Starting phenix.real_space_refine on Sun Mar 24 09:30:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/03_2024/8php_17670.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/03_2024/8php_17670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/03_2024/8php_17670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/03_2024/8php_17670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/03_2024/8php_17670.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/03_2024/8php_17670.pdb" } resolution = 2.56 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 26352 2.51 5 N 6708 2.21 5 O 7644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40812 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "B" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "C" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "E" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "F" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "G" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "H" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "I" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "J" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "K" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "L" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "M" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "N" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "O" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "P" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "Q" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "R" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "S" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "T" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "U" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "V" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "W" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2684 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 2 Chain: "X" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 717 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Time building chain proxies: 20.06, per 1000 atoms: 0.49 Number of scatterers: 40812 At special positions: 0 Unit cell: (199.23, 199.23, 120.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 7644 8.00 N 6708 7.00 C 26352 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: 14.02 Conformation dependent library (CDL) restraints added in 6.6 seconds 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9576 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 60.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 285 through 303 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 389 Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 92 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 145 through 163 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 285 through 303 Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 389 Processing helix chain 'C' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 92 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 109 through 126 Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 145 through 163 Processing helix chain 'E' and resid 14 through 22 Processing helix chain 'E' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL E 32 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR E 177 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 266 Processing helix chain 'E' and resid 285 through 303 Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS E 347 " --> pdb=" O SER E 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR E 349 " --> pdb=" O ASN E 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS E 350 " --> pdb=" O LEU E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 389 Processing helix chain 'E' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 403 " --> pdb=" O MET E 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 92 Processing helix chain 'F' and resid 95 through 98 Processing helix chain 'F' and resid 99 through 107 Processing helix chain 'F' and resid 109 through 126 Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 145 through 163 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL G 32 " --> pdb=" O TYR G 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR G 177 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 266 Processing helix chain 'G' and resid 285 through 303 Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS G 347 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR G 349 " --> pdb=" O ASN G 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS G 350 " --> pdb=" O LEU G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 389 Processing helix chain 'G' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS G 401 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS G 403 " --> pdb=" O MET G 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 92 Processing helix chain 'H' and resid 95 through 98 Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 109 through 126 Processing helix chain 'H' and resid 127 through 135 Processing helix chain 'H' and resid 145 through 163 Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL I 32 " --> pdb=" O TYR I 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 37 " --> pdb=" O ALA I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR I 177 " --> pdb=" O PHE I 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG I 183 " --> pdb=" O GLU I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 266 Processing helix chain 'I' and resid 285 through 303 Processing helix chain 'I' and resid 305 through 311 Processing helix chain 'I' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS I 347 " --> pdb=" O SER I 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR I 349 " --> pdb=" O ASN I 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 389 Processing helix chain 'I' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS I 401 " --> pdb=" O LEU I 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU I 402 " --> pdb=" O ALA I 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS I 403 " --> pdb=" O MET I 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 92 Processing helix chain 'J' and resid 95 through 98 Processing helix chain 'J' and resid 99 through 107 Processing helix chain 'J' and resid 109 through 126 Processing helix chain 'J' and resid 127 through 135 Processing helix chain 'J' and resid 145 through 163 Processing helix chain 'K' and resid 14 through 22 Processing helix chain 'K' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL K 32 " --> pdb=" O TYR K 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN K 68 " --> pdb=" O ASN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG K 183 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 266 Processing helix chain 'K' and resid 285 through 303 Processing helix chain 'K' and resid 305 through 311 Processing helix chain 'K' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS K 347 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR K 349 " --> pdb=" O ASN K 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS K 350 " --> pdb=" O LEU K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 389 Processing helix chain 'K' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU K 402 " --> pdb=" O ALA K 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 403 " --> pdb=" O MET K 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 92 Processing helix chain 'L' and resid 95 through 98 Processing helix chain 'L' and resid 99 through 107 Processing helix chain 'L' and resid 109 through 126 Processing helix chain 'L' and resid 127 through 135 Processing helix chain 'L' and resid 145 through 163 Processing helix chain 'M' and resid 14 through 22 Processing helix chain 'M' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL M 32 " --> pdb=" O TYR M 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA M 33 " --> pdb=" O ILE M 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU M 37 " --> pdb=" O ALA M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN M 68 " --> pdb=" O ASN M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR M 177 " --> pdb=" O PHE M 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 266 Processing helix chain 'M' and resid 285 through 303 Processing helix chain 'M' and resid 305 through 311 Processing