Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 11:28:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/10_2023/7tf7_25864.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/10_2023/7tf7_25864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/10_2023/7tf7_25864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/10_2023/7tf7_25864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/10_2023/7tf7_25864.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf7_25864/10_2023/7tf7_25864.pdb" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.106 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 192 5.16 5 C 25530 2.51 5 N 6670 2.21 5 O 7584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 39976 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "B" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "C" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "D" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "E" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3328 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "G" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "H" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3328 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "J" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "K" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Chain: "L" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3332 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 391} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU A 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU A 250 " occ=0.97 residue: pdb=" N LEU B 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 250 " occ=0.97 residue: pdb=" N LEU C 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU C 250 " occ=0.97 residue: pdb=" N LEU D 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU D 250 " occ=0.97 residue: pdb=" N LEU E 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU E 250 " occ=0.97 residue: pdb=" N LEU F 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 250 " occ=0.97 residue: pdb=" N LEU G 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU G 250 " occ=0.97 residue: pdb=" N LEU H 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU H 250 " occ=0.97 residue: pdb=" N LEU I 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU I 250 " occ=0.97 residue: pdb=" N LEU J 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU J 250 " occ=0.97 residue: pdb=" N LEU K 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU K 250 " occ=0.97 residue: pdb=" N LEU L 250 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 250 " occ=0.97 Time building chain proxies: 19.22, per 1000 atoms: 0.48 Number of scatterers: 39976 At special positions: 0 Unit cell: (161.04, 154.88, 124.08, 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 192 16.00 O 7584 8.00 N 6670 7.00 C 25530 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: 14.39 Conformation dependent library (CDL) restraints added in 5.3 seconds 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 36 sheets defined 41.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.570A pdb=" N ASP A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 204 through 225 removed outlier: 3.504A pdb=" N LYS A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.682A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.846A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 330 " --> pdb=" O GLY A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.636A pdb=" N GLU A 401 " --> pdb=" O LYS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 430 removed outlier: 3.934A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N HIS A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'B' and resid 5 through 17 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.585A pdb=" N ASP B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 179 removed outlier: 3.509A pdb=" N MET B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.532A pdb=" N ARG B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 282 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.675A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.780A pdb=" N SER B 329 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 330 " --> pdb=" O GLY B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.630A pdb=" N GLU B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 430 removed outlier: 3.806A pdb=" N LYS B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N HIS B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 440 Processing helix chain 'C' and resid 5 through 17 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.635A pdb=" N ASP C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 204 through 225 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.657A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.723A pdb=" N SER C 329 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 361 Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.619A pdb=" N GLU C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 430 removed outlier: 4.013A pdb=" N LYS C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN C 411 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N HIS C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'D' and resid 5 through 17 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.582A pdb=" N ASP D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 204 through 225 Processing helix chain 'D' and resid 268 through 282 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.677A pdb=" N ARG D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 294 through 299' Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.741A pdb=" N SER D 329 " --> pdb=" O ARG D 326 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 330 " --> pdb=" O GLY D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 330' Processing helix chain 'D' and resid 342 through 360 Processing helix chain 'D' and resid 391 through 401 removed outlier: 3.572A pdb=" N GLU D 401 " --> pdb=" O LYS D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 430 removed outlier: 4.082A pdb=" N LYS D 406 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN D 411 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N HIS D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 430 " --> pdb=" O ASP D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.577A pdb=" N ASP E 121 " --> pdb=" O LYS E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 removed outlier: 3.522A