Starting phenix.real_space_refine (version: dev) on Sat Apr 9 02:32:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2022/6smh_10235_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2022/6smh_10235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2022/6smh_10235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2022/6smh_10235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2022/6smh_10235_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6smh_10235/04_2022/6smh_10235_neut.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 39744 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 424, 'PCIS': 1} Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 424, 'PCIS': 1} Chain: "C" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 424, 'PCIS': 1} Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 22, 'TRANS': 424} Chain: "E" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 424, 'PCIS': 1} Chain: "F" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 424, 'PCIS': 1} Chain: "G" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 424, 'PCIS': 1} Chain: "H" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3495 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 424, 'PCIS': 1} Chain: "I" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "J" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1523 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 179, 'PCIS': 1} Chain: "K" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "L" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1457 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "M" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1465 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "N" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1473 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1473 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "P" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1479 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Time building chain proxies: 21.61, per 1000 atoms: 0.54 Number of scatterers: 39744 At special positions: 0 Unit cell: (167.5, 165, 132.5, 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 176 16.00 O 7342 8.00 N 7133 7.00 C 25093 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: 18.18 Conformation dependent library (CDL) restraints added in 6.1 seconds 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9232 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 28 sheets defined 44.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 178 through 192 Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.548A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.794A pdb=" N GLU A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 430 Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.534A pdb=" N GLU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 348 removed outlier: 4.167A pdb=" N MET B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 409 through 430 Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.503A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY B 439 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP B 440 " --> pdb=" O ARG B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA C 50 " --> pdb=" O PRO C 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 118 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.660A pdb=" N GLY C 193 " --> pdb=" O CYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.842A pdb=" N ARG C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 383 through 392 Processing helix chain 'C' and resid 409 through 431 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 118 Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.603A pdb=" N ALA D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 186 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 removed outlier: 4.044A pdb=" N PHE D 215 " --> pdb=" O TRP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 Processing helix chain 'D' and resid 270 through 285 Processing helix chain 'D' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 383 through 392 Processing helix chain 'D' and resid 409 through 431 Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.534A pdb=" N GLU D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY D 439 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP D 440 " --> pdb=" O ARG D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 151 through 160 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.546A pdb=" N CYS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 193 " --> pdb=" O CYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.776A pdb=" N ALA E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 282 Processing helix chain 'E' and resid 307 through 319 Processing helix chain 'E' and resid 332 through 345 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.793A pdb=" N GLU E 389 " --> pdb=" O PRO E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 431 Processing helix chain 'E' and resid 433 through 446 removed outlier: 3.535A pdb=" N GLU E 437 " --> pdb=" O ASP E 433 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY E 439 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ASP E 440 " --> pdb=" O ARG E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 459 removed outlier: 3.797A pdb=" N TRP E 459 " --> pdb=" O ALA E 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.535A pdb=" N ALA F 50 " --> pdb=" O PRO F 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 151 through 160 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.922A pdb=" N GLY F 193 " --> pdb=" O CYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 230 removed outlier: 3.897A pdb=" N PHE F 215 " --> pdb=" O TRP