helix chain 'M' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS M 347 " --> pdb=" O SER M 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR M 349 " --> pdb=" O ASN M 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS M 350 " --> pdb=" O LEU M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 389 Processing helix chain 'M' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS M 401 " --> pdb=" O LEU M 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU M 402 " --> pdb=" O ALA M 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS M 403 " --> pdb=" O MET M 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 92 Processing helix chain 'N' and resid 95 through 98 Processing helix chain 'N' and resid 99 through 107 Processing helix chain 'N' and resid 109 through 126 Processing helix chain 'N' and resid 127 through 135 Processing helix chain 'N' and resid 145 through 163 Processing helix chain 'O' and resid 14 through 22 Processing helix chain 'O' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL O 32 " --> pdb=" O TYR O 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA O 33 " --> pdb=" O ILE O 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 110 No H-bonds generated for 'chain 'O' and resid 108 through 110' Processing helix chain 'O' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR O 177 " --> pdb=" O PHE O 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG O 183 " --> pdb=" O GLU O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 266 Processing helix chain 'O' and resid 285 through 303 Processing helix chain 'O' and resid 305 through 311 Processing helix chain 'O' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS O 347 " --> pdb=" O SER O 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR O 349 " --> pdb=" O ASN O 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS O 350 " --> pdb=" O LEU O 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 365 through 389 Processing helix chain 'O' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS O 401 " --> pdb=" O LEU O 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU O 402 " --> pdb=" O ALA O 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS O 403 " --> pdb=" O MET O 399 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 92 Processing helix chain 'P' and resid 95 through 98 Processing helix chain 'P' and resid 99 through 107 Processing helix chain 'P' and resid 109 through 126 Processing helix chain 'P' and resid 127 through 135 Processing helix chain 'P' and resid 145 through 163 Processing helix chain 'Q' and resid 14 through 22 Processing helix chain 'Q' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL Q 32 " --> pdb=" O TYR Q 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA Q 33 " --> pdb=" O ILE Q 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Q 37 " --> pdb=" O ALA Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain 'Q' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR Q 177 " --> pdb=" O PHE Q 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Q 183 " --> pdb=" O GLU Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 266 Processing helix chain 'Q' and resid 285 through 303 Processing helix chain 'Q' and resid 305 through 311 Processing helix chain 'Q' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS Q 347 " --> pdb=" O SER Q 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR Q 349 " --> pdb=" O ASN Q 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS Q 350 " --> pdb=" O LEU Q 346 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 389 Processing helix chain 'Q' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS Q 401 " --> pdb=" O LEU Q 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU Q 402 " --> pdb=" O ALA Q 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS Q 403 " --> pdb=" O MET Q 399 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 92 Processing helix chain 'R' and resid 95 through 98 Processing helix chain 'R' and resid 99 through 107 Processing helix chain 'R' and resid 109 through 126 Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 145 through 163 Processing helix chain 'S' and resid 14 through 22 Processing helix chain 'S' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL S 32 " --> pdb=" O TYR S 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA S 33 " --> pdb=" O ILE S 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU S 37 " --> pdb=" O ALA S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN S 68 " --> pdb=" O ASN S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 108 through 110 No H-bonds generated for 'chain 'S' and resid 108 through 110' Processing helix chain 'S' and resid 163 through 184 removed outlier: 4.418A pdb=" N TYR S 177 " --> pdb=" O PHE S 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG S 183 " --> pdb=" O GLU S 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 258 through 266 Processing helix chain 'S' and resid 285 through 303 Processing helix chain 'S' and resid 305 through 311 Processing helix chain 'S' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS S 347 " --> pdb=" O SER S 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR S 349 " --> pdb=" O ASN S 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS S 350 " --> pdb=" O LEU S 346 " (cutoff:3.500A) Processing helix chain 'S' and resid 365 through 389 Processing helix chain 'S' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS S 401 " --> pdb=" O LEU S 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU S 402 " --> pdb=" O ALA S 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS S 403 " --> pdb=" O MET S 399 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 92 Processing helix chain 'T' and resid 95 through 98 Processing helix chain 'T' and resid 99 through 107 Processing helix chain 'T' and resid 109 through 126 Processing helix chain 'T' and resid 127 through 135 Processing helix chain 'T' and resid 145 through 163 Processing helix chain 'U' and resid 14 through 22 Processing helix chain 'U' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL U 32 " --> pdb=" O TYR U 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA U 33 " --> pdb=" O ILE U 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU U 37 " --> pdb=" O ALA U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR U 177 " --> pdb=" O PHE U 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG U 183 " --> pdb=" O GLU U 179 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 266 Processing helix chain 'U' and resid 285 through 303 Processing helix chain 'U' and resid 305 through 311 Processing helix chain 'U' and resid 327 through 353 removed outlier: 4.312A pdb=" N LYS U 347 " --> pdb=" O SER U 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR U 349 " --> pdb=" O ASN U 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS U 350 " --> pdb=" O LEU U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 365 through 389 Processing helix chain 'U' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS U 401 " --> pdb=" O LEU U 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU U 402 " --> pdb=" O ALA U 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS U 403 " --> pdb=" O MET U 399 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 92 Processing helix chain 'V' and resid 95 through 98 Processing helix chain 'V' and resid 99 through 107 Processing helix chain 'V' and resid 109 through 126 Processing helix chain 'V' and resid 127 through 135 Processing helix chain 'V' and resid 145 through 163 Processing helix chain 'W' and resid 14 through 22 Processing helix chain 'W' and resid 22 through 37 removed outlier: 4.518A pdb=" N VAL W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA W 33 " --> pdb=" O ILE W 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU W 37 " --> pdb=" O ALA W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 76 removed outlier: 3.751A pdb=" N ASN W 68 " --> pdb=" O ASN W 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 110 No H-bonds generated for 'chain 'W' and resid 108 through 110' Processing helix chain 'W' and resid 163 through 184 removed outlier: 4.417A pdb=" N TYR W 177 " --> pdb=" O PHE W 173 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG W 183 " --> pdb=" O GLU W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 258 through 266 