Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 25 13:05:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/08_2023/8php_17670.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/08_2023/8php_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_17670/08_2023/8php_17670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/08_2023/8php_17670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/08_2023/8php_17670.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8php_17670/08_2023/8php_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 19.41, per 1000 atoms: 0.48 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: 15.04 Conformation dependent library (CDL) restraints added in 5.2 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: 3.78 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: 14.32 Time building geometry restraints manager: 16.16 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 10.380 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 94.440 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.360 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.910 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 4.608 Fit side-chains outliers start: 0 outliers final: 4 residues processed: 924 average time/residue: 1.7604 time to fit residues: 1924.6672 Evaluate side-chains 544 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 540 time to evaluate : 4.888 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 4 average time/residue: 0.4952 time to fit residues: 10.0975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 41472 Z= 0.392 Angle : 0.581 8.502 55764 Z= 0.320 Chirality : 0.043 0.269 6300 Planarity : 0.004 0.039 7032 Dihedral : 4.078 22.133 5436 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 3.86 % 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: 1.77 (0.09), residues: 2940 sheet: -0.21 (0.21), residues: 600 loop : -0.11 (0.16), residues: 1332 *********************** 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 761 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 587 time to evaluate : 5.154 Fit side-chains outliers start: 174 outliers final: 60 residues processed: 691 average time/residue: 1.7449 time to fit residues: 1433.2932 Evaluate side-chains 612 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 552 time to evaluate : 4.921 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 36 residues processed: 24 average time/residue: 0.4288 time to fit residues: 24.5797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 362 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 436 optimal weight: 9.9990 chunk 471 optimal weight: 3.9990 chunk 388 optimal weight: 0.8980 chunk 433 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 350 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 262 ASN C 388 GLN E 388 GLN F 96 ASN F 99 ASN G 48 HIS G 262 ASN G 385 GLN G 388 GLN H 96 ASN I 262 ASN I 388 GLN K 388 GLN L 96 ASN L 99 ASN M 48 HIS M 262 ASN M 385 GLN M 388 GLN N 96 ASN O 262 ASN O 388 GLN Q 388 GLN R 96 ASN R 99 ASN S 48 HIS S 262 ASN S 385 GLN S 388 GLN T 96 ASN U 262 ASN U 388 GLN W 388 GLN X 96 ASN X 99 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 41472 Z= 0.156 Angle : 0.473 7.722 55764 Z= 0.260 Chirality : 0.039 0.184 6300 Planarity : 0.003 0.027 7032 Dihedral : 3.855 19.482 5436 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 2.30 % 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: 1.56 (0.12), residues: 4872 helix: 1.90 (0.10), residues: 2952 sheet: -0.31 (0.21), residues: 600 loop : -0.20 (0.16), residues: 1320 *********************** 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 656 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 552 time to evaluate : 4.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 36 residues processed: 632 average time/residue: 1.6851 time to fit residues: 1286.9122 Evaluate side-chains 568 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 532 time to evaluate : 4.967 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.4232 time to fit residues: 13.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 0.0770 chunk 328 optimal weight: 20.0000 chunk 226 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 208 optimal weight: 8.9990 chunk 293 optimal weight: 0.6980 chunk 438 optimal weight: 20.0000 chunk 463 optimal weight: 0.0470 chunk 228 optimal weight: 4.9990 chunk 415 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 385 GLN B 96 ASN C 388 GLN E 264 ASN E 388 GLN F 96 ASN G 264 ASN G 385 GLN H 96 ASN I 264 ASN I 388 GLN K 264 ASN K 388 GLN L 96 ASN M 264 ASN M 385 GLN N 96 ASN O 388 GLN Q 264 ASN Q 388 GLN R 96 ASN S 264 ASN S 385 GLN T 96 ASN U 388 GLN W 264 ASN W 388 GLN X 96 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 41472 Z= 0.115 Angle : 0.435 9.251 55764 Z= 0.237 Chirality : 0.037 0.156 6300 Planarity : 0.002 0.027 7032 Dihedral : 3.680 18.966 5436 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.42 % 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: 1.76 (0.12), residues: 4872 helix: 2.00 (0.10), residues: 2964 sheet: -0.12 (0.20), residues: 600 loop : -0.04 (0.16), residues: 1308 *********************** 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 608 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 544 time to evaluate : 4.782 Fit side-chains outliers