT: J 125 MET cc_start: 0.5989 (ttp) cc_final: 0.5722 (ttp) REVERT: J 148 LEU cc_start: 0.7362 (mm) cc_final: 0.7027 (mt) REVERT: J 177 MET cc_start: 0.5404 (ttt) cc_final: 0.4813 (mtp) REVERT: J 204 LYS cc_start: 0.5317 (ttpt) cc_final: 0.4748 (mptt) REVERT: J 242 MET cc_start: 0.7212 (tmm) cc_final: 0.6686 (tpp) REVERT: J 257 TYR cc_start: 0.7509 (t80) cc_final: 0.6993 (t80) REVERT: J 417 GLU cc_start: 0.6511 (tt0) cc_final: 0.5858 (mp0) REVERT: K 15 GLU cc_start: 0.7251 (tp30) cc_final: 0.6705 (tp30) REVERT: L 86 ARG cc_start: 0.6294 (tpp80) cc_final: 0.5003 (ttt90) REVERT: L 125 MET cc_start: 0.6167 (ttt) cc_final: 0.5853 (ttp) REVERT: L 242 MET cc_start: 0.7449 (tmm) cc_final: 0.6292 (tpp) REVERT: L 417 GLU cc_start: 0.6353 (tt0) cc_final: 0.5707 (mp0) REVERT: Q 86 ARG cc_start: 0.6130 (tpp80) cc_final: 0.5028 (ttt90) REVERT: Q 177 MET cc_start: 0.5557 (ttm) cc_final: 0.5083 (ttm) REVERT: Q 204 LYS cc_start: 0.5317 (ttpt) cc_final: 0.4615 (mptt) REVERT: Q 257 TYR cc_start: 0.7103 (t80) cc_final: 0.6762 (t80) REVERT: R 10 ARG cc_start: 0.6745 (ttp-110) cc_final: 0.6509 (ttp-110) REVERT: R 15 GLU cc_start: 0.7730 (mm-30) cc_final: 0.6818 (mm-30) REVERT: R 86 ARG cc_start: 0.5749 (tpp80) cc_final: 0.5204 (mmm160) REVERT: R 156 ASP cc_start: 0.6336 (m-30) cc_final: 0.5983 (m-30) REVERT: R 157 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6126 (tt) REVERT: R 366 ILE cc_start: 0.5675 (OUTLIER) cc_final: 0.4826 (mm) REVERT: S 86 ARG cc_start: 0.6326 (tpp80) cc_final: 0.5184 (ttt90) REVERT: S 125 MET cc_start: 0.5967 (ttp) cc_final: 0.5680 (ttp) REVERT: S 126 ASN cc_start: 0.6455 (OUTLIER) cc_final: 0.6003 (t0) REVERT: S 148 LEU cc_start: 0.7249 (mm) cc_final: 0.6985 (mt) REVERT: S 257 TYR cc_start: 0.7606 (t80) cc_final: 0.7048 (t80) REVERT: T 10 ARG cc_start: 0.6730 (ttp-110) cc_final: 0.6514 (ttp-110) REVERT: T 15 GLU cc_start: 0.7372 (tp30) cc_final: 0.7029 (tp30) REVERT: T 148 LEU cc_start: 0.7113 (mm) cc_final: 0.6860 (mt) REVERT: T 156 ASP cc_start: 0.6373 (m-30) cc_final: 0.6029 (m-30) REVERT: T 169 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6925 (tm-30) REVERT: T 242 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6367 (tpp) REVERT: T 366 ILE cc_start: 0.5536 (OUTLIER) cc_final: 0.4705 (mm) REVERT: T 439 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6077 (tp) REVERT: W 86 ARG cc_start: 0.5733 (tpp80) cc_final: 0.4837 (ttt90) REVERT: W 148 LEU cc_start: 0.7276 (mm) cc_final: 0.6976 (mt) REVERT: W 174 LEU cc_start: 0.3629 (OUTLIER) cc_final: 0.3353 (mt) REVERT: W 177 MET cc_start: 0.5207 (tpt) cc_final: 0.4419 (mmm) REVERT: W 257 TYR cc_start: 0.7597 (t80) cc_final: 0.7057 (t80) REVERT: W 317 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5554 (tpt) REVERT: W 319 ARG cc_start: 0.6397 (ttp80) cc_final: 0.5922 (ttt180) REVERT: W 417 GLU cc_start: 0.6512 (tt0) cc_final: 0.5919 (mp0) REVERT: X 61 ARG cc_start: 0.4120 (OUTLIER) cc_final: 0.2660 (ptt180) REVERT: X 242 MET cc_start: 0.7269 (tmm) cc_final: 0.6580 (tpp) outliers start: 115 outliers final: 73 residues processed: 648 average time/residue: 0.5686 time to fit residues: 589.5448 Evaluate side-chains 665 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 581 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 399 ARG Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 36 ILE Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 155 