Processing helix chain 'W' and resid 285 through 303 Processing helix chain 'W' and resid 305 through 311 Processing helix chain 'W' and resid 327 through 353 removed outlier: 4.311A pdb=" N LYS W 347 " --> pdb=" O SER W 343 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR W 349 " --> pdb=" O ASN W 345 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS W 350 " --> pdb=" O LEU W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 365 through 389 Processing helix chain 'W' and resid 393 through 403 removed outlier: 3.556A pdb=" N LYS W 401 " --> pdb=" O LEU W 397 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU W 402 " --> pdb=" O ALA W 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS W 403 " --> pdb=" O MET W 399 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 92 Processing helix chain 'X' and resid 95 through 98 Processing helix chain 'X' and resid 99 through 107 Processing helix chain 'X' and resid 109 through 126 Processing helix chain 'X' and resid 127 through 135 Processing helix chain 'X' and resid 145 through 163 Processing sheet with id= 1, first strand: chain 'A' and resid 41 through 45 Processing sheet with id= 2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR A 80 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id= 4, first strand: chain 'A' and resid 151 through 152 Processing sheet with id= 5, first strand: chain 'A' and resid 188 through 193 Processing sheet with id= 6, first strand: chain 'C' and resid 41 through 45 Processing sheet with id= 7, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR C 80 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 112 through 113 Processing sheet with id= 9, first strand: chain 'C' and resid 151 through 152 Processing sheet with id= 10, first strand: chain 'C' and resid 188 through 193 Processing sheet with id= 11, first strand: chain 'E' and resid 41 through 45 Processing sheet with id= 12, first strand: chain 'E' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR E 80 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 112 through 113 Processing sheet with id= 14, first strand: chain 'E' and resid 151 through 152 Processing sheet with id= 15, first strand: chain 'E' and resid 188 through 193 Processing sheet with id= 16, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 17, first strand: chain 'G' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR G 80 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 112 through 113 Processing sheet with id= 19, first strand: chain 'G' and resid 151 through 152 Processing sheet with id= 20, first strand: chain 'G' and resid 188 through 193 Processing sheet with id= 21, first strand: chain 'I' and resid 41 through 45 Processing sheet with id= 22, first strand: chain 'I' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR I 80 " --> pdb=" O LEU I 107 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 112 through 113 Processing sheet with id= 24, first strand: chain 'I' and resid 151 through 152 Processing sheet with id= 25, first strand: chain 'I' and resid 188 through 193 Processing sheet with id= 26, first strand: chain 'K' and resid 41 through 45 Processing sheet with id= 27, first strand: chain 'K' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR K 80 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 112 through 113 Processing sheet with id= 29, first strand: chain 'K' and resid 151 through 152 Processing sheet with id= 30, first strand: chain 'K' and resid 188 through 193 Processing sheet with id= 31, first strand: chain 'M' and resid 41 through 45 Processing sheet with id= 32, first strand: chain 'M' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR M 80 " --> pdb=" O LEU M 107 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'M' and resid 112 through 113 Processing sheet with id= 34, first strand: chain 'M' and resid 151 through 152 Processing sheet with id= 35, first strand: chain 'M' and resid 188 through 193 Processing sheet with id= 36, first strand: chain 'O' and resid 41 through 45 Processing sheet with id= 37, first strand: chain 'O' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR O 80 " --> pdb=" O LEU O 107 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 112 through 113 Processing sheet with id= 39, first strand: chain 'O' and resid 151 through 152 Processing sheet with id= 40, first strand: chain 'O' and resid 188 through 193 Processing sheet with id= 41, first strand: chain 'Q' and resid 41 through 45 Processing sheet with id= 42, first strand: chain 'Q' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR Q 80 " --> pdb=" O LEU Q 107 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 112 through 113 Processing sheet with id= 44, first strand: chain 'Q' and resid 151 through 152 Processing sheet with id= 45, first strand: chain 'Q' and resid 188 through 193 Processing sheet with id= 46, first strand: chain 'S' and resid 41 through 45 Processing sheet with id= 47, first strand: chain 'S' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR S 80 " --> pdb=" O LEU S 107 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 112 through 113 Processing sheet with id= 49, first strand: chain 'S' and resid 151 through 152 Processing sheet with id= 50, first strand: chain 'S' and resid 188 through 193 Processing sheet with id= 51, first strand: chain 'U' and resid 41 through 45 Processing sheet with id= 52, first strand: chain 'U' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR U 80 " --> pdb=" O LEU U 107 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'U' and resid 112 through 113 Processing sheet with id= 54, first strand: chain 'U' and resid 151 through 152 Processing sheet with id= 55, first strand: chain 'U' and resid 188 through 193 Processing sheet with id= 56, first strand: chain 'W' and resid 41 through 45 Processing sheet with id= 57, first strand: chain 'W' and resid 103 through 107 removed outlier: 4.663A pdb=" N TYR W 80 " --> pdb=" O LEU W 107 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 112 through 113 Processing sheet with id= 59, first strand: chain 'W' and resid 151 through 152 Processing sheet with id= 60, first strand: chain 'W' and resid 188 through 193 2388 hydrogen bonds defined for protein. 6984 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: 14.75 Time building geometry restraints manager: 15.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13080 1.34 - 1.46: 8704 1.46 - 1.58: 19520 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 41472 Sorted by residual: bond pdb=" CA VAL F 126 " pdb=" CB VAL F 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL X 126 " pdb=" CB VAL X 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL R 126 " pdb=" CB VAL R 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL L 126 " pdb=" CB VAL L 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 bond pdb=" CA VAL D 126 " pdb=" CB VAL D 126 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.72e-02 3.38e+03 2.70e-01 ... (remaining 41467 not shown) Histogram of bond angle deviations from ideal: 100.86 - 106.97: 480 106.97 - 113.07: 22360 113.07 - 119.18: 11236 119.18 - 125.29: 21508 125.29 - 131.39: 180 Bond angle restraints: 55764 Sorted by residual: angle pdb=" CG1 ILE X 143 " pdb=" CB ILE X 143 " pdb=" CG2 ILE X 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE R 143 " pdb=" CB ILE R 143 " pdb=" CG2 ILE R 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE L 143 " pdb=" CB ILE L 143 " pdb=" CG2 ILE L 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE F 143 " pdb=" CB ILE F 143 " pdb=" CG2 ILE F 143 " ideal model delta sigma weight residual 110.70 106.09 4.61 3.00e+00 1.11e-01 2.36e+00 angle pdb=" CG1 ILE J 143 " pdb=" CB ILE J 143 " pdb=" CG2 ILE J 143 " ideal model delta sigma weight residual 110.70 106.11 4.59 3.00e+00 1.11e-01 2.34e+00 ... (remaining 55759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 23256 16.51 - 33.02: 1608 33.02 - 49.53: 324 49.53 - 66.04: 156 66.04 - 82.55: 24 Dihedral angle restraints: 25368 sinusoidal: 10572 harmonic: 14796 Sorted by residual: dihedral pdb=" CB GLU E 266 " pdb=" CG GLU E 266 " pdb=" CD GLU E 266 " pdb=" OE1 GLU E 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.55 -82.55 1 3.00e+01 1.11e-03 9.28e+00 dihedral pdb=" CB GLU W 266 " pdb=" CG GLU W 266 " pdb=" CD GLU W 266 " pdb=" OE1 GLU W 