start: 64 outliers final: 24 residues processed: 596 average time/residue: 1.7655 time to fit residues: 1253.5170 Evaluate side-chains 536 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 512 time to evaluate : 5.259 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.3940 time to fit residues: 9.5160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 345 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 395 optimal weight: 3.9990 chunk 320 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 416 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 359 ASN A 388 GLN C 314 GLN C 359 ASN C 388 GLN E 264 ASN E 388 GLN F 96 ASN G 264 ASN G 359 ASN G 388 GLN I 264 ASN I 314 GLN I 359 ASN I 388 GLN K 264 ASN K 388 GLN L 96 ASN M 264 ASN M 359 ASN M 388 GLN O 314 GLN O 388 GLN Q 264 ASN Q 388 GLN R 96 ASN S 264 ASN S 388 GLN U 314 GLN U 388 GLN W 264 ASN W 388 GLN X 96 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3113 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= 0.364 Angle : 0.545 7.356 55764 Z= 0.299 Chirality : 0.041 0.147 6300 Planarity : 0.003 0.036 7032 Dihedral : 4.021 20.715 5436 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 2.48 % 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: 1.74 (0.10), residues: 2952 sheet: -0.25 (0.21), residues: 600 loop : -0.25 (0.16), residues: 1320 *********************** 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 608 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 496 time to evaluate : 5.205 Fit side-chains outliers start: 112 outliers final: 48 residues processed: 580 average time/residue: 1.7489 time to fit residues: 1210.6615 Evaluate side-chains 552 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 504 time to evaluate : 4.954 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 4 average time/residue: 0.4100 time to fit residues: 9.8086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 91 optimal weight: 0.1980 chunk 272 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 464 optimal weight: 4.9990 chunk 385 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 186 ASN A 385 GLN A 388 GLN C 388 GLN E 188 ASN E 264 ASN E 359 ASN E 385 GLN E 388 GLN F 96 ASN G 186 ASN G 385 GLN G 388 GLN I 388 GLN K 264 ASN K 359 ASN K 385 GLN 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 359 ASN O 388 GLN Q 264 ASN Q 359 ASN Q 385 GLN Q 388 GLN R 96 ASN S 121 HIS S 186 ASN S 359 ASN S 385 GLN S 388 GLN U 359 ASN U 388 GLN W 264 ASN W 359 ASN W 385 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 41472 Z= 0.249 Angle : 0.507 8.708 55764 Z= 0.279 Chirality : 0.040 0.148 6300 Planarity : 0.003 0.026 7032 Dihedral : 3.957 19.679 5436 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 2.30 % 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: 1.48 (0.12), residues: 4872 helix: 1.83 (0.10), residues: 2940 sheet: 0.03 (0.21), residues: 576 loop : -0.40 (0.15), residues: 1356 *********************** 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 612 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 508 time to evaluate : 5.036 Fit side-chains outliers start: 104 outliers final: 56 residues processed: 580 average time/residue: 1.6650 time to fit residues: 1161.2283 Evaluate side-chains 544 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 488 time to evaluate : 4.760 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 44 residues processed: 12 average time/residue: 0.7043 time to fit residues: 18.7862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 264 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 390 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 320 ASN C 388 GLN E 385 GLN E 388 GLN F 96 ASN G 121 HIS G 264 ASN G 385 GLN G 388 GLN I 264 ASN I 320 ASN I 388 GLN K 385 GLN K 388 GLN L 96 ASN M 121 HIS M 264 ASN M 385 GLN M 388 GLN O 264 ASN O 320 ASN O 388 GLN Q 385 GLN Q 388 GLN R 96 ASN S 121 HIS S 264 ASN S 385 GLN S 388 GLN U 320 ASN U 388 GLN W 385 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 41472 Z= 0.159 Angle : 0.493 11.064 55764 Z= 0.268 Chirality : 0.039 0.200 6300 Planarity : 0.003 0.025 7032 Dihedral : 3.829 19.530 5436 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.12), residues: 4872 helix: 2.02 (0.10), residues: 2940 sheet: 0.07 (0.21), residues: 576 loop : -0.35 (0.16), residues: 1356 *********************** 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 572 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 492 time to evaluate : 4.712 Fit side-chains outliers start: 80 outliers final: 52 residues processed: 552 average time/residue: 1.7790 time to fit residues: 1173.5932 Evaluate side-chains 540 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 488 time to evaluate : 4.853 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 44 residues processed: 8 average time/residue: 0.3725 time to fit residues: 12.1977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 276 optimal weight: 20.0000 chunk 139 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 388 GLN E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN 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 264 ASN O 388 GLN Q 388 GLN R 96 ASN S 121 HIS S 264 ASN S 385 GLN S 388 GLN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 41472 Z= 0.256 Angle : 0.525 10.306 55764 Z= 0.286 Chirality : 0.040 0.155 6300 Planarity : 0.003 0.025 7032 Dihedral : 3.947 20.603 5436 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 2.15 % 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: 1.52 (0.12), residues: 4872 helix: 1.88 (0.10), residues: 2940 sheet: 0.08 (0.21), residues: 576 loop : -0.42 (0.16), residues: 1356 *********************** 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 589 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 492 time to evaluate : 4.688 Fit side-chains outliers start: 97 outliers final: 56 residues processed: 560 average time/residue: 1.6838 time to fit residues: 1133.9265 Evaluate side-chains 532 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 476 time to evaluate : 4.612 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 44 residues processed: 12 average time/residue: 0.3646 time to fit residues: 14.9723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 404 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 187 optimal weight: 9.9990 chunk 338 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 389 optimal weight: 0.9990 chunk 407 optimal weight: 0.0020 chunk 429 optimal weight: 1.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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 48 HIS C 264 ASN C 388 GLN E 385 GLN E 388 GLN F 96 ASN G 121 HIS G 264 ASN G 385 GLN G 388 GLN I 48 HIS I 264 ASN I 388 GLN K 385 GLN K 388 GLN L 96 ASN M 121 HIS M 264 ASN M 385 GLN M 388 GLN O 48 HIS O 264 ASN O 388 GLN Q 385 GLN Q 388 GLN R 96 ASN S 121 HIS S 264 ASN S 385 GLN S 388 GLN U 48 HIS U 186 ASN U 388 GLN W 385 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 41472 Z= 0.174 Angle : 0.488 11.238 55764 Z= 0.268 Chirality : 0.038 0.149 6300 Planarity : 0.003 0.025 7032 Dihedral : 3.859 20.644 5436 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 1.42 % 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: 1.69 (0.12), residues: 4872 helix: 2.03 (0.10), residues: 2940 sheet: 0.14 (0.22), residues: 576 loop : -0.41 (0.16), residues: 1356 *********************** 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 540 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 476 time to evaluate : 4.823 Fit side-chains outliers start: 64 outliers final: 44 residues processed: 524 average time/residue: 1.8081 time to fit residues: 1129.4742 Evaluate side-chains 516 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 472 time to evaluate : 4.792 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 4 average time/residue: 0.3948 time to fit residues: 9.2793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 10.0000 chunk 455 optimal weight: 0.9990 chunk 278 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 478 optimal weight: 10.0000 chunk 440 optimal weight: 5.9990 chunk 380 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 48 HIS C 186 ASN C 264 ASN C 388 GLN E 388 GLN F 96 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN 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 264 ASN 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 264 ASN S 385 GLN S 388 GLN U 48 HIS U 186 ASN U 388 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 41472 Z= 0.326 Angle : 0.562 11.352 55764 Z= 0.305 Chirality : 0.041 0.225 6300 Planarity : 0.003 0.031 7032 Dihedral : 4.049 21.738 5436 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.12), residues: 4872 helix: 1.82 (0.10), residues: 2940 sheet: 0.16 (0.22), residues: 576 loop : -0.52 (0.15), residues: 1356 ********************** 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 540 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 480 time to evaluate : 5.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 44 residues processed: 532 average time/residue: 1.7330 time to fit residues: 1107.5660 Evaluate side-chains 516 residues out of total 4512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 472 time to evaluate : 4.870 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 40 residues processed: 8 average time/residue: 0.4002 time to fit residues: 12.5202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.9980 chunk 405 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 381 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 391 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 264 ASN C 388 GLN E 385 GLN E 388 GLN F 96 ASN G 121 HIS G 264 ASN G 385 GLN G 388 GLN I 264 ASN I 388 GLN K 385 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 385 GLN Q 388 GLN R 96 ASN S 121 HIS S 264 ASN S 385 GLN S 388 GLN U 264 ASN U 388 GLN W 385 GLN W 388 GLN X 96 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.121632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.076034 restraints weight = 62550.860| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.38 r_work: 0.2711 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 41472 Z= 0.130 Angle : 0.471 8.427 55764 Z= 0.253 Chirality : 0.038 0.235 6300 Planarity : 0.002 0.026 7032 Dihedral : 3.785 20.259 5436 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 1.06 % 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: 2.05 (0.12), residues: 4872 helix: 2.29 (0.10), residues: 2868 sheet: 0.24 (0.22), residues: 576 loop : -0.02 (0.16), residues: 1428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18666.38 seconds wall clock time: 330 minutes 20.94 seconds (19820.94 seconds total)