F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 258 removed outlier: 4.286A pdb=" N GLU F 252 " --> pdb=" O MET F 248 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 307 through 318 Processing helix chain 'F' and resid 332 through 344 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 391 Processing helix chain 'F' and resid 409 through 430 Processing helix chain 'F' and resid 438 through 446 Processing helix chain 'F' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA G 50 " --> pdb=" O PRO G 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 118 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'G' and resid 151 through 160 Processing helix chain 'G' and resid 178 through 192 removed outlier: 4.354A pdb=" N GLY G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 257 removed outlier: 3.601A pdb=" N ALA G 254 " --> pdb=" O ARG G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 285 Processing helix chain 'G' and resid 307 through 318 removed outlier: 3.548A pdb=" N LEU G 311 " --> pdb=" O HIS G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 344 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 391 removed outlier: 4.419A pdb=" N GLU G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE G 390 " --> pdb=" O ALA G 386 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 430 Processing helix chain 'G' and resid 437 through 446 Processing helix chain 'G' and resid 449 through 457 Processing helix chain 'H' and resid 46 through 59 removed outlier: 3.534A pdb=" N ALA H 50 " --> pdb=" O PRO H 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'H' and resid 151 through 160 Processing helix chain 'H' and resid 178 through 192 Processing helix chain 'H' and resid 210 through 230 removed outlier: 3.842A pdb=" N ARG H 214 " --> pdb=" O ARG H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 257 Processing helix chain 'H' and resid 270 through 285 Processing helix chain 'H' and resid 295 through 300 removed outlier: 3.733A pdb=" N ASP H 299 " --> pdb=" O HIS H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 318 removed outlier: 3.547A pdb=" N LEU H 311 " --> pdb=" O HIS H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 348 removed outlier: 4.220A pdb=" N MET H 346 " --> pdb=" O PHE H 342 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG H 347 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 392 Processing helix chain 'H' and resid 409 through 430 Processing helix chain 'H' and resid 437 through 446 Processing helix chain 'H' and resid 449 through 459 removed outlier: 3.796A pdb=" N TRP H 459 " --> pdb=" O ALA H 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.536A pdb=" N LEU I 21 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 34 removed outlier: 3.695A pdb=" N ALA I 32 " --> pdb=" O TRP I 28 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 48 removed outlier: 3.675A pdb=" N LEU I 48 " --> pdb=" O PRO I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 63 through 66 Processing helix chain 'I' and resid 67 through 75 removed outlier: 3.653A pdb=" N ILE I 72 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU I 73 " --> pdb=" O TYR I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 121 through 130 removed outlier: 4.319A pdb=" N ALA I 125 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP I 130 " --> pdb=" O LYS I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 157 removed outlier: 3.530A pdb=" N CYS I 153 " --> pdb=" O VAL I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 168 Processing helix chain 'I' and resid 179 through 185 removed outlier: 3.733A pdb=" N LEU I 185 " --> pdb=" O GLY I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 44 through 52 removed outlier: 3.773A pdb=" N LEU J 48 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE J 49 " --> pdb=" O PRO J 45 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLU J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.535A pdb=" N VAL J 64 " --> pdb=" O ASN J 60 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET J 66 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.527A pdb=" N LEU J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.676A pdb=" N ALA J 108 " --> pdb=" O ARG J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 removed outlier: 3.792A pdb=" N GLU J 113 " --> pdb=" O GLN J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 132 removed outlier: 3.561A pdb=" N ALA J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.902A pdb=" N VAL J 149 " --> pdb=" O PRO J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 removed outlier: 4.010A pdb=" N CYS J 153 " --> pdb=" O ALA J 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 150 through 153' Processing helix chain 'J' and resid 179 through 187 removed outlier: 3.766A pdb=" N ARG J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU J 187 " --> pdb=" O ARG J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 195 removed outlier: 3.893A pdb=" N SER J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 24 removed outlier: 3.721A pdb=" N LEU K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG K 22 " --> pdb=" O LEU K 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS K 24 " --> pdb=" O GLN K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 38 removed outlier: 3.723A pdb=" N ALA K 32 " --> pdb=" O TRP K 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 44 through 52 removed outlier: 3.997A pdb=" N LEU K 48 " --> pdb=" O ASN K 44 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE K 49 " --> pdb=" O PRO K 45 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLU K 50 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 51 " --> pdb=" O THR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 72 removed