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.55 -82.55 1 3.00e+01 1.11e-03 9.28e+00 dihedral pdb=" CB GLU Q 266 " pdb=" CG GLU Q 266 " pdb=" CD GLU Q 266 " pdb=" OE1 GLU Q 266 " ideal model delta sinusoidal sigma weight residual 0.00 82.55 -82.55 1 3.00e+01 1.11e-03 9.28e+00 ... (remaining 25365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4284 0.027 - 0.053: 1244 0.053 - 0.080: 496 0.080 - 0.106: 120 0.106 - 0.133: 156 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CB ILE V 140 " pdb=" CA ILE V 140 " pdb=" CG1 ILE V 140 " pdb=" CG2 ILE V 140 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB ILE P 140 " pdb=" CA ILE P 140 " pdb=" CG1 ILE P 140 " pdb=" CG2 ILE P 140 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB ILE D 140 " pdb=" CA ILE D 140 " pdb=" CG1 ILE D 140 " pdb=" CG2 ILE D 140 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 6297 not shown) Planarity restraints: 7032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 159 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO K 160 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO K 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO K 160 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 159 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO E 160 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 160 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 160 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Q 159 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO Q 160 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO Q 160 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO Q 160 " -0.017 5.00e-02 4.00e+02 ... (remaining 7029 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 13924 2.87 - 3.37: 38392 3.37 - 3.88: 67436 3.88 - 4.39: 78492 4.39 - 4.90: 130356 Nonbonded interactions: 328600 Sorted by model distance: nonbonded pdb=" OD2 ASP U 35 " pdb=" OH TYR U 329 " model vdw 2.357 2.440 nonbonded pdb=" OD2 ASP C 35 " pdb=" OH TYR C 329 " model vdw 2.357 2.440 nonbonded pdb=" OD2 ASP O 35 " pdb=" OH TYR O 329 " model vdw 2.357 2.440 nonbonded pdb=" OD2 ASP I 35 " pdb=" OH TYR I 329 " model vdw 2.357 2.440 nonbonded pdb=" OD2 ASP E 35 " pdb=" OH TYR E 329 " model vdw 2.357 2.440 ... (remaining 328595 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 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 9.080 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 96.150 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.370 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.001 0.015 41472 Z= 0.087 Angle : 0.319 4.606 55764 Z= 0.174 Chirality : 0.036 0.133 6300 Planarity : 0.002 0.030 7032 Dihedral : 12.915 82.551 15792 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.55 (0.12), residues: 4872 helix: 1.70 (0.09), residues: 2916 sheet: -0.11 (0.22), residues: 624 loop : 0.29 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 121 PHE 0.008 0.001 PHE A 189 TYR 0.010 0.001 TYR G 177 ARG 0.002 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 924 time to evaluate : 5.280 Fit side-chains REVERT: A 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8331 (tppp) REVERT: E 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) REVERT: G 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8331 (tppp) REVERT: K 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) REVERT: M 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8332 (tppp) REVERT: Q 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) REVERT: S 86 LYS cc_start: 0.8678 (tptt) cc_final: 0.8331 (tppp) REVERT: W 111 TYR cc_start: 0.9179 (m-10) cc_final: 0.8892 (m-80) outliers start: 0 outliers final: 4 residues processed: 924 average time/residue: 1.7404 time to fit residues: 1904.2240 Evaluate side-chains 552 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 548 time to evaluate : 5.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain S residue 118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 245 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 chunk 435 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 188 ASN A 262 ASN A 314 GLN A 388 GLN B 96 ASN B 97 HIS C 48 HIS C 186 ASN C 188 ASN C 262 ASN C 314 GLN C 385 GLN C 388 GLN D 97 HIS E 121 HIS E 186 ASN E 188 ASN E 314 GLN E 320 ASN E 388 GLN F 96 ASN F 97 HIS F 99 ASN G 186 ASN G 188 ASN G 262 ASN G 314 GLN G 388 GLN H 96 ASN H 97 HIS I 48 HIS I 186 ASN I 188 ASN I 262 ASN I 314 GLN I 385 GLN I 388 GLN J 97 HIS K 186 ASN K 188 ASN K 314 GLN K 320 ASN K 388 GLN L 96 ASN L 97 HIS L 99 ASN M 186 ASN M 188 ASN M 262 ASN M 314 GLN M 388 GLN N 96 ASN N 97 HIS O 48 HIS O 186 ASN O 188 ASN O 262 ASN O 314 GLN O 385 GLN O 388 GLN P 97 HIS Q 186 ASN Q 188 ASN Q 314 GLN Q 320 ASN Q 388 GLN R 96 ASN R 97 HIS R 99 ASN S 186 ASN S 188 ASN S 262 ASN S 314 GLN S 388 GLN T 96 ASN T 97 HIS U 48 HIS U 186 ASN U 188 ASN U 262 ASN U 314 GLN U 385 GLN U 388 GLN V 97 HIS W 186 ASN W 188 ASN W 314 GLN W 320 ASN W 388 GLN X 96 ASN X 97 HIS X 99 ASN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 41472 Z= 0.393 Angle : 0.583 8.415 55764 Z= 0.320 Chirality : 0.043 0.267 6300 Planarity : 0.004 0.037 7032 Dihedral : 4.433 59.751 5444 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.90 % Allowed : 7.80 % Favored : 88.30 % 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: 1.44 (0.12), residues: 4872 helix: 1.75 (0.09), residues: 2940 sheet: -0.21 (0.21), residues: 600 loop : -0.14 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 121 PHE 0.022 0.002 PHE U 269 TYR 0.023 0.002 TYR E 177 ARG 0.006 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 596 time to evaluate : 4.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 157 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7892 (ptt90) REVERT: A 339 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: C 110 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: C 157 ARG cc_start: 0.8537 (ptp90) cc_final: 0.8254 (ptt90) REVERT: C 339 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8520 (mp-120) REVERT: E 110 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: E 111 TYR cc_start: 0.9202 (m-10) cc_final: 0.8920 (m-80) REVERT: G 110 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: G 157 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7891 (ptt90) REVERT: G 339 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: I 110 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: I 157 ARG cc_start: 0.8536 (ptp90) cc_final: 0.8253 (ptt90) REVERT: I 339 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8521 (mp-120) REVERT: K 110 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: K 111 TYR cc_start: 0.9201 (m-10) cc_final: 0.8920 (m-80) REVERT: M 110 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: M 157 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7891 (ptt90) REVERT: M 339 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: O 110 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: O 157 ARG cc_start: 0.8537 (ptp90) cc_final: 0.8254 (ptt90) REVERT: O 339 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8520 (mp-120) REVERT: Q 110 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: Q 111 TYR cc_start: 0.9201 (m-10) cc_final: 0.8920 (m-80) REVERT: S 110 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: S 157 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7891 (ptt90) REVERT: S 339 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: U 110 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: U 157 ARG cc_start: 0.8536 (ptp90) cc_final: 0.8253 (ptt90) REVERT: U 339 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8520 (mp-120) REVERT: W 110 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: W 111 TYR cc_start: 0.9202 (m-10) cc_final: 0.8921 (m-80) outliers start: 176 outliers final: 60 residues processed: 704 average time/residue: 1.6954 time to fit residues: 1417.8317 Evaluate side-chains 636 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 552 time to evaluate : 4.