PHE Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 242 MET Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 439 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 155 PHE Chi-restraints excluded: chain W residue 174 LEU Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 317 MET Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 61 ARG Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 303 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 323 optimal weight: 5.9990 chunk 346 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 400 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN E 149 ASN E 210 GLN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 ASN K 149 ASN ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 ASN ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 313 ASN R 149 ASN ** S 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 313 ASN ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42356 Z= 0.239 Angle : 0.583 7.625 57523 Z= 0.297 Chirality : 0.042 0.165 6312 Planarity : 0.004 0.039 7523 Dihedral : 4.699 41.903 5847 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.76 % Allowed : 15.99 % Favored : 81.25 % 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: -0.32 (0.12), residues: 5268 helix: 0.84 (0.11), residues: 2136 sheet: -0.79 (0.19), residues: 792 loop : -0.93 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 76 HIS 0.005 0.001 HIS R 243 PHE 0.018 0.002 PHE E 133 TYR 0.022 0.002 TYR E 257 ARG 0.005 0.000 ARG E 86 *********************** 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 703 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 585 time to evaluate : 5.084 Fit side-chains revert: symmetry clash REVERT: B 61 ARG cc_start: 0.4079 (ptt90) cc_final: 0.3641 (ptm-80) REVERT: B 169 GLU cc_start: 0.7362 (tp30) cc_final: 0.6938 (tp30) REVERT: B 204 LYS cc_start: 0.5039 (ttpt) cc_final: 0.4520 (mptt) REVERT: B 257 TYR cc_start: 0.7603 (t80) cc_final: 0.6985 (t80) REVERT: B 324 ARG cc_start: 0.6000 (mmp80) cc_final: 0.5427 (mmp-170) REVERT: B 417 GLU cc_start: 0.6507 (tt0) cc_final: 0.5921 (mp0) REVERT: E 139 ASP cc_start: 0.5644 (m-30) cc_final: 0.4213 (p0) REVERT: E 242 MET cc_start: 0.7124 (tmm) cc_final: 0.6435 (tpp) REVERT: F 15 GLU cc_start: 0.7212 (tp30) cc_final: 0.6973 (tp30) REVERT: F 61 ARG cc_start: 0.3824 (ptt90) cc_final: 0.3234 (ptm-80) REVERT: F 273 MET cc_start: 0.6245 (mmp) cc_final: 0.5956 (mmp) REVERT: F 360 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6491 (mtt) REVERT: F 417 GLU cc_start: 0.6445 (tt0) cc_final: 0.5724 (mp0) REVERT: F 439 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6184 (tp) REVERT: J 125 MET cc_start: 0.5955 (ttp) cc_final: 0.5674 (ttp) REVERT: J 148 LEU cc_start: 0.7353 (mm) cc_final: 0.7096 (mt) REVERT: J 204 LYS cc_start: 0.5481 (ttpt) cc_final: 0.4850 (mptt) REVERT: J 242 MET cc_start: 0.7201 (tmm) cc_final: 0.6713 (tpp) REVERT: J 257 TYR cc_start: 0.7601 (t80) cc_final: 0.7035 (t80) REVERT: J 417 GLU cc_start: 0.6608 (tt0) cc_final: 0.5923 (mp0) REVERT: K 15 GLU cc_start: 0.7243 (tp30) cc_final: 0.6696 (tp30) REVERT: L 86 ARG cc_start: 0.6262 (tpp80) cc_final: 0.5037 (ttt90) REVERT: L 125 MET cc_start: 0.6218 (ttt) cc_final: 0.5892 (ttp) REVERT: L 204 LYS cc_start: 0.5491 (ttpt) cc_final: 0.4880 (mptt) REVERT: L 242 MET cc_start: 0.7456 (tmm) cc_final: 0.6655 (tpp) REVERT: L 417 GLU cc_start: 