outlier: 4.126A pdb=" N ALA K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET K 66 " --> pdb=" O ILE K 62 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 96 removed outlier: 3.614A pdb=" N LEU K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 109 removed outlier: 3.723A pdb=" N SER K 105 " --> pdb=" O GLN K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 112 No H-bonds generated for 'chain 'K' and resid 110 through 112' Processing helix chain 'K' and resid 121 through 132 Processing helix chain 'K' and resid 144 through 156 removed outlier: 4.114A pdb=" N CYS K 153 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TRP K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 186 removed outlier: 3.506A pdb=" N ARG K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 28 through 39 removed outlier: 4.069A pdb=" N ALA L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.985A pdb=" N LEU L 48 " --> pdb=" O ASN L 44 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 44 through 49' Processing helix chain 'L' and resid 55 through 62 Processing helix chain 'L' and resid 64 through 72 Processing helix chain 'L' and resid 89 through 96 removed outlier: 3.794A pdb=" N LEU L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 115 removed outlier: 4.744A pdb=" N SER L 105 " --> pdb=" O GLN L 101 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 132 removed outlier: 3.595A pdb=" N ALA L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 153 removed outlier: 3.580A pdb=" N CYS L 153 " --> pdb=" O VAL L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 166 removed outlier: 3.995A pdb=" N ARG L 166 " --> pdb=" O LEU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 186 removed outlier: 3.526A pdb=" N ARG L 183 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 23 Processing helix chain 'M' and resid 28 through 39 removed outlier: 4.023A pdb=" N ALA M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 49 removed outlier: 3.794A pdb=" N LEU M 48 " --> pdb=" O ASN M 44 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE M 49 " --> pdb=" O PRO M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 55 through 72 removed outlier: 3.638A pdb=" N GLN M 61 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR M 63 " --> pdb=" O GLN M 59 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL M 64 " --> pdb=" O ASN M 60 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA M 65 " --> pdb=" O GLN M 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET M 66 " --> pdb=" O ILE M 62 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 removed outlier: 3.914A pdb=" N LEU M 96 " --> pdb=" O LEU M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 115 removed outlier: 4.095A pdb=" N SER M 105 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS M 107 " --> pdb=" O GLN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 134 removed outlier: 3.776A pdb=" N LEU M 134 " --> pdb=" O ASP M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 163 through 168 removed outlier: 3.784A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG M 168 " --> pdb=" O THR M 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 163 through 168' Processing helix chain 'M' and resid 179 through 185 removed outlier: 3.940A pdb=" N ARG M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 190 removed outlier: 3.544A pdb=" N LEU M 190 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 24 removed outlier: 4.123A pdb=" N LEU N 21 " --> pdb=" O LEU N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 39 removed outlier: 4.064A pdb=" N ALA N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.843A pdb=" N LEU N 48 " --> pdb=" O ASN N 44 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE N 49 " --> pdb=" O PRO N 45 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU N 50 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA N 51 " --> pdb=" O THR N 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 44 through 52' Processing helix chain 'N' and resid 60 through 72 removed outlier: 3.691A pdb=" N ALA N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET N 66 " --> pdb=" O ILE N 62 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 96 removed outlier: 3.572A pdb=" N LEU N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 114 Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 144 through 156 removed outlier: 3.560A pdb=" N ALA N 148 " --> pdb=" O HIS N 144 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL N 149 " --> pdb=" O PRO N 145 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS N 153 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP N 154 " --> pdb=" O ALA N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 167 removed outlier: 3.901A pdb=" N SER N 167 " --> pdb=" O LEU N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 186 Processing helix chain 'N' and resid 187 through 190 Processing helix chain 'O' and resid 18 through 23 Processing helix chain 'O' and resid 28 through 39 removed outlier: 4.001A pdb=" N ALA O 34 " --> pdb=" O ALA O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 49 removed outlier: 3.816A pdb=" N LEU O 48 " --> pdb=" O ASN O 44 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE O 49 " --> pdb=" O PRO O 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 44 through 49' Processing helix chain 'O' and resid 60 through 72 removed outlier: 3.531A pdb=" N VAL O 64 " --> pdb=" O ASN O 60 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA O 65 " --> pdb=" O GLN O 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET O 66 " --> pdb=" O ILE O 62 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.738A pdb=" N TYR O 85 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN O 86 " --> pdb=" O GLU O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 86' Processing helix chain 'O' and resid 89 through 96 removed outlier: 3.691A pdb=" N LEU O 96 " --> pdb=" O LEU O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 115 removed outlier: 3.687A pdb=" N LEU O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 128 Processing helix chain 'O' and resid 129 through 132 Processing helix chain 'O' and resid 144 through 151 Processing helix chain 'O' and resid 179 through 185 removed outlier: 3.810A pdb=" N ARG O 183 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 193 Processing helix chain 'P' and resid 18 through 24 Processing helix chain 'P' and resid 28 through 39 removed outlier: 4.016A pdb=" N ALA P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 52 removed outlier: 3.804A pdb=" N LEU P 48 " --> pdb=" O ASN P 44 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE P 49 " --> pdb=" O PRO P 45 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU P 50 " --> pdb=" O GLN P 46 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 44 through 52' Processing helix chain 'P' and resid 60 through 72 removed outlier: 4.237A pdb=" N ALA P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET P 66 " --> pdb=" O ILE P 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN P 67 " --> pdb=" O THR P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 96 Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.892A pdb=" N SER P 105 " --> pdb=" O GLN P 101 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA P 108 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN P 109 " --> pdb=" O SER P 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU P 110 " --> pdb=" O LEU P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 removed outlier: 3.573A pdb=" N ALA P 125 " --> pdb=" O ILE P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 151 Processing helix chain 'P' and resid 162 through 167 removed outlier: 3.636A pdb=" N SER P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 185 removed outlier: 3.574A pdb=" N ARG P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 189 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.775A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 133 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.293A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N HIS A 235 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET A 263 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 197 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN A 238 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A 323 " --> pdb=" O VAL A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.775A pdb=" N ALA B 36 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 133 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.292A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET B 166 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 323 " --> pdb=" O VAL B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.987A pdb=" N ASP C 134 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG C 38 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 132 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER C 40 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU C 130 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 196 through 198 removed outlier: 6.499A pdb=" N LEU C 167 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LYS C 198 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS C 169 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET C 166 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU C 323 " --> pdb=" O VAL C 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 237 through 238 removed outlier: 6.206A pdb=" N LEU C 237 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 262 " --> pdb=" O HIS C 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 81 through 86 removed outlier: 4.001A pdb=" N HIS D 83 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE D 97 " --> pdb=" O HIS D 83 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D 39 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA D 35 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA D 36 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 133 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 166 through 169 removed outlier: 6.354A pdb=" N MET D 166 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N PHE D 399 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY D 168 " --> pdb=" O PHE D 399 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLN D 398 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA D 375 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 323 " --> pdb=" O VAL D 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 196 through 198 removed outlier: 6.919A pdb=" N THR D 197 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN D 238 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS D 235 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET D 263 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU D 237 " --> pdb=" O MET D 263 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 262 " --> pdb=" O HIS D 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB6, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.775A pdb=" N ALA E 36 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 133 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 166 through 167 removed outlier: 6.353A pdb=" N MET E 166 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEU E 323 " --> pdb=" O VAL E 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AB9, first strand: chain 'F' and resid 85 through 86 removed outlier: 3.666A pdb=" N GLU F 85 