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 393 ASN Chi-restraints excluded: chain F residue 99 ASN Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 157 ARG Chi-restraints excluded: chain G residue 339 GLN Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 375 LYS Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain I residue 393 ASN Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 325 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain K residue 393 ASN Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 110 GLU Chi-restraints excluded: chain M residue 157 ARG Chi-restraints excluded: chain M residue 339 GLN Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 375 LYS Chi-restraints excluded: chain O residue 389 SER Chi-restraints excluded: chain O residue 393 ASN Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 325 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain Q residue 393 ASN Chi-restraints excluded: chain R residue 99 ASN Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 110 GLU Chi-restraints excluded: chain S residue 157 ARG Chi-restraints excluded: chain S residue 339 GLN Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 375 LYS Chi-restraints excluded: chain U residue 389 SER Chi-restraints excluded: chain U residue 393 ASN Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain W residue 393 ASN Chi-restraints excluded: chain X residue 99 ASN Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.0980 chunk 135 optimal weight: 0.9980 chunk 362 optimal weight: 0.0570 chunk 296 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 436 optimal weight: 9.9990 chunk 471 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 433 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 350 optimal weight: 0.0010 overall best weight: 1.0306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 262 ASN A 385 GLN A 388 GLN B 96 ASN C 388 GLN E 388 GLN F 96 ASN G 48 HIS G 262 ASN G 385 GLN G 388 GLN H 96 ASN I 388 GLN K 388 GLN L 96 ASN M 48 HIS M 262 ASN M 385 GLN M 388 GLN N 96 ASN O 388 GLN Q 388 GLN R 96 ASN S 48 HIS S 262 ASN S 385 GLN S 388 GLN T 96 ASN U 388 GLN W 121 HIS W 388 GLN X 96 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 41472 Z= 0.136 Angle : 0.452 7.518 55764 Z= 0.249 Chirality : 0.038 0.180 6300 Planarity : 0.003 0.027 7032 Dihedral : 3.787 18.685 5436 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.95 % Allowed : 11.35 % Favored : 86.70 % 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: 1.72 (0.12), residues: 4872 helix: 1.95 (0.10), residues: 2952 sheet: -0.06 (0.21), residues: 576 loop : -0.03 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS U 121 PHE 0.012 0.001 PHE U 189 TYR 0.016 0.001 TYR C 177 ARG 0.006 0.000 ARG Q 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 544 time to evaluate : 4.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 339 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8513 (mp-120) REVERT: C 399 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8618 (tmm) REVERT: E 111 TYR cc_start: 0.9181 (m-10) cc_final: 0.8847 (m-80) REVERT: E 113 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7725 (tpp-160) REVERT: I 339 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8512 (mp-120) REVERT: I 399 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8618 (tmm) REVERT: K 111 TYR cc_start: 0.9181 (m-10) cc_final: 0.8848 (m-80) REVERT: K 113 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7726 (tpp-160) REVERT: O 339 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8513 (mp-120) REVERT: O 399 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8618 (tmm) REVERT: Q 111 TYR cc_start: 0.9181 (m-10) cc_final: 0.8847 (m-80) REVERT: Q 113 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7725 (tpp-160) REVERT: U 339 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8512 (mp-120) REVERT: U 399 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8619 (tmm) REVERT: W 111 TYR cc_start: 0.9181 (m-10) cc_final: 0.8847 (m-80) REVERT: W 113 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7725 (tpp-160) outliers start: 88 outliers final: 24 residues processed: 604 average time/residue: 1.6279 time to fit residues: 1178.2336 Evaluate side-chains 556 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 524 time to evaluate : 4.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 141 SER Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 325 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 141 SER Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 325 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 141 SER Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 226 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 208 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 438 optimal weight: 20.0000 chunk 463 optimal weight: 0.1980 chunk 228 optimal weight: 5.9990 chunk 415 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 388 GLN C 262 ASN C 388 GLN E 388 GLN F 96 ASN G 385 GLN G 388 GLN I 262 ASN I 388 GLN K 264 ASN K 388 GLN L 96 ASN M 385 GLN M 388 GLN O 262 ASN O 388 GLN Q 388 GLN R 96 ASN S 385 GLN S 388 GLN U 262 ASN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41472 Z= 0.184 Angle : 0.475 8.479 55764 Z= 0.258 Chirality : 0.039 0.164 6300 Planarity : 0.003 0.025 7032 Dihedral : 3.814 19.611 5436 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.39 % Allowed : 11.35 % Favored : 86.26 % 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: 1.61 (0.12), residues: 4872 helix: 1.89 (0.10), residues: 2964 sheet: -0.09 (0.21), residues: 576 loop : -0.16 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 121 PHE 0.013 0.001 PHE U 269 TYR 0.020 0.001 TYR A 177 ARG 0.004 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 508 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8881 (m-40) REVERT: C 339 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8565 (mp-120) REVERT: C 399 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8657 (tmm) REVERT: E 111 TYR cc_start: 0.9186 (m-10) cc_final: 0.8865 (m-80) REVERT: G 64 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8881 (m-40) REVERT: I 339 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8566 (mp-120) REVERT: I 399 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8658 (tmm) REVERT: K 111 TYR cc_start: 0.9187 (m-10) cc_final: 0.8866 (m-80) REVERT: M 64 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8881 (m-40) REVERT: O 339 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8566 (mp-120) REVERT: O 399 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8658 (tmm) REVERT: Q 111 TYR cc_start: 0.9187 (m-10) cc_final: 0.8865 (m-80) REVERT: S 64 ASN cc_start: 0.9114 (OUTLIER) cc_final: 0.8882 (m-40) REVERT: U 339 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8565 (mp-120) REVERT: U 399 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8658 (tmm) REVERT: W 111 TYR cc_start: 0.9187 (m-10) cc_final: 0.8866 (m-80) outliers start: 108 outliers final: 40 residues processed: 596 average time/residue: 1.6399 time to fit residues: 1173.3906 Evaluate side-chains 548 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 496 time to evaluate : 5.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 325 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 118 ASP Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain Q residue 64 ASN Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 325 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain W residue 64 ASN Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 395 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 416 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 385 GLN A 388 GLN C 262 ASN C 359 ASN C 388 GLN E 359 ASN E 388 GLN F 96 ASN G 359 ASN G 385 GLN G 388 GLN I 262 ASN I 359 ASN I 388 GLN K 264 ASN K 359 ASN K 388 GLN L 96 ASN M 359 ASN M 385 GLN M 388 GLN O 262 ASN O 359 ASN O 388 GLN Q 388 GLN R 96 ASN ** S 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 385 GLN S 388 GLN U 262 ASN U 359 ASN U 388 GLN W 359 ASN W 388 GLN X 96 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 41472 Z= 0.290 Angle : 0.509 6.860 55764 Z= 0.282 Chirality : 0.040 0.145 6300 Planarity : 0.003 0.030 7032 Dihedral : 3.987 20.183 5436 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.86 % Allowed : 11.41 % Favored : 85.73 % 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: 1.39 (0.12), residues: 4872 helix: 1.75 (0.10), residues: 2952 sheet: -0.28 (0.21), residues: 600 loop : -0.27 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS U 121 PHE 0.018 0.001 PHE U 269 TYR 0.023 0.002 TYR K 177 ARG 0.003 0.000 ARG J 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 508 time to evaluate : 4.