0.6434 (tt0) cc_final: 0.5732 (mp0) REVERT: Q 86 ARG cc_start: 0.6173 (tpp80) cc_final: 0.5045 (ttt90) REVERT: Q 177 MET cc_start: 0.5573 (ttm) cc_final: 0.5090 (ttm) REVERT: Q 204 LYS cc_start: 0.5329 (ttpt) cc_final: 0.4609 (mptt) REVERT: R 15 GLU cc_start: 0.7754 (mm-30) cc_final: 0.6571 (tp30) REVERT: R 156 ASP cc_start: 0.6342 (m-30) cc_final: 0.5936 (m-30) REVERT: R 157 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6201 (tt) REVERT: R 366 ILE cc_start: 0.5757 (OUTLIER) cc_final: 0.4886 (mm) REVERT: R 417 GLU cc_start: 0.6435 (tt0) cc_final: 0.5683 (mp0) REVERT: S 86 ARG cc_start: 0.6392 (tpp80) cc_final: 0.5269 (ttt90) REVERT: S 125 MET cc_start: 0.6096 (ttp) cc_final: 0.5797 (ttp) REVERT: S 126 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.6037 (t0) REVERT: S 139 ASP cc_start: 0.6244 (p0) cc_final: 0.5932 (m-30) REVERT: S 257 TYR cc_start: 0.7618 (t80) cc_final: 0.6967 (t80) REVERT: T 10 ARG cc_start: 0.6895 (ttp-110) cc_final: 0.6669 (ttp-110) REVERT: T 15 GLU cc_start: 0.7412 (tp30) cc_final: 0.7034 (tp30) REVERT: T 148 LEU cc_start: 0.7135 (mm) cc_final: 0.6892 (mt) REVERT: T 156 ASP cc_start: 0.6481 (m-30) cc_final: 0.6054 (m-30) REVERT: T 169 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6981 (tm-30) REVERT: T 242 MET cc_start: 0.7595 (tmm) cc_final: 0.7129 (tpp) REVERT: T 366 ILE cc_start: 0.5642 (OUTLIER) cc_final: 0.4809 (mm) REVERT: T 417 GLU cc_start: 0.6462 (tt0) cc_final: 0.5680 (mp0) REVERT: T 439 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6220 (tp) REVERT: W 86 ARG cc_start: 0.5637 (tpp80) cc_final: 0.4784 (ttt90) REVERT: W 148 LEU cc_start: 0.7296 (mm) cc_final: 0.7017 (mt) REVERT: W 177 MET cc_start: 0.5272 (tpt) cc_final: 0.4404 (mmm) REVERT: W 221 ARG cc_start: 0.5790 (mpt90) cc_final: 0.5559 (mpt-90) REVERT: W 257 TYR cc_start: 0.7637 (t80) cc_final: 0.7082 (t80) REVERT: W 317 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5467 (tpt) REVERT: W 319 ARG cc_start: 0.6456 (ttp80) cc_final: 0.5982 (ttt180) REVERT: W 417 GLU cc_start: 0.6528 (tt0) cc_final: 0.5939 (mp0) REVERT: X 61 ARG cc_start: 0.3979 (OUTLIER) cc_final: 0.2455 (ptt180) REVERT: X 242 MET cc_start: 0.7244 (tmm) cc_final: 0.6567 (tpp) outliers start: 118 outliers final: 87 residues processed: 648 average time/residue: 0.5681 time to fit residues: 585.3564 Evaluate side-chains 659 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 563 time to evaluate : 4.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 439 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 399 ARG Chi-restraints excluded: chain K residue 418 LEU Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 114 LEU Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 155 PHE Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 399 ARG Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 366 ILE Chi-restraints excluded: chain R residue 373 MET Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 155 PHE Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain S residue 439 LEU Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 123 THR Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain T residue 439 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 155 PHE Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 317 MET Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 61 ARG Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 