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA F 36 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU F 133 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N GLY F 305 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU F 130 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 166 through 167 removed outlier: 6.353A pdb=" N MET F 166 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU F 323 " --> pdb=" O VAL F 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 237 through 238 removed outlier: 5.759A pdb=" N LEU F 237 " --> pdb=" O MET F 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AC4, first strand: chain 'G' and resid 36 through 39 Processing sheet with id=AC5, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'G' and resid 234 through 235 removed outlier: 3.670A pdb=" N THR G 197 " --> pdb=" O GLY G 234 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU G 167 " --> pdb=" O PHE G 196 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LYS G 198 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N CYS G 169 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET G 166 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 261 through 263 removed outlier: 6.319A pdb=" N ILE G 262 " --> pdb=" O HIS G 289 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 85 through 86 removed outlier: 3.865A pdb=" N PHE H 39 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA H 36 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 133 " --> pdb=" O ALA H 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 287 through 289 removed outlier: 6.292A pdb=" N ILE H 262 " --> pdb=" O HIS H 289 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS H 235 " --> pdb=" O ILE H 261 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N MET H 263 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU H 237 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR H 197 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN H 238 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU H 167 " --> pdb=" O PHE H 196 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LYS H 198 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS H 169 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET H 166 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU H 323 " --> pdb=" O VAL H 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 350 through 351 1366 hydrogen bonds defined for protein. 3972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.23 Time building geometry restraints manager: 19.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11298 1.33 - 1.45: 7612 1.45 - 1.57: 21483 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 40657 Sorted by residual: bond pdb=" C GLN I 137 " pdb=" N PRO I 138 " ideal model delta sigma weight residual 1.333 1.367 -0.034 7.80e-03 1.64e+04 1.94e+01 bond pdb=" N GLN D 206 " pdb=" CA GLN D 206 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N VAL E 239 " pdb=" CA VAL E 239 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.04e-02 9.25e+03 1.35e+01 bond pdb=" N ILE C 379 " pdb=" CA ILE C 379 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" N HIS O 144 " pdb=" CA HIS O 144 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.04e-02 9.25e+03 1.02e+01 ... (remaining 40652 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.89: 959 105.89 - 113.00: 20718 113.00 - 120.11: 16265 120.11 - 127.23: 16580 127.23 - 134.34: 549 Bond angle restraints: 55071 Sorted by residual: angle pdb=" N ILE P 170 " pdb=" CA ILE P 170 " pdb=" C ILE P 170 " ideal model delta sigma weight residual 113.71 107.30 6.41 9.50e-01 1.11e+00 4.55e+01 angle pdb=" N ILE M 170 " pdb=" CA ILE M 170 " pdb=" C ILE M 170 " ideal model delta sigma weight residual 113.22 104.94 8.28 1.23e+00 6.61e-01 4.53e+01 angle pdb=" N ILE K 170 " pdb=" CA ILE K 170 " pdb=" C ILE K 170 " ideal model delta sigma weight residual 113.53 107.13 6.40 9.80e-01 1.04e+00 4.26e+01 angle pdb=" C SER E 367 " pdb=" N MET E 368 " pdb=" CA MET E 368 " ideal model delta sigma weight residual 121.61 113.22 8.39 1.39e+00 5.18e-01 3.64e+01 angle pdb=" C SER B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 121.61 113.23 8.38 1.39e+00 5.18e-01 3.63e+01 ... (remaining 55066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 22451 26.44 - 52.87: 1473 52.87 - 79.31: 288 79.31 - 105.74: 30 105.74 - 132.18: 1 Dihedral angle restraints: 24243 sinusoidal: 9890 harmonic: 14353 Sorted by residual: dihedral pdb=" CA LYS D 172 " pdb=" C LYS D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta harmonic sigma weight residual 180.00 47.82 132.18 0 5.00e+00 4.00e-02 6.99e+02 dihedral pdb=" CD ARG J 27 " pdb=" NE ARG J 27 " pdb=" CZ ARG J 27 " pdb=" NH1 ARG J 27 " ideal model delta sinusoidal sigma weight residual 0.00 89.93 -89.93 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CD ARG H 191 " pdb=" NE ARG H 191 " pdb=" CZ ARG H 191 " pdb=" NH1 ARG H 191 " ideal model delta sinusoidal sigma weight residual 0.00 -89.10 89.10 1 1.00e+01 1.00e-02 9.45e+01 ... (remaining 24240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3767 0.062 - 0.125: 1665 0.125 - 0.187: 433 0.187 - 0.250: 35 0.250 - 0.312: 17 Chirality restraints: 5917 Sorted by residual: chirality pdb=" CB VAL I 81 " pdb=" CA VAL I 81 " pdb=" CG1 VAL I 81 " pdb=" CG2 VAL I 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE H 203 " pdb=" CA ILE H 203 " pdb=" CG1 ILE H 203 " pdb=" CG2 ILE H 203 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 5914 not shown) Planarity restraints: 7264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 27 " -1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG J 27 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG J 27 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG J 27 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG J 27 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 191 " -1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG H 191 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG H 191 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG H 191 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG H 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 428 " 1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG E 428 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 428 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 428 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG E 428 " 0.016 2.00e-02 2.50e+03 ... (remaining 7261 not shown) Histogram of nonbonded interaction distances: 0.29 - 1.21: 60 1.21 - 2.14: 519 2.14 - 3.06: 26676 3.06 - 3.98: 105877 3.98 - 4.90: 185538 Warning: very small nonbonded interaction distances. Nonbonded interactions: 318670 Sorted by model distance: nonbonded pdb=" C ILE C 351 " pdb=" CG2 THR C 362 " model vdw 0.292 3.690 nonbonded pdb=" O HIS F 295 " pdb=" CG ASP F 299 " model vdw 0.375 3.270 nonbonded pdb=" CG2 VAL F 328 " pdb=" NZ LYS F 336 " model vdw 0.483 3.540 nonbonded pdb=" NH2 ARG D 212 " pdb=" CE2 PHE D 253 " model vdw 0.501 3.420 nonbonded pdb=" CE2 TYR E 236 " pdb=" CE1 HIS E 289 " model vdw 0.502 3.560 ... (remaining 318665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 13 through 191) selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 13 through 191) selection = (chain 'N' and resid 13 through 191) selection = (chain 'O' and resid 13 through 191) selection = (chain 'P' and resid 13 through 191) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 25093 2.51 5 N 7133 2.21 5 O 7342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.180 Check model and map are aligned: 0.630 Convert atoms to be neutral: 0.350 Process input model: 99.940 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.009 0.059 40657 Z= 0.571 Angle : 1.334 14.129 55071 Z= 0.867 Chirality : 0.072 0.312 5917 Planarity : 0.039 0.494 7264 Dihedral : 17.186 132.177 15011 Min Nonbonded Distance : 0.292 Molprobity Statistics. All-atom Clashscore : 54.20 Ramachandran Plot: Outliers : 2.20 % Allowed : 11.96 % Favored : 85.84 % Rotamer Outliers : 14.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.34 % 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: -4.97 (0.09), residues: 4993 helix: -2.91 (0.08), residues: 2050 sheet: -3.44 (0.19), residues: 440 loop : -3.67 (0.10), residues: 2503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2047 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 603 poor density : 1444 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 603 outliers final: 366 residues processed: 1898 average time/residue: 0.5479 time to fit residues: 1626.0397 Evaluate side-chains 1182 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 816 time to evaluate : 4.693 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 366 outliers final: 42 residues processed: 366 average time/residue: 0.4854 time to fit residues: 294.6375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 5.9990 chunk 373 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 386 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 447 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 112 ASN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 160 ASN B 209 GLN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 146 GLN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN D 160 ASN D 202 ASN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 HIS E 112 ASN E 160 ASN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 ASN F 112 ASN F 160 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS G 112 ASN ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN G 284 ASN G 324 HIS G 426 GLN H 112 ASN H 160 ASN ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN K 67 GLN K 86 GLN K 109 GLN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN L 175 GLN M 46 GLN M 59 GLN M 140 ASN N 67 GLN O 46 GLN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 152 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 40657 Z= 0.323 Angle : 0.822 13.429 55071 Z= 0.422 Chirality : 0.049 0.316 5917 Planarity : 0.006 0.082 7264 Dihedral : 6.572 63.952 5490 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.67 % Favored : 89.95 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.15 % 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: -3.45 (0.10), residues: 4993 helix: -1.30 (0.10), residues: 2113 sheet: -2.71 (0.22), residues: 392 loop : -3.18 (0.11), residues: 2488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1136 time to evaluate : 5.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 1153 average time/residue: 0.5405 time to fit residues: 1008.2916 Evaluate side-chains 776 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 771 time to evaluate : 4.779 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4023 time to fit residues: 10.1366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 372 optimal weight: 8.9990 chunk 304 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 448 optimal weight: 6.9990 chunk 484 optimal weight: 0.9980 chunk 399 optimal weight: 0.9990 chunk 444 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 359 optimal weight: 9.