Starting phenix.real_space_refine on Sun Mar 10 21:49:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/03_2024/7xok_33350.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/03_2024/7xok_33350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/03_2024/7xok_33350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/03_2024/7xok_33350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/03_2024/7xok_33350.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xok_33350/03_2024/7xok_33350.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 33558 2.51 5 N 9310 2.21 5 O 10822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 188": "OD1" <-> "OD2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "G TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 354": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 53970 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "G" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "H" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "I" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "J" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "L" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "N" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 20.85, per 1000 atoms: 0.39 Number of scatterers: 53970 At special positions: 0 Unit cell: (155.73, 160.08, 155.73, 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 280 16.00 O 10822 8.00 N 9310 7.00 C 33558 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: 16.14 Conformation dependent library (CDL) restraints added in 7.5 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 84 sheets defined 59.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.65 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.144A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.501A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 229 through 244 removed outlier: 4.374A pdb=" N MET A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.710A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 427 removed outlier: 4.039A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.128A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.629A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 229 through 244 removed outlier: 4.324A pdb=" N MET B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.954A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 458 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.039A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 64 through 86 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.602A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 removed outlier: 3.845A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 458 Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.500A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.102A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.510A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.558A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 229 through 244 removed outlier: 4.521A pdb=" N MET D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 256 through 269 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 374 Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.913A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 458 Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.545A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 29 removed outlier: 4.191A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 64 through 86 Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.591A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 229 through 244 removed outlier: 4.362A pdb=" N MET E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 427 removed outlier: 4.026A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 458 Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 29 removed outlier: 4.232A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.519A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.558A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 427 removed outlier: 3.966A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 458 Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.103A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 59 Processing helix chain 'G' and resid 64 through 86 Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.700A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 removed outlier: 4.236A pdb=" N GLY G 375 " --> pdb=" O LYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 427 removed outlier: 3.828A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 458 Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 Processing helix chain 'H' and resid 9 through 29 removed outlier: 4.131A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 Processing helix chain 'H' and resid 64 through 86 Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.627A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 229 through 244 removed outlier: 4.359A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 256 through 269 Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 375 removed outlier: 4.095A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 427 removed outlier: 3.826A pdb=" N ILE H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 458 Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 497 through 516 Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.093A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 64 through 86 Processing helix chain 'I' and resid 88 through 110 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.572A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 229 through 244 removed outlier: 4.418A pdb=" N MET I 233 " --> pdb=" O ASN I 229 " (cutoff:3.500A) Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.840A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA I 260 " --> pdb=" O GLY I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 removed outlier: 4.236A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 removed outlier: 3.851A pdb=" N ILE I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 458 Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.037A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'J' and resid 64 through 86 Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.611A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 244 removed outlier: 4.234A