4.9990 chunk 487 optimal weight: 0.9990 chunk 444 optimal weight: 0.4980 chunk 474 optimal weight: 5.9990 chunk 285 optimal weight: 0.4980 chunk 206 optimal weight: 2.9990 chunk 372 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 428 optimal weight: 7.9990 chunk 448 optimal weight: 4.9990 chunk 472 optimal weight: 0.0040 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN 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** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 HIS ** 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 ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 42356 Z= 0.152 Angle : 0.522 6.646 57523 Z= 0.267 Chirality : 0.040 0.161 6312 Planarity : 0.004 0.039 7523 Dihedral : 4.252 33.144 5844 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.96 % Allowed : 17.32 % Favored : 80.71 % 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: -0.08 (0.12), residues: 5268 helix: 1.00 (0.11), residues: 2136 sheet: -0.64 (0.20), residues: 744 loop : -0.77 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 81 HIS 0.006 0.001 HIS Q 185 PHE 0.017 0.001 PHE E 133 TYR 0.013 0.001 TYR K 199 ARG 0.009 0.000 ARG X 86 *********************** 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 699 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 615 time to evaluate : 4.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.3968 (ptt90) cc_final: 0.3745 (ptm160) REVERT: B 257 TYR cc_start: 0.7542 (t80) cc_final: 0.7056 (t80) REVERT: B 324 ARG cc_start: 0.5824 (mmp80) cc_final: 0.5267 (mmm160) REVERT: B 439 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.6065 (tp) REVERT: E 86 ARG cc_start: 0.5528 (mtp-110) cc_final: 0.5322 (mtp-110) REVERT: E 242 MET cc_start: 0.7247 (tmm) cc_final: 0.6357 (tpp) REVERT: F 15 GLU cc_start: 0.7207 (tp30) cc_final: 0.6985 (tp30) REVERT: F 61 ARG cc_start: 0.3760 (ptt90) cc_final: 0.3340 (ptm-80) REVERT: F 156 ASP cc_start: 0.6229 (m-30) cc_final: 0.5908 (m-30) REVERT: F 242 MET cc_start: 0.7100 (tmm) cc_final: 0.5987 (tmm) REVERT: F 273 MET cc_start: 0.6197 (mmp) cc_final: 0.5855 (mmt) REVERT: J 125 MET cc_start: 0.5815 (ttp) cc_final: 0.5536 (ttp) REVERT: J 134 PHE cc_start: 0.7788 (m-80) cc_final: 0.7558 (m-80) REVERT: J 148 LEU cc_start: 0.7312 (mm) cc_final: 0.7071 (mt) REVERT: J 242 MET cc_start: 0.7134 (tmm) cc_final: 0.6547 (tpp) REVERT: J 257 TYR cc_start: 0.7537 (t80) cc_final: 0.7026 (t80) REVERT: K 15 GLU cc_start: 0.7260 (tp30) cc_final: 0.6745 (tp30) REVERT: L 86 ARG cc_start: 0.6214 (tpp80) cc_final: 0.4827 (tpt170) REVERT: L 125 MET cc_start: 0.6087 (ttt) cc_final: 0.5776 (ttp) REVERT: L 156 ASP cc_start: 0.6443 (m-30) cc_final: 0.6187 (m-30) REVERT: L 242 MET cc_start: 0.7375 (tmm) cc_final: 0.6991 (tmm) REVERT: Q 86 ARG cc_start: 0.6199 (tpp80) cc_final: 0.5095 (ttt90) REVERT: Q 177 MET cc_start: 0.5569 (ttm) cc_final: 0.5126 (ttm) REVERT: Q 257 TYR cc_start: 0.7086 (t80) cc_final: 0.6797 (t80) REVERT: R 15 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6319 (tp30) REVERT: R 86 ARG cc_start: 0.6670 (mmm-85) cc_final: 0.4882 (ttt180) REVERT: R 156 ASP cc_start: 0.6351 (m-30) cc_final: 0.6106 (m-30) REVERT: R 157 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6023 (tt) REVERT: R 243 HIS cc_start: 0.7215 (m-70) cc_final: 0.7013 (m-70) REVERT: S 15 GLU cc_start: 0.7598 (tp30) cc_final: 0.7146 (mm-30) REVERT: S 86 ARG cc_start: 0.6380 (tpp80) cc_final: 0.5154 (ttt90) REVERT: S 125 MET cc_start: 0.5916 (ttp) cc_final: 0.5623 (ttp) REVERT: S 126 ASN cc_start: 0.6556 (OUTLIER) cc_final: 0.6140 (t0) REVERT: S 198 LYS cc_start: 0.6769 (mtpp) cc_final: 0.6419 (mmmt) REVERT: S 257 TYR cc_start: 0.7513 (t80) cc_final: 0.6968 (t80) REVERT: T 10 ARG cc_start: 0.6922 (ttp-110) cc_final: 0.6696 (ttp-110) REVERT: T 15 GLU cc_start: 0.7408 (tp30) cc_final: 0.7092 (tp30) REVERT: T 148 LEU cc_start: 0.7119 (mm) cc_final: 0.6903 (mt) REVERT: T 169 GLU cc_start: 0.7394 (tm-30) cc_final: 0.6781 (tp30) REVERT: T 242 MET cc_start: 0.7370 (tmm) cc_final: 0.6931 (tpp) REVERT: T 273 MET cc_start: 0.5523 (mmm) cc_final: 0.5270 (mmp) REVERT: T 366 ILE cc_start: 0.5530 (OUTLIER) cc_final: 0.4695 (mm) REVERT: W 86 ARG cc_start: 0.5672 (tpp80) cc_final: 0.4811 (ttt90) REVERT: W 134 PHE cc_start: 0.7817 (m-80) cc_final: 0.7615 (m-80) REVERT: W 148 LEU cc_start: 0.7192 (mm) cc_final: 0.6935 (mt) REVERT: W 177 MET cc_start: 0.5246 (tpt) cc_final: 0.4402 (mmm) REVERT: W 198 LYS cc_start: 0.6609 (mtpp) cc_final: 0.6246 (mmmt) REVERT: W 257 TYR cc_start: 0.7605 (t80) cc_final: 0.7099 (t80) REVERT: W 317 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5662 (tpt) REVERT: W 319 ARG cc_start: 0.6430 (ttp80) cc_final: 0.6008 (ttt180) REVERT: W 417 GLU cc_start: 0.6482 (tt0) cc_final: 0.5876 (mp0) REVERT: X 242 MET cc_start: 0.7298 (tmm) cc_final: 0.6522 (tpp) outliers start: 84 outliers final: 58 residues processed: 654 average time/residue: 0.5649 time to fit residues: 591.5451 Evaluate side-chains 640 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 577 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 317 MET Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 87 VAL Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 87 VAL Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 317 MET Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 5.9990 chunk 501 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 348 optimal weight: 5.9990 chunk 526 optimal weight: 0.3980 chunk 484 optimal weight: 10.0000 chunk 418 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 323 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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** E 149 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 245 ASN K 313 ASN ** Q 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 429 GLN ** R 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 223 HIS 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: 0.6203 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 42356 Z= 0.317 Angle : 0.657 8.570 57523 Z= 0.333 Chirality : 0.045 0.194 6312 Planarity : 0.005 0.085 7523 Dihedral : 4.958 29.518 5844 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.05 % Allowed : 17.42 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.52 (0.12), residues: 5268 helix: 0.69 (0.11), residues: 2136 sheet: -0.80 (0.20), residues: 792 loop : -1.10 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 76 HIS 0.007 0.002 HIS X 193 PHE 0.032 0.002 PHE Q 212 TYR 0.017 0.002 TYR T 416 ARG 0.009 0.001 ARG X 86 ********************** 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 665 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 577 time to evaluate : 5.