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8890 (m-40) REVERT: A 399 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8646 (tmm) REVERT: C 157 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8285 (ptt90) REVERT: C 339 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8508 (mp-120) REVERT: C 399 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8663 (tmm) REVERT: E 110 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: G 64 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8890 (m-40) REVERT: G 399 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8646 (tmm) REVERT: I 157 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8285 (ptt90) REVERT: I 339 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8510 (mp-120) REVERT: I 399 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8663 (tmm) REVERT: K 110 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: M 64 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8890 (m-40) REVERT: M 399 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8645 (tmm) REVERT: O 157 ARG cc_start: 0.8557 (ptp90) cc_final: 0.8285 (ptt90) REVERT: O 339 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8509 (mp-120) REVERT: O 399 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8664 (tmm) REVERT: Q 110 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: S 64 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8891 (m-40) REVERT: S 399 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8645 (tmm) REVERT: U 157 ARG cc_start: 0.8558 (ptp90) cc_final: 0.8285 (ptt90) REVERT: U 339 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8509 (mp-120) REVERT: U 399 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8664 (tmm) REVERT: W 110 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8079 (mp0) outliers start: 129 outliers final: 49 residues processed: 593 average time/residue: 1.6517 time to fit residues: 1172.4622 Evaluate side-chains 565 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 496 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain G residue 393 ASN Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 325 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 325 ASP Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 393 ASN Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 325 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 325 ASP Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain S residue 393 ASN Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 6.9990 chunk 417 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 464 optimal weight: 4.9990 chunk 385 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 385 GLN A 388 GLN C 262 ASN C 388 GLN E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 GLN G 388 GLN I 262 ASN I 388 GLN K 264 ASN K 388 GLN L 96 ASN ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 ASN M 385 GLN M 388 GLN O 262 ASN O 388 GLN Q 359 ASN Q 388 GLN R 96 ASN ** S 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 359 ASN S 385 GLN S 388 GLN U 262 ASN U 388 GLN W 264 ASN W 388 GLN X 96 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 41472 Z= 0.306 Angle : 0.531 8.971 55764 Z= 0.292 Chirality : 0.041 0.263 6300 Planarity : 0.003 0.030 7032 Dihedral : 4.031 20.207 5436 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.55 % Allowed : 12.03 % Favored : 85.42 % 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: 1.28 (0.12), residues: 4872 helix: 1.69 (0.10), residues: 2952 sheet: -0.19 (0.21), residues: 600 loop : -0.47 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS I 121 PHE 0.018 0.001 PHE G 269 TYR 0.024 0.002 TYR E 177 ARG 0.003 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 492 time to evaluate : 4.731 Fit side-chains REVERT: A 64 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8895 (m-40) REVERT: A 399 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8644 (tmm) REVERT: C 110 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: C 157 ARG cc_start: 0.8571 (ptp90) cc_final: 0.8310 (ptt90) REVERT: C 339 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8534 (mp-120) REVERT: C 399 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (tmm) REVERT: E 110 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: E 111 TYR cc_start: 0.9219 (m-80) cc_final: 0.8994 (m-80) REVERT: G 64 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8895 (m-40) REVERT: G 399 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8644 (tmm) REVERT: I 110 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: I 157 ARG cc_start: 0.8571 (ptp90) cc_final: 0.8311 (ptt90) REVERT: I 339 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8533 (mp-120) REVERT: I 399 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (tmm) REVERT: K 110 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: K 111 TYR cc_start: 0.9220 (m-80) cc_final: 0.8995 (m-80) REVERT: M 64 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8896 (m-40) REVERT: M 399 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8644 (tmm) REVERT: O 110 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: O 157 ARG cc_start: 0.8571 (ptp90) cc_final: 0.8310 (ptt90) REVERT: O 339 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8533 (mp-120) REVERT: O 399 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (tmm) REVERT: Q 110 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: Q 111 TYR cc_start: 0.9219 (m-80) cc_final: 0.8994 (m-80) REVERT: S 64 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8895 (m-40) REVERT: S 399 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8644 (tmm) REVERT: U 110 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: U 157 ARG cc_start: 0.8571 (ptp90) cc_final: 0.8310 (ptt90) REVERT: U 339 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8534 (mp-120) REVERT: U 399 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8652 (tmm) REVERT: W 110 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: W 111 TYR cc_start: 0.9219 (m-80) cc_final: 0.8995 (m-80) outliers start: 115 outliers final: 55 residues processed: 575 average time/residue: 1.6270 time to fit residues: 1121.3704 Evaluate side-chains 575 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 496 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 389 SER Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 325 ASP Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 389 SER Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 325 ASP Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 389 SER Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain W residue 110 GLU Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 339 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 390 optimal weight: 6.9990 chunk 259 optimal weight: 4.9990 chunk 462 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 264 ASN A 385 GLN A 388 GLN C 186 ASN C 388 GLN E 264 ASN E 388 GLN F 96 ASN G 121 HIS G 186 ASN G 264 ASN G 385 GLN G 388 GLN I 186 ASN I 264 ASN I 388 GLN K 388 GLN L 96 ASN M 121 HIS M 264 ASN M 385 GLN M 388 GLN O 186 ASN O 264 ASN O 388 GLN Q 264 ASN Q 388 GLN R 96 ASN S 121 HIS S 186 ASN S 264 ASN S 385 GLN S 388 GLN U 186 ASN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41472 Z= 0.204 Angle : 0.493 9.290 55764 Z= 0.272 Chirality : 0.040 0.159 6300 Planarity : 0.003 0.024 7032 Dihedral : 3.919 19.728 5436 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.13 % Allowed : 12.63 % Favored : 85.24 % 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: 1.53 (0.12), residues: 4872 helix: 1.92 (0.10), residues: 2940 sheet: 0.12 (0.22), residues: 576 loop : -0.53 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 121 PHE 0.013 0.001 PHE O 189 TYR 0.021 0.001 TYR E 177 ARG 0.003 0.000 ARG P 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 496 time to evaluate : 4.