pdb=" N MET E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 225 removed outlier: 3.504A pdb=" N ARG E 223 " --> pdb=" O LYS E 219 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS E 224 " --> pdb=" O THR E 220 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 282 Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.676A pdb=" N ARG E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 299 " --> pdb=" O SER E 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 294 through 299' Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.777A pdb=" N SER E 329 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 330 " --> pdb=" O GLY E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 330' Processing helix chain 'E' and resid 342 through 361 Processing helix chain 'E' and resid 391 through 401 removed outlier: 3.632A pdb=" N GLU E 401 " --> pdb=" O LYS E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 430 removed outlier: 3.868A pdb=" N LYS E 406 " --> pdb=" O ASN E 402 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN E 411 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N HIS E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 440 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.581A pdb=" N ASP F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 179 Processing helix chain 'F' and resid 204 through 225 removed outlier: 3.536A pdb=" N ARG F 223 " --> pdb=" O LYS F 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS F 224 " --> pdb=" O THR F 220 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS F 225 " --> pdb=" O ILE F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 285 through 290 Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.682A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 294 through 299' Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.807A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 330 " --> pdb=" O GLY F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 330' Processing helix chain 'F' and resid 342 through 361 Processing helix chain 'F' and resid 391 through 401 removed outlier: 3.622A pdb=" N GLU F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 410 removed outlier: 3.846A pdb=" N LYS F 406 " --> pdb=" O ASN F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 430 removed outlier: 3.796A pdb=" N THR F 430 " --> pdb=" O ASP F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 440 Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'G' and resid 41 through 47 Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.611A pdb=" N ASP G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 Processing helix chain 'G' and resid 204 through 225 Processing helix chain 'G' and resid 268 through 282 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.680A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 299' Processing helix chain 'G' and resid 326 through 330 removed outlier: 3.741A pdb=" N SER G 329 " --> pdb=" O ARG G 326 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR G 330 " --> pdb=" O GLY G 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 326 through 330' Processing helix chain 'G' and resid 342 through 360 Processing helix chain 'G' and resid 391 through 401 removed outlier: 3.576A pdb=" N GLU G 401 " --> pdb=" O LYS G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 430 removed outlier: 4.084A pdb=" N LYS G 406 " --> pdb=" O ASN G 402 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASN G 411 " --> pdb=" O LYS G 407 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N HIS G 412 " --> pdb=" O ALA G 408 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE G 413 " --> pdb=" O LEU G 409 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR G 430 " --> pdb=" O ASP G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 440 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 107 through 121 removed outlier: 3.601A pdb=" N ASP H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 179 Processing helix chain 'H' and resid 204 through 225 Processing helix chain 'H' and resid 268 through 282 Processing helix chain 'H' and resid 285 through 290 Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.650A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU H 299 " --> pdb=" O SER H 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 294 through 299' Processing helix chain 'H' and resid 326 through 330 removed outlier: 3.798A pdb=" N SER H 329 " --> pdb=" O ARG H 326 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR H 330 " --> pdb=" O GLY H 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 326 through 330' Processing helix chain 'H' and resid 342 through 361 Processing helix chain 'H' and resid 391 through 401 removed outlier: 3.575A pdb=" N GLU H 401 " --> pdb=" O LYS H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 430 removed outlier: 4.012A pdb=" N LYS H 406 " --> pdb=" O ASN H 402 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN H 411 " --> pdb=" O LYS H 407 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N HIS H 412 " --> pdb=" O ALA H 408 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE H 413 " --> pdb=" O LEU H 409 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR H 430 " --> pdb=" O ASP H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 440 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 107 through 121 removed outlier: 3.630A pdb=" N ASP I 121 " --> pdb=" O LYS I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 179 Processing helix chain 'I' and resid 204 through 225 Processing helix chain 'I' and resid 268 through 281 Processing helix chain 'I' and resid 285 through 290 Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.659A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 330 removed outlier: 3.706A pdb=" N SER I 329 " --> pdb=" O ARG I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 361 Processing helix chain 'I' and resid 391 through 401 removed outlier: 3.602A pdb=" N GLU I 401 " --> pdb=" O LYS I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 430 removed outlier: 4.021A pdb=" N LYS I 406 " --> pdb=" O ASN I 402 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN I 411 " --> pdb=" O LYS I 407 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N HIS I 412 " --> pdb=" O ALA I 408 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE I 413 " --> pdb=" O LEU I 409 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR I 430 " --> pdb=" O ASP I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 440 Processing