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 ASN E 202 ASN E 209 GLN ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 HIS ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 HIS H 204 ASN H 291 HIS H 324 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN J 58 GLN L 75 GLN ** L 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 GLN N 152 GLN O 101 GLN P 140 ASN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 40657 Z= 0.211 Angle : 0.727 13.620 55071 Z= 0.365 Chirality : 0.045 0.233 5917 Planarity : 0.005 0.065 7264 Dihedral : 5.965 43.290 5490 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.53 % Favored : 90.11 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.11), residues: 4993 helix: -0.62 (0.11), residues: 2082 sheet: -2.52 (0.24), residues: 376 loop : -2.81 (0.11), residues: 2535 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1127 time to evaluate : 4.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 1132 average time/residue: 0.5066 time to fit residues: 931.8911 Evaluate side-chains 766 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 765 time to evaluate : 4.862 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4159 time to fit residues: 7.1923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 443 optimal weight: 20.0000 chunk 337 optimal weight: 0.6980 chunk 232 optimal weight: 0.0270 chunk 49 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 450 optimal weight: 6.9990 chunk 476 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 426 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS A 324 HIS A 426 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 324 HIS C 380 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 ASN E 209 GLN ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 301 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN L 58 GLN L 60 ASN L 75 GLN M 58 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN O 86 GLN P 46 GLN ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 40657 Z= 0.262 Angle : 0.709 11.369 55071 Z= 0.360 Chirality : 0.045 0.257 5917 Planarity : 0.005 0.119 7264 Dihedral : 5.795 45.110 5490 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.03 % Favored : 89.65 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 4993 helix: -0.35 (0.11), residues: 2084 sheet: -2.34 (0.25), residues: 376 loop : -2.66 (0.11), residues: 2533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1015 time to evaluate : 4.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 1019 average time/residue: 0.5430 time to fit residues: 910.4836 Evaluate side-chains 730 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 727 time to evaluate : 5.270 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4293 time to fit residues: 8.9943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 396 optimal weight: 9.9990 chunk 270 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 354 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 406 optimal weight: 20.0000 chunk 329 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 427 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN G 324 HIS G 417 ASN H 209 GLN H 274 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 417 ASN ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 GLN L 60 ASN ** L 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN M 58 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.129 40657 Z= 0.207 Angle : 0.691 14.017 55071 Z= 0.347 Chirality : 0.044 0.252 5917 Planarity : 0.005 0.130 7264 Dihedral : 5.547 44.697 5490 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.67 % Favored : 90.03 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.12), residues: 4993 helix: -0.14 (0.12), residues: 2100 sheet: -2.47 (0.21), residues: 488 loop : -2.61 (0.12), residues: 2405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1036 time to evaluate : 5.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 1040 average time/residue: 0.4995 time to fit residues: 853.6034 Evaluate side-chains 744 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 4.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 0.6980 chunk 429 optimal weight: 0.0070 chunk 94 optimal weight: 3.9990 chunk 279 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 476 optimal weight: 2.9990 chunk 395 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN A 291 HIS A 417 ASN B 204 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 GLN L 58 GLN L 60 ASN L 75 GLN M 140 ASN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN O 60 ASN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN P 144 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.117 40657 Z= 0.202 Angle : 0.685 13.483 55071 Z= 0.342 Chirality : 0.044 0.239 5917 Planarity : 0.005 0.130 7264 Dihedral : 5.452 41.675 5490 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.31 % Favored : 90.41 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 4993 helix: 0.01 (0.12), residues: 2101 sheet: -2.42 (0.21), residues: 480 loop : -2.52 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1004 time to evaluate : 4.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1006 average time/residue: 0.5120 time to fit residues: 846.0141 Evaluate side-chains 723 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 723 time to evaluate : 4.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 459 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 348 optimal weight: 6.9990 chunk 269 optimal weight: 20.0000 chunk 401 optimal weight: 0.9990 chunk 266 optimal weight: 8.9990 chunk 475 optimal weight: 20.0000 chunk 297 optimal weight: 2.9990 chunk 289 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 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 274 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 HIS ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 209 GLN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN H 274 ASN ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN L 75 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.176 40657 Z= 0.226 Angle : 0.711 18.791 55071 Z= 0.356 Chirality : 0.045 0.238 5917 Planarity : 0.005 0.140 7264 Dihedral : 5.443 41.542 5490 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.65 % Favored : 90.09 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 4993 helix: 0.06 (0.12), residues: 2099 sheet: -2.27 (0.20), residues: 488 loop : -2.47 (0.12), residues: 2406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 953 time to evaluate : 5.