pdb=" N MET J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 256 through 269 Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 374 Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 427 removed outlier: 3.866A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 458 Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 9 through 29 removed outlier: 4.139A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 59 Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.580A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 244 removed outlier: 4.296A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 338 through 355 Processing helix chain 'K' and resid 358 through 374 Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 427 removed outlier: 3.890A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 458 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 removed outlier: 3.513A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 516 Processing helix chain 'L' and resid 9 through 29 removed outlier: 4.141A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 Processing helix chain 'L' and resid 64 through 86 Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.569A pdb=" N GLY L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 229 through 244 removed outlier: 4.427A pdb=" N MET L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 269 Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 338 through 356 removed outlier: 3.620A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 374 Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 427 removed outlier: 3.954A pdb=" N ILE L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 458 Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 9 through 29 removed outlier: 4.126A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 Processing helix chain 'M' and resid 64 through 86 Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.534A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 232 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 256 through 269 Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 313 through 317 Processing helix chain 'M' and resid 338 through 356 removed outlier: 3.752A pdb=" N ILE M 342 " --> pdb=" O GLU M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 375 removed outlier: 4.125A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 427 removed outlier: 3.957A pdb=" N ILE M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 433 through 458 Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 497 through 516 Processing helix chain 'N' and resid 9 through 29 removed outlier: 4.062A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Processing helix chain 'N' and resid 64 through 86 Processing helix chain 'N' and resid 88 through 110 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.642A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 229 through 244 removed outlier: 4.396A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 256 through 269 Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 338 through 356 removed outlier: 3.590A pdb=" N ILE N 342 " --> pdb=" O GLU N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 374 Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 427 removed outlier: 3.897A pdb=" N ILE N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 458 Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 461 through 472 removed outlier: 3.505A pdb=" N VAL N 465 " --> pdb=" O GLU N 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.492A pdb=" N ASN G 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS A 519 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.345A pdb=" N ASN A 37 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS B 519 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.203A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 8.432A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.508A pdb=" N GLU A 484 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 50 removed outlier: 7.012A pdb=" N ASN B 37 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N VAL C 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 39 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ASP C 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.479A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.169A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 213 through 216 removed outlier: 8.344A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.846A pdb=" N ASN C 37 " --> pdb=" O CYS D 519 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL D 521 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 39 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP D 523 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.531A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.201A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 251 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 213 through 216 removed outlier: 8.174A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 479 removed outlier: 3.501A pdb=" N GLU C 484 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.526A pdb=" N ASN D 37 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS E 519 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 174 through 179 Processing sheet with id=AC4, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.328A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.328A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 251 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AC7, first strand: chain 'D' and resid 476 through 479 removed outlier: 3.610A pdb=" N GLU D 484 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.919A pdb=" N ASN E 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL F 521 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASP F 523 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AD1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.271A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.271A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA E 251 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'E' and resid 476 through 479 removed outlier: 3.508A pdb=" N GLU E 484 " --> pdb=" O ASN E 479 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.536A pdb=" N ASN F 37 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS G 519 