helix chain 'J' and resid 5 through 17 Processing helix chain 'J' and resid 41 through 47 Processing helix chain 'J' and resid 107 through 121 removed outlier: 3.623A pdb=" N ASP J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 179 Processing helix chain 'J' and resid 204 through 225 Processing helix chain 'J' and resid 268 through 281 Processing helix chain 'J' and resid 285 through 290 Processing helix chain 'J' and resid 294 through 299 removed outlier: 3.676A pdb=" N ARG J 298 " --> pdb=" O ASN J 294 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 294 through 299' Processing helix chain 'J' and resid 326 through 330 removed outlier: 3.688A pdb=" N SER J 329 " --> pdb=" O ARG J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 360 Processing helix chain 'J' and resid 391 through 401 removed outlier: 3.608A pdb=" N GLU J 401 " --> pdb=" O LYS J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 402 through 430 removed outlier: 4.082A pdb=" N LYS J 406 " --> pdb=" O ASN J 402 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN J 411 " --> pdb=" O LYS J 407 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N HIS J 412 " --> pdb=" O ALA J 408 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE J 413 " --> pdb=" O LEU J 409 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR J 430 " --> pdb=" O ASP J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 440 Processing helix chain 'K' and resid 5 through 17 Processing helix chain 'K' and resid 41 through 47 Processing helix chain 'K' and resid 107 through 121 removed outlier: 3.623A pdb=" N ASP K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 179 Processing helix chain 'K' and resid 204 through 225 Processing helix chain 'K' and resid 268 through 281 Processing helix chain 'K' and resid 285 through 290 Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.674A pdb=" N ARG K 298 " --> pdb=" O ASN K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 330 removed outlier: 3.682A pdb=" N SER K 329 " --> pdb=" O ARG K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 360 Processing helix chain 'K' and resid 391 through 401 removed outlier: 3.608A pdb=" N GLU K 401 " --> pdb=" O LYS K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 430 removed outlier: 4.082A pdb=" N LYS K 406 " --> pdb=" O ASN K 402 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN K 411 " --> pdb=" O LYS K 407 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N HIS K 412 " --> pdb=" O ALA K 408 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE K 413 " --> pdb=" O LEU K 409 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR K 430 " --> pdb=" O ASP K 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 440 Processing helix chain 'L' and resid 5 through 17 Processing helix chain 'L' and resid 41 through 47 Processing helix chain 'L' and resid 107 through 121 removed outlier: 3.614A pdb=" N ASP L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 179 Processing helix chain 'L' and resid 204 through 225 Processing helix chain 'L' and resid 268 through 281 Processing helix chain 'L' and resid 285 through 290 Processing helix chain 'L' and resid 294 through 299 removed outlier: 3.657A pdb=" N ARG L 298 " --> pdb=" O ASN L 294 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU L 299 " --> pdb=" O SER L 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 294 through 299' Processing helix chain 'L' and resid 326 through 330 removed outlier: 3.799A pdb=" N SER L 329 " --> pdb=" O ARG L 326 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L 330 " --> pdb=" O GLY L 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 326 through 330' Processing helix chain 'L' and resid 342 through 361 Processing helix chain 'L' and resid 391 through 401 removed outlier: 3.561A pdb=" N GLU L 401 " --> pdb=" O LYS L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 430 removed outlier: 4.022A pdb=" N LYS L 406 " --> pdb=" O ASN L 402 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN L 411 " --> pdb=" O LYS L 407 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N HIS L 412 " --> pdb=" O ALA L 408 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR L 430 " --> pdb=" O ASP L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 6.314A pdb=" N TYR A 20 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 92 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG A 22 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS A 94 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN A 24 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL A 96 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N THR A 26 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 11.906A pdb=" N VAL A 89 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N TRP A 77 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N ARG A 91 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP A 75 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 93 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET A 50 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 140 removed outlier: 7.285A pdb=" N LEU A 137 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU A 149 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS A 139 " --> pdb=" O THR A 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 146 through 150 current: chain 'A' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 194 through 199 current: chain 'A' and resid 320 through 321 Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 309 removed outlier: 4.025A pdb=" N GLN A 386 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.471A pdb=" N THR B 26 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL B 96 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N VAL B 89 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N TRP B 77 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N ARG B 91 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASP B 75 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 93 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET B 50 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 140 removed outlier: 7.375A pdb=" N LEU B 137 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU B 149 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS B 139 " --> pdb=" O THR B 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 146 through 150 current: chain 'B' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 194 through 199 current: chain 'B' and resid 320 through 