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8880 (m-40) REVERT: A 399 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (tmm) REVERT: C 157 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8276 (ptt90) REVERT: C 339 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8536 (mp-120) REVERT: C 399 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8640 (tmm) REVERT: E 111 TYR cc_start: 0.9198 (m-80) cc_final: 0.8971 (m-80) REVERT: E 113 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7766 (tpp-160) REVERT: E 399 MET cc_start: 0.8675 (tmt) cc_final: 0.8450 (tmm) REVERT: G 64 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8881 (m-40) REVERT: G 399 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (tmm) REVERT: I 157 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8275 (ptt90) REVERT: I 339 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8536 (mp-120) REVERT: I 399 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8641 (tmm) REVERT: K 111 TYR cc_start: 0.9198 (m-80) cc_final: 0.8971 (m-80) REVERT: K 113 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7766 (tpp-160) REVERT: K 399 MET cc_start: 0.8675 (tmt) cc_final: 0.8449 (tmm) REVERT: M 64 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8881 (m-40) REVERT: M 399 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8629 (tmm) REVERT: O 157 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8275 (ptt90) REVERT: O 339 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8536 (mp-120) REVERT: O 399 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8641 (tmm) REVERT: Q 111 TYR cc_start: 0.9194 (m-80) cc_final: 0.8966 (m-80) REVERT: Q 113 ARG cc_start: 0.7979 (tpp-160) cc_final: 0.7764 (tpp-160) REVERT: Q 399 MET cc_start: 0.8675 (tmt) cc_final: 0.8449 (tmm) REVERT: S 64 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8881 (m-40) REVERT: S 399 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8628 (tmm) REVERT: U 157 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8275 (ptt90) REVERT: U 339 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8535 (mp-120) REVERT: U 399 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8641 (tmm) REVERT: W 111 TYR cc_start: 0.9194 (m-80) cc_final: 0.8966 (m-80) REVERT: W 113 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7764 (tpp-160) REVERT: W 399 MET cc_start: 0.8675 (tmt) cc_final: 0.8450 (tmm) outliers start: 96 outliers final: 48 residues processed: 552 average time/residue: 1.6182 time to fit residues: 1073.6536 Evaluate side-chains 552 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 484 time to evaluate : 5.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 64 ASN Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 157 ARG Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 64 ASN Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 157 ARG Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 363 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN A 388 GLN C 388 GLN E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 GLN G 388 GLN I 264 ASN I 388 GLN K 388 GLN L 96 ASN ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 264 ASN M 385 GLN M 388 GLN O 186 ASN O 264 ASN O 388 GLN Q 388 GLN R 96 ASN ** S 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 385 GLN S 388 GLN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41472 Z= 0.304 Angle : 0.524 10.933 55764 Z= 0.290 Chirality : 0.041 0.180 6300 Planarity : 0.003 0.030 7032 Dihedral : 4.039 20.475 5436 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.30 % Allowed : 12.37 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.12), residues: 4872 helix: 1.79 (0.10), residues: 2928 sheet: -0.11 (0.22), residues: 600 loop : -0.60 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS U 121 PHE 0.017 0.001 PHE A 269 TYR 0.024 0.001 TYR W 177 ARG 0.003 0.000 ARG J 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 496 time to evaluate : 4.663 Fit side-chains REVERT: C 110 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: C 157 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8340 (ptt90) REVERT: C 339 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8529 (mp-120) REVERT: C 399 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8631 (tmm) REVERT: D 156 LYS cc_start: 0.8018 (mptt) cc_final: 0.7664 (mttt) REVERT: E 111 TYR cc_start: 0.9212 (m-80) cc_final: 0.8978 (m-80) REVERT: F 156 LYS cc_start: 0.8050 (mppt) cc_final: 0.7762 (mtmt) REVERT: I 110 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: I 157 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8341 (ptt90) REVERT: I 339 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8529 (mp-120) REVERT: I 399 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8631 (tmm) REVERT: J 156 LYS cc_start: 0.8018 (mptt) cc_final: 0.7664 (mttt) REVERT: K 111 TYR cc_start: 0.9212 (m-80) cc_final: 0.8977 (m-80) REVERT: L 156 LYS cc_start: 0.8050 (mppt) cc_final: 0.7762 (mtmt) REVERT: O 110 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: O 157 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8341 (ptt90) REVERT: O 339 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8529 (mp-120) REVERT: O 399 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8631 (tmm) REVERT: P 156 LYS cc_start: 0.8018 (mptt) cc_final: 0.7664 (mttt) REVERT: Q 111 TYR cc_start: 0.9212 (m-80) cc_final: 0.8977 (m-80) REVERT: R 156 LYS cc_start: 0.8050 (mppt) cc_final: 0.7762 (mtmt) REVERT: U 110 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: U 157 ARG cc_start: 0.8569 (ptp90) cc_final: 0.8339 (ptt90) REVERT: U 339 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8529 (mp-120) REVERT: U 399 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8631 (tmm) REVERT: V 156 LYS cc_start: 0.8020 (mptt) cc_final: 0.7665 (mttt) REVERT: W 111 TYR cc_start: 0.9213 (m-80) cc_final: 0.8977 (m-80) REVERT: X 156 LYS cc_start: 0.8050 (mppt) cc_final: 0.7761 (mtmt) outliers start: 104 outliers final: 64 residues processed: 568 average time/residue: 1.7015 time to fit residues: 1161.4188 Evaluate side-chains 560 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 484 time to evaluate : 4.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 325 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 110 GLU Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 118 ASP Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 325 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 110 GLU Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 118 ASP Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 2.9990 chunk 443 optimal weight: 8.9990 chunk 404 optimal weight: 7.9990 chunk 431 optimal weight: 9.9990 chunk 259 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 338 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 389 optimal weight: 0.8980 chunk 407 optimal weight: 0.7980 chunk 429 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 385 GLN A 388 GLN C 264 ASN C 320 ASN C 388 GLN E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 GLN G 388 GLN I 264 ASN I 320 ASN I 388 GLN K 388 GLN L 96 ASN ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 264 ASN M 385 GLN M 388 GLN O 186 ASN O 264 ASN O 320 ASN O 388 GLN Q 388 GLN R 96 ASN S 121 HIS S 385 GLN S 388 GLN U 264 ASN U 320 ASN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 41472 Z= 0.158 Angle : 0.471 9.916 55764 Z= 0.262 Chirality : 0.039 0.159 6300 Planarity : 0.002 0.025 7032 Dihedral : 3.859 19.800 5436 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.75 % Allowed : 13.23 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.12), residues: 4872 helix: 2.03 (0.10), residues: 2940 sheet: 0.19 (0.22), residues: 576 loop : -0.50 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 121 PHE 0.012 0.001 PHE O 189 TYR 0.019 0.001 TYR I 177 ARG 0.003 0.000 ARG E 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 494 time to evaluate : 4.882 Fit side-chains REVERT: C 157 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8256 (ptt90) REVERT: C 339 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8518 (mp-120) REVERT: C 399 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8630 (tmm) REVERT: D 156 LYS cc_start: 0.7997 (mptt) cc_final: 0.7668 (mttt) REVERT: E 111 TYR cc_start: 0.9209 (m-80) cc_final: 0.9005 (m-80) REVERT: E 113 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7744 (tpp-160) REVERT: F 156 LYS cc_start: 0.8010 (mppt) cc_final: 0.7738 (mtmt) REVERT: I 157 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8257 (ptt90) REVERT: I 339 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8518 (mp-120) REVERT: I 399 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8630 (tmm) REVERT: J 156 LYS cc_start: 0.7997 (mptt) cc_final: 0.7669 (mttt) REVERT: K 111 TYR cc_start: 