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 958 average time/residue: 0.5091 time to fit residues: 808.1591 Evaluate side-chains 697 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 697 time to evaluate : 5.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 293 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 323 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS B 112 ASN B 150 HIS ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS B 417 ASN C 150 HIS C 274 ASN C 291 HIS ** C 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 ASN F 426 GLN G 274 ASN G 426 GLN ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 274 ASN ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 HIS H 324 HIS ** H 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN L 60 ASN L 67 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.132 40657 Z= 0.385 Angle : 0.807 11.506 55071 Z= 0.411 Chirality : 0.048 0.340 5917 Planarity : 0.005 0.101 7264 Dihedral : 5.943 43.133 5490 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.00 % Favored : 88.74 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.12), residues: 4993 helix: -0.15 (0.11), residues: 2075 sheet: -2.19 (0.22), residues: 432 loop : -2.49 (0.12), residues: 2486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 867 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 871 average time/residue: 0.5217 time to fit residues: 745.4652 Evaluate side-chains 621 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 621 time to evaluate : 4.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 415 optimal weight: 2.9990 chunk 442 optimal weight: 0.0870 chunk 266 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 347 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 chunk 400 optimal weight: 5.9990 chunk 418 optimal weight: 20.0000 chunk 441 optimal weight: 6.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN M 140 ASN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN ** O 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.315 40657 Z= 0.273 Angle : 0.743 17.795 55071 Z= 0.374 Chirality : 0.046 0.289 5917 Planarity : 0.005 0.152 7264 Dihedral : 5.775 42.031 5490 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.21 % Favored : 89.51 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.12), residues: 4993 helix: -0.09 (0.11), residues: 2108 sheet: -2.21 (0.22), residues: 416 loop : -2.53 (0.12), residues: 2469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 911 time to evaluate : 4.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 915 average time/residue: 0.4966 time to fit residues: 753.4150 Evaluate side-chains 668 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 4.991 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 9.9990 chunk 468 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 491 optimal weight: 9.9990 chunk 452 optimal weight: 10.0000 chunk 391 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 302 optimal weight: 0.0970 chunk 239 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN L 60 ASN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN P 140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.677 40657 Z= 0.373 Angle : 0.857 73.898 55071 Z= 0.417 Chirality : 0.049 0.661 5917 Planarity : 0.005 0.126 7264 Dihedral : 5.769 41.724 5490 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.43 % Favored : 89.24 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.43 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.12), residues: 4993 helix: -0.13 (0.11), residues: 2126 sheet: -2.19 (0.22), residues: 432 loop : -2.58 (0.12), residues: 2435 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9986 Ramachandran restraints generated. 4993 Oldfield, 0 Emsley, 4993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 853 time to evaluate : 5.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 856 average time/residue: 0.5020 time to fit residues: 715.6256 Evaluate side-chains 650 residues out of total 4128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 5.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 310 optimal weight: 9.9990 chunk 416 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 360 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 391 optimal weight: 30.0000 chunk 163 optimal weight: 9.9990 chunk 402 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 291 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN M 103 GLN ** N 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118177 restraints weight = 82922.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121549 restraints weight = 48164.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123740 restraints weight = 30093.504| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.389 40657 Z= 0.402 Angle : 0.883 53.315 55071 Z= 0.444 Chirality : 0.049 0.400 5917 Planarity : 0.006 0.128 7264 Dihedral : 6.060 44.834 5490 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.90 % Favored : 87.76 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.12), residues: 4993 helix: -0.34 (0.11), residues: 2122 sheet: -2.27 (0.22), residues: 432 loop : -2.59 (0.12), residues: 2439 =============================================================================== Job complete usr+sys time: 12660.49 seconds wall clock time: 227 minutes 9.81 seconds (13629.81 seconds total)