321 Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 309 removed outlier: 4.106A pdb=" N GLN B 386 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.485A pdb=" N THR C 26 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL C 96 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 11.897A pdb=" N VAL C 89 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N TRP C 77 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 9.958A pdb=" N ARG C 91 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASP C 75 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE C 93 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET C 50 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 126 through 140 removed outlier: 7.349A pdb=" N LEU C 137 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU C 149 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS C 139 " --> pdb=" O THR C 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 146 through 150 current: chain 'C' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 194 through 199 current: chain 'C' and resid 320 through 321 Processing sheet with id=AA9, first strand: chain 'C' and resid 308 through 309 removed outlier: 4.076A pdb=" N GLN C 386 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 32 through 38 removed outlier: 5.496A pdb=" N THR D 26 " --> pdb=" O CYS D 94 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL D 96 " --> pdb=" O THR D 26 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N VAL D 89 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N TRP D 77 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ARG D 91 " --> pdb=" O ASP D 75 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP D 75 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE D 93 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N MET D 50 " --> pdb=" O LEU D 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 126 through 140 removed outlier: 7.347A pdb=" N LEU D 137 " --> pdb=" O GLU D 149 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU D 149 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS D 139 " --> pdb=" O THR D 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 146 through 150 current: chain 'D' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 194 through 199 current: chain 'D' and resid 320 through 321 Processing sheet with id=AB3, first strand: chain 'D' and resid 308 through 309 removed outlier: 4.105A pdb=" N GLN D 386 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 38 removed outlier: 5.460A pdb=" N THR E 26 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL E 96 " --> pdb=" O THR E 26 " (cutoff:3.500A) removed outlier: 11.897A pdb=" N VAL E 89 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N TRP E 77 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N ARG E 91 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ASP E 75 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE E 93 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET E 50 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 126 through 140 removed outlier: 7.367A pdb=" N LEU E 137 " --> pdb=" O GLU E 149 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU E 149 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS E 139 " --> pdb=" O THR E 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 146 through 150 current: chain 'E' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 194 through 199 current: chain 'E' and resid 320 through 321 Processing sheet with id=AB6, first strand: chain 'E' and resid 308 through 309 removed outlier: 4.079A pdb=" N GLN E 386 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 32 through 38 removed outlier: 6.293A pdb=" N TYR F 20 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU F 92 " --> pdb=" O TYR F 20 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG F 22 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS F 94 " --> pdb=" O ARG F 22 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLN F 24 " --> pdb=" O CYS F 94 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL F 96 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N THR F 26 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N VAL F 89 " --> pdb=" O TRP F 77 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N TRP F 77 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 10.026A pdb=" N ARG F 91 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ASP F 75 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE F 93 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET F 50 " --> pdb=" O LEU F 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 126 through 140 removed outlier: 7.296A pdb=" N LEU F 137 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU F 149 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS F 139 " --> pdb=" O THR F 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 146 through 150 current: chain 'F' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 194 through 199 current: chain 'F' and resid 320 through 321 Processing sheet with id=AB9, first strand: chain 'F' and resid 308 through 309 removed outlier: 4.061A pdb=" N GLN F 386 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.478A pdb=" N THR G 26 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL G 96 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N VAL G 89 " --> pdb=" O TRP G 77 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N TRP G 77 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N ARG G 91 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP G 75 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE G 93 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET G 50 " --> pdb=" O LEU G 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 126 through 140 removed outlier: 5.410A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 146 through 150 current: chain 'G' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 194 through 199 current: chain 'G' and resid 320 through 321 Processing sheet with id=AC3, first strand: chain 'G' and resid 308 through 309 removed outlier: 4.113A pdb=" N GLN G 386 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.489A pdb=" N THR H 26 " --> pdb=" O CYS H 94 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL H 96 " --> pdb=" O THR H 26 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N VAL H 89 " --> pdb=" O TRP H 77 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N TRP H 77 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N ARG