0.9209 (m-80) cc_final: 0.9005 (m-80) REVERT: K 113 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7742 (tpp-160) REVERT: L 156 LYS cc_start: 0.8010 (mppt) cc_final: 0.7738 (mtmt) REVERT: O 157 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8256 (ptt90) REVERT: O 339 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8519 (mp-120) REVERT: O 399 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8630 (tmm) REVERT: P 156 LYS cc_start: 0.7996 (mptt) cc_final: 0.7667 (mttt) REVERT: Q 111 TYR cc_start: 0.9209 (m-80) cc_final: 0.9006 (m-80) REVERT: Q 113 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7742 (tpp-160) REVERT: R 156 LYS cc_start: 0.8010 (mppt) cc_final: 0.7737 (mtmt) REVERT: U 157 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8257 (ptt90) REVERT: U 339 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8518 (mp-120) REVERT: U 399 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8631 (tmm) REVERT: V 156 LYS cc_start: 0.7996 (mptt) cc_final: 0.7667 (mttt) REVERT: W 111 TYR cc_start: 0.9209 (m-80) cc_final: 0.9005 (m-80) REVERT: W 113 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7742 (tpp-160) REVERT: X 156 LYS cc_start: 0.8010 (mppt) cc_final: 0.7737 (mtmt) outliers start: 79 outliers final: 56 residues processed: 545 average time/residue: 1.6802 time to fit residues: 1093.5813 Evaluate side-chains 544 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 476 time to evaluate : 4.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 157 ARG Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 325 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 157 ARG Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 325 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 157 ARG Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 325 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 278 optimal weight: 20.0000 chunk 216 optimal weight: 0.0670 chunk 316 optimal weight: 10.0000 chunk 478 optimal weight: 5.9990 chunk 440 optimal weight: 6.9990 chunk 380 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN A 388 GLN C 48 HIS C 264 ASN C 388 GLN E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 GLN G 388 GLN I 48 HIS I 264 ASN I 388 GLN K 388 GLN L 96 ASN ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 385 GLN M 388 GLN O 48 HIS O 264 ASN O 388 GLN Q 388 GLN R 96 ASN ** S 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 385 GLN S 388 GLN U 48 HIS U 264 ASN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41472 Z= 0.282 Angle : 0.534 9.607 55764 Z= 0.293 Chirality : 0.041 0.209 6300 Planarity : 0.003 0.027 7032 Dihedral : 4.017 20.768 5436 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 13.45 % Favored : 85.11 % 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: 1.47 (0.12), residues: 4872 helix: 1.86 (0.10), residues: 2940 sheet: 0.19 (0.22), residues: 576 loop : -0.57 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 121 PHE 0.016 0.001 PHE S 269 TYR 0.023 0.001 TYR W 177 ARG 0.002 0.000 ARG J 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9744 Ramachandran restraints generated. 4872 Oldfield, 0 Emsley, 4872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 484 time to evaluate : 5.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: C 157 ARG cc_start: 0.8560 (ptp90) cc_final: 0.8307 (ptt90) REVERT: C 339 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8538 (mp-120) REVERT: C 399 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8635 (tmm) REVERT: D 156 LYS cc_start: 0.8035 (mptt) cc_final: 0.7670 (mttt) REVERT: E 111 TYR cc_start: 0.9205 (m-80) cc_final: 0.8982 (m-80) REVERT: E 158 TYR cc_start: 0.8852 (m-80) cc_final: 0.8579 (m-80) REVERT: I 157 ARG cc_start: 0.8560 (ptp90) cc_final: 0.8307 (ptt90) REVERT: I 339 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8538 (mp-120) REVERT: I 399 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8629 (tmm) REVERT: J 156 LYS cc_start: 0.8036 (mptt) cc_final: 0.7671 (mttt) REVERT: K 111 TYR cc_start: 0.9205 (m-80) cc_final: 0.8982 (m-80) REVERT: K 158 TYR cc_start: 0.8852 (m-80) cc_final: 0.8580 (m-80) REVERT: O 157 ARG cc_start: 0.8560 (ptp90) cc_final: 0.8306 (ptt90) REVERT: O 339 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8538 (mp-120) REVERT: O 399 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8629 (tmm) REVERT: P 156 LYS cc_start: 0.8035 (mptt) cc_final: 0.7669 (mttt) REVERT: Q 111 TYR cc_start: 0.9205 (m-80) cc_final: 0.8982 (m-80) REVERT: Q 158 TYR cc_start: 0.8854 (m-80) cc_final: 0.8579 (m-80) REVERT: U 157 ARG cc_start: 0.8560 (ptp90) cc_final: 0.8307 (ptt90) REVERT: U 339 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8538 (mp-120) REVERT: U 399 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8631 (tmm) REVERT: V 156 LYS cc_start: 0.8036 (mptt) cc_final: 0.7670 (mttt) REVERT: W 111 TYR cc_start: 0.9204 (m-80) cc_final: 0.8981 (m-80) REVERT: W 158 TYR cc_start: 0.8852 (m-80) cc_final: 0.8580 (m-80) outliers start: 65 outliers final: 56 residues processed: 525 average time/residue: 1.6754 time to fit residues: 1050.4246 Evaluate side-chains 541 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 476 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain G residue 389 SER Chi-restraints excluded: chain G residue 399 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 159 ILE Chi-restraints excluded: chain I residue 64 ASN Chi-restraints excluded: chain I residue 98 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 339 GLN Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 151 LEU Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 118 ASP Chi-restraints excluded: chain K residue 389 SER Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain M residue 389 SER Chi-restraints excluded: chain M residue 399 MET Chi-restraints excluded: chain N residue 141 SER Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain O residue 64 ASN Chi-restraints excluded: chain O residue 98 ILE Chi-restraints excluded: chain O residue 117 VAL Chi-restraints excluded: chain O residue 325 ASP Chi-restraints excluded: chain O residue 339 GLN Chi-restraints excluded: chain O residue 399 MET Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 118 ASP Chi-restraints excluded: chain Q residue 389 SER Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain S residue 389 SER Chi-restraints excluded: chain S residue 399 MET Chi-restraints excluded: chain T residue 141 SER Chi-restraints excluded: chain T residue 159 ILE Chi-restraints excluded: chain U residue 64 ASN Chi-restraints excluded: chain U residue 98 ILE Chi-restraints excluded: chain U residue 117 VAL Chi-restraints excluded: chain U residue 325 ASP Chi-restraints excluded: chain U residue 339 GLN Chi-restraints excluded: chain U residue 399 MET Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 118 ASP Chi-restraints excluded: chain W residue 389 SER Chi-restraints excluded: chain X residue 141 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.6980 chunk 405 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 381 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 391 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 385 GLN A 388 GLN C 264 ASN C 388 GLN E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 GLN G 388 GLN I 388 GLN K 388 GLN L 96 ASN ** M 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 385 GLN M 388 GLN O 264 ASN O 388 GLN Q 388 GLN R 96 ASN S 121 HIS S 385 GLN S 388 GLN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.071727 restraints weight = 62744.733| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.42 r_work: 0.2627 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41472 Z= 0.209 Angle : 0.524 11.840 55764 Z= 0.288 Chirality : 0.040 0.248 6300 Planarity : 0.003 0.023 7032 Dihedral : 3.947 20.493 5436 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.80 % Allowed : 13.45 % Favored : 84.75 % 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: 1.80 (0.12), residues: 4872 helix: 2.08 (0.10), residues: 2868 sheet: 0.22 (0.22), residues: 576 loop : -0.16 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS I 121 PHE 0.013 0.001 PHE A 269 TYR 0.021 0.001 TYR E 177 ARG 0.003 0.000 ARG Q 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18467.40 seconds wall clock time: 325 minutes 19.86 seconds (19519.86 seconds total)