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 148 LEU cc_start: 0.7233 (mm) cc_final: 0.6965 (mt) REVERT: B 204 LYS cc_start: 0.5149 (ttpt) cc_final: 0.4645 (mptt) REVERT: B 257 TYR cc_start: 0.7603 (t80) cc_final: 0.6972 (t80) REVERT: B 324 ARG cc_start: 0.6009 (mmp80) cc_final: 0.5277 (mmm160) REVERT: B 392 GLU cc_start: 0.6339 (mp0) cc_final: 0.5754 (tt0) REVERT: B 417 GLU cc_start: 0.6583 (tt0) cc_final: 0.5758 (mp0) REVERT: E 242 MET cc_start: 0.7211 (tmm) cc_final: 0.6493 (tpp) REVERT: E 392 GLU cc_start: 0.6738 (mp0) cc_final: 0.6061 (tt0) REVERT: F 15 GLU cc_start: 0.7217 (tp30) cc_final: 0.6955 (tp30) REVERT: F 61 ARG cc_start: 0.3788 (OUTLIER) cc_final: 0.3192 (ptm-80) REVERT: F 204 LYS cc_start: 0.5469 (ttpt) cc_final: 0.4772 (mptt) REVERT: F 273 MET cc_start: 0.6216 (mmp) cc_final: 0.5973 (mmt) REVERT: F 360 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6411 (mtt) REVERT: F 417 GLU cc_start: 0.6517 (tt0) cc_final: 0.5701 (mp0) REVERT: J 125 MET cc_start: 0.5972 (ttp) cc_final: 0.5680 (ttp) REVERT: J 148 LEU cc_start: 0.7334 (mm) cc_final: 0.7106 (mt) REVERT: J 204 LYS cc_start: 0.5303 (ttpt) cc_final: 0.4691 (mptt) REVERT: J 242 MET cc_start: 0.7258 (tmm) cc_final: 0.6780 (tpp) REVERT: J 257 TYR cc_start: 0.7658 (t80) cc_final: 0.7088 (t80) REVERT: J 417 GLU cc_start: 0.6655 (tt0) cc_final: 0.5887 (mp0) REVERT: K 15 GLU cc_start: 0.7229 (tp30) cc_final: 0.6656 (tp30) REVERT: L 86 ARG cc_start: 0.6481 (tpp80) cc_final: 0.4907 (tpt170) REVERT: L 204 LYS cc_start: 0.5514 (ttpt) cc_final: 0.4855 (mptt) REVERT: L 242 MET cc_start: 0.7457 (tmm) cc_final: 0.6038 (tmm) REVERT: L 417 GLU cc_start: 0.6479 (tt0) cc_final: 0.5715 (mp0) REVERT: Q 86 ARG cc_start: 0.6073 (tpp80) cc_final: 0.4943 (ttt90) REVERT: Q 177 MET cc_start: 0.5885 (ttm) cc_final: 0.5371 (ttm) REVERT: Q 204 LYS cc_start: 0.5431 (ttpt) cc_final: 0.4734 (mptt) REVERT: R 86 ARG cc_start: 0.6829 (mmm-85) cc_final: 0.5412 (mtp85) REVERT: R 156 ASP cc_start: 0.6499 (m-30) cc_final: 0.6021 (m-30) REVERT: R 157 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6308 (tt) REVERT: R 417 GLU cc_start: 0.6456 (tt0) cc_final: 0.5687 (mp0) REVERT: S 15 GLU cc_start: 0.7544 (tp30) cc_final: 0.6262 (mm-30) REVERT: S 61 ARG cc_start: 0.4179 (OUTLIER) cc_final: 0.2765 (ptt180) REVERT: S 86 ARG cc_start: 0.6396 (tpp80) cc_final: 0.5748 (mmm160) REVERT: S 125 MET cc_start: 0.6027 (ttp) cc_final: 0.5721 (ttp) REVERT: S 126 ASN cc_start: 0.6535 (OUTLIER) cc_final: 0.6038 (t0) REVERT: S 204 LYS cc_start: 0.5355 (ttpt) cc_final: 0.4744 (mptt) REVERT: S 257 TYR cc_start: 0.7627 (t80) cc_final: 0.6914 (t80) REVERT: T 10 ARG cc_start: 0.6918 (ttp-110) cc_final: 0.6682 (ttp-110) REVERT: T 15 GLU cc_start: 0.7397 (tp30) cc_final: 0.6942 (tp30) REVERT: T 148 LEU cc_start: 0.7150 (mm) cc_final: 0.6870 (mt) REVERT: T 169 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7063 (tm-30) REVERT: T 242 MET cc_start: 0.7700 (tmm) cc_final: 0.6812 (tpp) REVERT: T 366 ILE cc_start: 0.5762 (OUTLIER) cc_final: 0.4917 (mm) REVERT: T 417 GLU cc_start: 0.6415 (tt0) cc_final: 0.5729 (mm-30) REVERT: W 86 ARG cc_start: 0.5587 (tpp80) cc_final: 0.4755 (ttt90) REVERT: W 177 MET cc_start: 0.5370 (tpt) cc_final: 0.4484 (mmm) REVERT: W 257 TYR cc_start: 0.7667 (t80) cc_final: 0.7089 (t80) REVERT: W 317 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5375 (tpt) REVERT: W 417 GLU cc_start: 0.6615 (tt0) cc_final: 0.5917 (mp0) REVERT: X 242 MET cc_start: 0.7207 (tmm) cc_final: 0.6516 (tpp) outliers start: 88 outliers final: 66 residues processed: 623 average time/residue: 0.5693 time to fit residues: 565.3118 Evaluate side-chains 628 residues out of total 4548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 555 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 36 ILE Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 155 PHE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 283 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 385 SER Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 216 VAL Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 418 LEU Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain L residue 283 MET Chi-restraints excluded: chain L residue 317 MET Chi-restraints excluded: chain L residue 373 MET Chi-restraints excluded: chain Q residue 77 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 157 LEU Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 317 MET Chi-restraints excluded: chain Q residue 418 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 237 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 47 ASN Chi-restraints excluded: chain S residue 61 ARG Chi-restraints excluded: chain S residue 77 VAL Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 126 ASN Chi-restraints excluded: chain S residue 146 THR Chi-restraints excluded: chain S residue 237 VAL Chi-restraints excluded: chain S residue 403 ILE Chi-restraints excluded: chain T residue 39 SER Chi-restraints excluded: chain T residue 146 THR Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 283 MET Chi-restraints excluded: chain T residue 366 ILE Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain W residue 123 THR Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 317 MET Chi-restraints excluded: chain W residue 403 ILE Chi-restraints excluded: chain X residue 77 VAL Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 0.9980 chunk 446 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 419 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 430 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** E 149 ASN ** 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 226 HIS ** 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 ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.233908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.220137 restraints weight = 49987.452| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.32 r_work: 0.4317 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.4217 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4222 r_free = 0.4222 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4222 r_free = 0.4222 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42356 Z= 0.179 Angle : 0.560 6.817 57523 Z= 0.287 Chirality : 0.041 0.164 6312 Planarity : 0.004 0.067 7523 Dihedral : 4.541 34.158 5844 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.80 % Allowed : 18.02 % Favored : 80.18 % 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: -0.28 (0.12), residues: 5268 helix: 0.86 (0.11), residues: 2136 sheet: -0.71 (0.21), residues: 744 loop : -0.92 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 423 HIS 0.005 0.001 HIS K 185 PHE 0.030 0.002 PHE Q 212 TYR 0.017 0.001 TYR T 416 ARG 0.008 0.000 ARG X 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11337.57 seconds wall clock time: 203 minutes 41.48 seconds (12221.48 seconds total)