H 91 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP H 75 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE H 93 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET H 50 " --> pdb=" O LEU H 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 126 through 140 removed outlier: 7.287A pdb=" N LEU H 137 " --> pdb=" O GLU H 149 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU H 149 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS H 139 " --> pdb=" O THR H 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 146 through 150 current: chain 'H' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 194 through 199 current: chain 'H' and resid 320 through 321 Processing sheet with id=AC6, first strand: chain 'H' and resid 308 through 309 removed outlier: 4.096A pdb=" N GLN H 386 " --> pdb=" O ILE H 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 32 through 38 removed outlier: 6.292A pdb=" N TYR I 20 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU I 92 " --> pdb=" O TYR I 20 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ARG I 22 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS I 94 " --> pdb=" O ARG I 22 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN I 24 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL I 96 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N THR I 26 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 11.884A pdb=" N VAL I 89 " --> pdb=" O TRP I 77 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N TRP I 77 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 9.981A pdb=" N ARG I 91 " --> pdb=" O ASP I 75 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ASP I 75 " --> pdb=" O ARG I 91 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE I 93 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N MET I 50 " --> pdb=" O LEU I 70 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 126 through 140 removed outlier: 7.358A pdb=" N LEU I 137 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU I 149 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS I 139 " --> pdb=" O THR I 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 146 through 150 current: chain 'I' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 194 through 199 current: chain 'I' and resid 320 through 321 Processing sheet with id=AC9, first strand: chain 'I' and resid 308 through 309 removed outlier: 4.055A pdb=" N GLN I 386 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 32 through 38 removed outlier: 5.484A pdb=" N THR J 26 " --> pdb=" O CYS J 94 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL J 96 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N VAL J 89 " --> pdb=" O TRP J 77 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N TRP J 77 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N ARG J 91 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASP J 75 " --> pdb=" O ARG J 91 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE J 93 " --> pdb=" O ASP J 73 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET J 50 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 126 through 140 removed outlier: 7.323A pdb=" N LEU J 137 " --> pdb=" O GLU J 149 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU J 149 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS J 139 " --> pdb=" O THR J 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 146 through 150 current: chain 'J' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 194 through 199 current: chain 'J' and resid 320 through 321 Processing sheet with id=AD3, first strand: chain 'J' and resid 308 through 309 removed outlier: 4.055A pdb=" N GLN J 386 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 32 through 38 removed outlier: 6.299A pdb=" N TYR K 20 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU K 92 " --> pdb=" O TYR K 20 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ARG K 22 " --> pdb=" O LEU K 92 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS K 94 " --> pdb=" O ARG K 22 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN K 24 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL K 96 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N THR K 26 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 11.858A pdb=" N VAL K 89 " --> pdb=" O TRP K 77 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N TRP K 77 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N ARG K 91 " --> pdb=" O ASP K 75 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ASP K 75 " --> pdb=" O ARG K 91 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE K 93 " --> pdb=" O ASP K 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET K 50 " --> pdb=" O LEU K 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 126 through 140 removed outlier: 7.340A pdb=" N LEU K 137 " --> pdb=" O GLU K 149 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU K 149 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS K 139 " --> pdb=" O THR K 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 146 through 150 current: chain 'K' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 194 through 199 current: chain 'K' and resid 320 through 321 Processing sheet with id=AD6, first strand: chain 'K' and resid 308 through 309 removed outlier: 4.056A pdb=" N GLN K 386 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 32 through 38 removed outlier: 5.492A pdb=" N THR L 26 " --> pdb=" O CYS L 94 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL L 96 " --> pdb=" O THR L 26 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL L 89 " --> pdb=" O PHE L 80 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 78 " --> pdb=" O ARG L 91 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE L 93 " --> pdb=" O THR L 76 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR L 76 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N ASP L 95 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N LEU L 74 " --> pdb=" O ASP L 95 " (cutoff:3.500A) removed outlier: 10.202A pdb=" N TYR L 97 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET L 50 " --> pdb=" O LEU L 70 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 126 through 140 removed outlier: 7.284A pdb=" N LEU L 137 " --> pdb=" O GLU L 149 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU L 149 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LYS L 139 " --> pdb=" O THR L 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 146 through 150 current: chain 'L' and resid 194 through 199 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 194 through 199 current: chain 'L' and resid 320 through 321 Processing sheet with id=AD9, first strand: chain 'L' and resid 308 through 309 removed outlier: 3.956A pdb=" N GLN L 386 " --> pdb=" O ILE L 309 " (cutoff:3.500A) 1557 hydrogen bonds defined for protein. 4623 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: 12.93 Time building geometry restraints manager: 15.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13141 1.34 - 1.46: 9152 1.46 - 1.58: 18283 1.58 - 1.70: 0 1.70 - 1.82: 324 Bond restraints: 40900 Sorted by residual: bond pdb=" N LYS H 254 " pdb=" CA LYS H 254 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.30e+00 bond pdb=" N LYS E 254 " pdb=" CA LYS E 254 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" N ILE G 32 " pdb=" CA ILE G 32 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.10e-02 8.26e+03 8.89e+00 bond pdb=" N VAL C 334 " pdb=" CA VAL C 334 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.84e+00 bond pdb=" N ARG C 335 " pdb=" CA ARG C 335 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.22e-02 6.72e+03 7.59e+00 ... (remaining 40895 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.46: 1289 106.46 - 113.34: 21511 113.34 - 120.22: 15445 120.22 - 127.11: 16652 127.11 - 133.99: 463 Bond angle restraints: 55360 Sorted by residual: angle pdb=" N MET C 441 " pdb=" CA MET C 441 " pdb=" CB MET C 441 " ideal model delta sigma weight residual 114.17 109.75 4.42 1.14e+00 7.69e-01 1.50e+01 angle pdb=" CA LYS A 254 " pdb=" CB LYS A 254 " pdb=" CG LYS A 254 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA LYS B 254 " pdb=" CB LYS B 254 " pdb=" CG LYS B 254 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" N MET I 441 " pdb=" CA MET I 441 " pdb=" CB MET I 441 " ideal model delta sigma weight residual 114.17 109.80 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N MET L 441 " pdb=" CA MET L 441 " pdb=" CB MET L 441 " ideal model delta sigma weight residual 114.17 109.90 4.27 1.14e+00 7.69e-01 1.40e+01 ... (remaining 55355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 22052 17.92 - 35.85: 1836 35.85 - 53.77: 534 53.77 - 71.70: 131 71.70 - 89.62: 51 Dihedral angle restraints: 24604 sinusoidal: 10144 harmonic: 14460 Sorted by residual: dihedral pdb=" CA SER E 317 " pdb=" C SER E 317 " pdb=" N PRO E 318 " pdb=" CA PRO E 318 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER A 317 " pdb=" C SER A 317 " pdb=" N PRO A 318 " pdb=" CA PRO A 318 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA SER L 317 " pdb=" C SER L 317 " pdb=" N PRO L 318 " pdb=" CA PRO L 318 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 24601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4265 0.043 - 0.086: 1306 0.086 - 0.129: 374 0.129 - 0.172: 18 0.172 - 0.215: 1 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CA VAL C 334 " pdb=" N VAL C 334 " pdb=" C VAL C 334 " pdb=" CB VAL C 334 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA MET J 51 " pdb=" N MET J 51 " pdb=" C MET J 51 " pdb=" CB MET J 51 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA MET G 51 " pdb=" N MET G 51 " pdb=" C MET G 51 " pdb=" CB MET G 51 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 5961 not shown) Planarity restraints: 7260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 317 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO K 318 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO K 318 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 318 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 317 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO D 318 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 318 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 318 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER J 317 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO J 318 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO J 318 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 318 " -0.027 5.00e-02 4.00e+02 ... (remaining 7257 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2297 2.73 - 3.27: 39345 3.27 - 3.81: 68541 3.81 - 4.36: 87739 4.36 - 4.90: 146186 Nonbonded interactions: 344108 Sorted by model distance: nonbonded pdb=" OD2 ASP E 53 " pdb=" OG SER E 55 " model vdw 2.187 2.440 nonbonded pdb=" OD2 ASP B 53 " pdb=" OG SER B 55 " model vdw 2.189 2.440 nonbonded pdb=" OD2 ASP A 53 " pdb=" OG SER A 55 " model vdw 2.189 2.440 nonbonded pdb=" OD2 ASP D 53 " pdb=" OG SER D 55 " model vdw 2.199 2.440 nonbonded pdb=" OD2 ASP F 53 " pdb=" OG SER F 55 " model vdw 2.202 2.440 ... (remaining 344103 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' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'B' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'C' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'D' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = chain 'E' selection = (chain 'F' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'G' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = chain 'H' selection = (chain 'I' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'J' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'K' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) selection = (chain 'L' and (resid 4 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 444)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.97 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 15.710 Check model and map are aligned: 0.580 Set scattering table: 0.320 Process input model: 91.510 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.150 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:14.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 40900 Z= 0.273 Angle : 0.611 10.151 55360 Z= 0.355 Chirality : 0.043 0.215 5964 Planarity : 0.004 0.048 7260 Dihedral : 15.424 89.620 15268 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 1.43 % Allowed : 15.48 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.01 (0.12), residues: 4884 helix: 1.66 (0.12), residues: 1992 sheet: 0.02 (0.18), residues: 912 loop : 0.10 (0.15), residues: 1980 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 849 time to evaluate : 4.591 Fit side-chains outliers start: 62 outliers final: 34 residues processed: 900 average time/residue: 1.7431 time to fit residues: 1860.8207 Evaluate side-chains 639 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 605 time to evaluate : 4.516 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 34 residues processed: 0 time to fit residues: 6.1466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 385 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 287 optimal weight: 10.0000 chunk 446 optimal weight: 1.9990 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 111 ASN A 443 GLN ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 443 GLN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 HIS D 443 GLN E 111 ASN E 443 GLN F 111 ASN F 212 GLN F 225 HIS F 443 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 HIS G 226 ASN G 443 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 ASN H 245 HIS H 443 GLN I 111 ASN I 443 GLN J 111 ASN J 443 GLN K 111 ASN K 443 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN L 111 ASN L 443 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 40900 Z= 0.329 Angle : 0.691 9.180 55360 Z= 0.373 Chirality : 0.047 0.167 5964 Planarity : 0.006 0.055 7260 Dihedral : 5.215 28.669 5364 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 4.47 % Allowed : 11.49 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.12), residues: 4884 helix: 1.55 (0.11), residues: 2028 sheet: -0.03 (0.17), residues: 912 loop : 0.08 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 659 time to evaluate : 4.700 Fit side-chains outliers start: 194 outliers final: 60 residues processed: 812 average time/residue: 1.7087 time to fit residues: 1657.3958 Evaluate side-chains 686 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 626 time to evaluate : 4.574 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 59 residues processed: 1 average time/residue: 1.9740 time to fit residues: 8.5257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 371 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 447 optimal weight: 4.9990 chunk 483 optimal weight: 2.9990 chunk 398 optimal weight: 10.0000 chunk 443 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 chunk 359 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 ASN B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 443 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 17 ASN F 24 GLN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN G 128 ASN G 443 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 GLN K 443 GLN ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 245 HIS L 443 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40900 Z= 0.247 Angle : 0.596 7.925 55360 Z= 0.325 Chirality : 0.044 0.160 5964 Planarity : 0.005 0.049 7260 Dihedral : 5.064 28.034 5364 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.83 % Allowed : 12.41 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.03 (0.12), residues: 4884 helix: 1.69 (0.11), residues: 2028 sheet: -0.07 (0.17), residues: 912 loop : 0.11 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 621 time to evaluate : 4.959 Fit side-chains outliers start: 123 outliers final: 74 residues processed: 730 average time/residue: 1.5160 time to fit residues: 1330.3877 Evaluate side-chains 684 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 610 time to evaluate : 4.569 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 73 residues processed: 1 average time/residue: 2.6006 time to fit residues: 9.3645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 449 optimal weight: 0.9990 chunk 475 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 425 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 443 GLN B 24 GLN B 128 ASN B 225 HIS B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN C 443 GLN D 24 GLN D 128 ASN D 443 GLN E 24 GLN E 128 ASN E 225 HIS E 226 ASN E 443 GLN F 17 ASN F 443 GLN G 24 GLN G 443 GLN H 24 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN K 443 GLN L 24 GLN L 128 ASN L 443 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 40900 Z= 0.334 Angle : 0.664 8.085 55360 Z= 0.366 Chirality : 0.047 0.171 5964 Planarity : 0.006 0.050 7260 Dihedral : 5.363 29.613 5364 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.18 % Allowed : 12.41 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.12), residues: 4884 helix: 1.49 (0.11), residues: 2028 sheet: -0.18 (0.17), residues: 912 loop : -0.00 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 614 time to evaluate : 4.577 Fit side-chains outliers start: 138 outliers final: 80 residues processed: 731 average time/residue: 1.6896 time to fit residues: 1480.8202 Evaluate side-chains 686 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 606 time to evaluate : 4.753 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 77 residues processed: 3 average time/residue: 1.9871 time to fit residues: 13.5102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 196 optimal weight: 0.0980 chunk 405 optimal weight: 4.9990 chunk 328 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 426 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN D 24 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 17 ASN F 24 GLN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 24 GLN L 443 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 40900 Z= 0.318 Angle : 0.646 7.550 55360 Z= 0.356 Chirality : 0.047 0.178 5964 Planarity : 0.006 0.049 7260 Dihedral : 5.338 29.321 5364 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.74 % Allowed : 13.17 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.12), residues: 4884 helix: 1.51 (0.11), residues: 2028 sheet: -0.24 (0.17), residues: 912 loop : -0.06 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 609 time to evaluate : 4.897 Fit side-chains outliers start: 119 outliers final: 90 residues processed: 711 average time/residue: 1.6787 time to fit residues: 1432.3398 Evaluate side-chains 701 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 611 time to evaluate : 4.530 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 87 residues processed: 3 average time/residue: 1.3689 time to fit residues: 11.0608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 2.9990 chunk 428 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 476 optimal weight: 5.9990 chunk 395 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN D 24 GLN ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 17 ASN F 24 GLN F 245 HIS F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 40900 Z= 0.277 Angle : 0.611 7.140 55360 Z= 0.337 Chirality : 0.045 0.173 5964 Planarity : 0.006 0.050 7260 Dihedral : 5.256 29.004 5364 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.35 % Allowed : 13.43 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.12), residues: 4884 helix: 1.60 (0.11), residues: 2028 sheet: -0.22 (0.17), residues: 912 loop : -0.04 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 612 time to evaluate : 4.588 Fit side-chains outliers start: 102 outliers final: 86 residues processed: 710 average time/residue: 1.6810 time to fit residues: 1430.1058 Evaluate side-chains 694 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 608 time to evaluate : 4.540 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 86 residues processed: 0 time to fit residues: 6.1610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 271 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 400 optimal weight: 4.9990 chunk 265 optimal weight: 0.9990 chunk 474 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 289 optimal weight: 0.7980 chunk 218 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN E 443 GLN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN K 17 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40900 Z= 0.179 Angle : 0.523 6.558 55360 Z= 0.286 Chirality : 0.042 0.150 5964 Planarity : 0.005 0.049 7260 Dihedral : 4.880 27.121 5364 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.28 % Allowed : 13.47 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.15 (0.12), residues: 4884 helix: 1.90 (0.12), residues: 2028 sheet: -0.18 (0.17), residues: 912 loop : 0.12 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 621 time to evaluate : 4.569 Fit side-chains outliers start: 99 outliers final: 82 residues processed: 715 average time/residue: 1.6591 time to fit residues: 1423.0434 Evaluate side-chains 696 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 614 time to evaluate : 4.533 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 81 residues processed: 1 average time/residue: 2.0031 time to fit residues: 8.6460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 0.5980 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 301 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 372 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN ** H 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 40900 Z= 0.211 Angle : 0.552 6.853 55360 Z= 0.303 Chirality : 0.043 0.155 5964 Planarity : 0.005 0.049 7260 Dihedral : 4.978 27.514 5364 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.16 % Allowed : 13.52 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.12 (0.12), residues: 4884 helix: 1.86 (0.11), residues: 2028 sheet: -0.19 (0.17), residues: 912 loop : 0.13 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 610 time to evaluate : 4.457 Fit side-chains outliers start: 94 outliers final: 83 residues processed: 699 average time/residue: 1.6833 time to fit residues: 1409.4345 Evaluate side-chains 691 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 608 time to evaluate : 4.595 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 83 residues processed: 0 time to fit residues: 6.3392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 2.9990 chunk 454 optimal weight: 9.9990 chunk 414 optimal weight: 10.0000 chunk 441 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 399 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 440 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 40900 Z= 0.242 Angle : 0.583 6.986 55360 Z= 0.321 Chirality : 0.044 0.159 5964 Planarity : 0.005 0.049 7260 Dihedral : 5.084 27.714 5364 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.19 % Allowed : 13.31 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.03 (0.12), residues: 4884 helix: 1.78 (0.11), residues: 2028 sheet: -0.20 (0.17), residues: 912 loop : 0.08 (0.14), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 605 time to evaluate : 5.013 Fit side-chains outliers start: 95 outliers final: 83 residues processed: 696 average time/residue: 1.6353 time to fit residues: 1370.1205 Evaluate side-chains 687 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 604 time to evaluate : 4.628 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 83 residues processed: 0 time to fit residues: 6.3207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 10.0000 chunk 467 optimal weight: 1.9990 chunk 285 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 490 optimal weight: 0.9990 chunk 451 optimal weight: 10.0000 chunk 390 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 301 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40900 Z= 0.206 Angle : 0.548 6.857 55360 Z= 0.301 Chirality : 0.043 0.152 5964 Planarity : 0.005 0.050 7260 Dihedral : 4.974 27.480 5364 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.91 % Allowed : 13.50 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.11 (0.12), residues: 4884 helix: 1.86 (0.11), residues: 2028 sheet: -0.19 (0.17), residues: 912 loop : 0.12 (0.14), residues: 1944 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 610 time to evaluate : 4.644 Fit side-chains outliers start: 83 outliers final: 82 residues processed: 693 average time/residue: 1.7001 time to fit residues: 1410.9972 Evaluate side-chains 691 residues out of total 4344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 609 time to evaluate : 4.558 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 82 residues processed: 0 time to fit residues: 6.2208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 10.0000 chunk 415 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 359 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 390 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 401 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN F 443 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN H 443 GLN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 443 GLN ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 443 GLN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN L 443 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136564 restraints weight = 34072.338| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.10 r_work: 0.3439 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40900 Z= 0.144 Angle : 0.483 5.857 55360 Z= 0.263 Chirality : 0.041 0.143 5964 Planarity : 0.004 0.051 7260 Dihedral : 4.522 26.073 5364 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.96 % Allowed : 13.50 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.43 (0.12), residues: 4884 helix: 2.14 (0.12), residues: 2028 sheet: -0.10 (0.17), residues: 912 loop : 0.31 (0.14), residues: 1944 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19843.64 seconds wall clock time: 349 minutes 40.12 seconds (20980.12 seconds total)