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AD7, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.575A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.575A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'F' and resid 476 through 479 removed outlier: 3.607A pdb=" N GLU F 484 " --> pdb=" O ASN F 479 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.557A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.200A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.200A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 251 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE6, first strand: chain 'G' and resid 476 through 479 removed outlier: 3.508A pdb=" N GLU G 484 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.396A pdb=" N ASN N 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS H 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.388A pdb=" N ASN H 37 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS I 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS I 7 " --> pdb=" O MET I 520 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.482A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.191A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 213 through 216 removed outlier: 8.507A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'H' and resid 476 through 479 removed outlier: 3.539A pdb=" N GLU H 484 " --> pdb=" O ASN H 479 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.982A pdb=" N ASN I 37 " --> pdb=" O CYS J 519 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL J 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL I 39 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N ASP J 523 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 174 through 179 Processing sheet with id=AF7, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.344A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 213 through 216 removed outlier: 8.458A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG1, first strand: chain 'I' and resid 476 through 478 Processing sheet with id=AG2, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.977A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG4, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.264A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 251 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 213 through 216 removed outlier: 8.405A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG7, first strand: chain 'J' and resid 476 through 479 removed outlier: 3.510A pdb=" N GLU J 484 " --> pdb=" O ASN J 479 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 48 through 50 removed outlier: 6.490A pdb=" N ASN K 37 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS L 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS L 7 " --> pdb=" O MET L 520 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AH1, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.226A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA K 251 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 213 through 216 removed outlier: 8.417A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH4, first strand: chain 'K' and resid 476 through 479 removed outlier: 3.571A pdb=" N GLU K 484 " --> pdb=" O ASN K 479 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.886A pdb=" N ASN L 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL M 521 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL L 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ASP M 523 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AH7, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.193A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.193A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI1, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AI2, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.871A pdb=" N ASN M 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL N 521 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL M 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP N 523 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.584A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 193 through 195 removed outlier: 6.181A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 193 through 195 removed outlier: 6.181A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA M 251 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'M' and resid 476 through 479 removed outlier: 3.610A pdb=" N GLU M 484 " --> pdb=" O ASN M 479 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 174 through 179 Processing sheet with id=AI9, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.252A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 213 through 216 removed outlier: 8.346A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'N' and resid 476 through 479 3822 hydrogen bonds defined for protein. 11004 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: 23.57 Time building geometry restraints manager: 17.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18690 1.34 - 1.46: 4397 1.46 - 1.57: 30757 1.57 - 1.69: 0 1.69 - 1.81: 518 Bond restraints: 54362 Sorted by residual: bond pdb=" CB MET G 520 " pdb=" CG MET G 520 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CB MET E 520 " pdb=" CG MET E 520 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.74e+00 bond pdb=" CB MET C 520 " pdb=" CG MET C 520 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CA MET E 520 " pdb=" CB MET E 520 " ideal model delta sigma weight residual 1.535 1.505 0.031 2.09e-02 2.29e+03 2.15e+00 bond pdb=" SD MET B 520 " pdb=" CE MET B 520 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.81e+00 ... (remaining 54357 not shown) Histogram of bond angle deviations from ideal: 94.70 - 102.03: 230 102.03 - 109.36: 2758 109.36 - 116.69: 35811 116.69 - 124.02: 34084 124.02 - 131.35: 519 Bond angle restraints: 73402 Sorted by residual: angle pdb=" CB ARG H 350 " pdb=" CG ARG H 350 " pdb=" CD ARG H 350 " ideal model delta sigma weight residual 111.30 121.96 -10.66 2.30e+00 1.89e-01 2.15e+01 angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" CB GLU D 164 " ideal model delta sigma weight residual 110.28 116.12 -5.84 1.55e+00 4.16e-01 1.42e+01 angle pdb=" N GLU M 354 " pdb=" CA GLU M 354 " pdb=" CB GLU M 354 " ideal model delta sigma weight residual 110.28 116.10 -5.82 1.55e+00 4.16e-01 1.41e+01 angle pdb=" N GLU H 164 " pdb=" CA GLU H 164 " pdb=" CB GLU H 164 " ideal model delta sigma weight residual 110.16 115.59 -5.43 1.48e+00 4.57e-01 1.34e+01 angle pdb=" N GLN N 352 " pdb=" CA GLN N 352 " pdb=" CB GLN N 352 " ideal model delta sigma weight residual 110.16 115.27 -5.11 1.48e+00 4.57e-01 1.19e+01 ... (remaining 73397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 30381 16.35 - 32.70: 2689 32.70 - 49.04: 546 49.04 - 65.39: 109 65.39 - 81.74: 43 Dihedral angle restraints: 33768 sinusoidal: 13076 harmonic: 20692 Sorted by residual: dihedral pdb=" CA MET C 233 " pdb=" C MET C 233 " pdb=" N LEU C 234 " pdb=" CA LEU C 234 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA MET M 233 " pdb=" C MET M 233 " pdb=" N LEU M 234 " pdb=" CA LEU M 234 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA MET F 233 " pdb=" C MET F 233 " pdb=" N LEU F 234 " pdb=" CA LEU F 234 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 33765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 6527 0.037 - 0.074: 1672 0.074 - 0.111: 637 0.111 - 0.148: 93 0.148 - 0.185: 3 Chirality restraints: 8932 Sorted by residual: chirality pdb=" CA ARG H 350 " pdb=" N ARG H 350 " pdb=" C ARG H 350 " pdb=" CB ARG H 350 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA MET F 447 " pdb=" N MET F 447 " pdb=" C MET F 447 " pdb=" CB MET F 447 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA GLU M 354 " pdb=" N GLU M 354 " pdb=" C GLU M 354 " pdb=" CB GLU M 354 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 8929 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 362 " 0.162 9.50e-02 1.11e+02 7.31e-02 3.93e+00 pdb=" NE ARG H 362 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG H 362 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 362 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 362 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 351 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C GLN H 351 " -0.027 2.00e-02 2.50e+03 pdb=" O GLN H 351 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN H 352 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 350 " 0.116 9.50e-02 1.11e+02 5.26e-02 2.31e+00 pdb=" NE ARG H 350 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG H 350 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG H 350 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 350 " -0.000 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1381 2.71 - 3.26: 57207 3.26 - 3.80: 94154 3.80 - 4.35: 111710 4.35 - 4.90: 191924 Nonbonded interactions: 456376 Sorted by model distance: nonbonded pdb=" OD2 ASP N 291 " pdb=" NH1 ARG N 368 " model vdw 2.160 2.520 nonbonded pdb=" OG SER A 358 " pdb=" OD2 ASP A 361 " model vdw 2.202 2.440 nonbonded pdb=" OD2 ASP A 291 " pdb=" NH1 ARG A 368 " model vdw 2.203 2.520 nonbonded pdb=" OD2 ASP F 291 " pdb=" NH2 ARG F 368 " model vdw 2.215 2.520 nonbonded pdb=" OG SER G 463 " pdb=" OG SER M 463 " model vdw 2.215 2.440 ... (remaining 456371 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 7.530 Check model and map are aligned: 0.590 Set scattering table: 0.400 Process input model: 111.990 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.003 0.058 54362 Z= 0.227 Angle : 0.496 10.656 73402 Z= 0.271 Chirality : 0.039 0.185 8932 Planarity : 0.003 0.073 9618 Dihedral : 13.145 81.741 20496 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.10), residues: 7308 helix: 2.32 (0.08), residues: 4242 sheet: 1.06 (0.15), residues: 1148 loop : -0.15 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 401 PHE 0.008 0.001 PHE G 204 TYR 0.013 0.001 TYR G 360 ARG 0.014 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.615 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.8079 (mmm) cc_final: 0.7799 (mmm) REVERT: C 389 MET cc_start: 0.8905 (tmm) cc_final: 0.8516 (tmm) REVERT: F 59 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8468 (mm-30) REVERT: F 114 MET cc_start: 0.8519 (mmm) cc_final: 0.8282 (mmm) REVERT: H 193 MET cc_start: 0.8479 (ttm) cc_final: 0.8159 (ttm) REVERT: I 307 MET cc_start: 0.8613 (pmm) cc_final: 0.8392 (pmm) REVERT: K 44 PHE cc_start: 0.8091 (m-80) cc_final: 0.7870 (m-10) REVERT: L 138 CYS cc_start: 0.7909 (t) cc_final: 0.7693 (t) outliers start: 0 outliers final: 1 residues processed: 384 average time/residue: 1.3974 time to fit residues: 671.9392 Evaluate side-chains 306 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 473 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 9.9990 chunk 551 optimal weight: 40.0000 chunk 306 optimal weight: 0.9990 chunk 188 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 294 optimal weight: 30.0000 chunk 570 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 346 optimal weight: 50.0000 chunk 424 optimal weight: 5.9990 chunk 661 optimal weight: 30.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 54362 Z= 0.250 Angle : 0.520 8.597 73402 Z= 0.279 Chirality : 0.041 0.183 8932 Planarity : 0.003 0.044 9618 Dihedral : 3.999 122.146 7730 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.74 % Allowed : 5.96 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.10), residues: 7308 helix: 2.34 (0.08), residues: 4242 sheet: 0.87 (0.15), residues: 1064 loop : -0.16 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 401 PHE 0.019 0.001 PHE F 204 TYR 0.014 0.001 TYR D 360 ARG 0.008 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 328 time to evaluate : 4.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.8140 (mmm) cc_final: 0.7840 (mmm) REVERT: A 193 MET cc_start: 0.8664 (ptp) cc_final: 0.8264 (ptt) REVERT: B 267 MET cc_start: 0.8408 (mmm) cc_final: 0.8064 (mpp) REVERT: B 389 MET cc_start: 0.8659 (tmm) cc_final: 0.8369 (tmm) REVERT: C 389 MET cc_start: 0.8976 (tmm) cc_final: 0.8582 (tmm) REVERT: D 111 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8237 (mpm) REVERT: D 144 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9155 (mp) REVERT: D 389 MET cc_start: 0.8788 (tmm) cc_final: 0.8565 (tmt) REVERT: E 16 MET cc_start: 0.8659 (mtm) cc_final: 0.8175 (mtt) REVERT: E 111 MET cc_start: 0.8721 (mpp) cc_final: 0.8376 (mpt) REVERT: F 59 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8461 (mm-30) REVERT: F 114 MET cc_start: 0.8555 (mmm) cc_final: 0.8300 (mmm) REVERT: F 204 PHE cc_start: 0.8119 (m-80) cc_final: 0.7875 (m-80) REVERT: G 397 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8527 (mm-30) REVERT: H 193 MET cc_start: 0.8659 (ttm) cc_final: 0.8308 (ttm) REVERT: H 491 MET cc_start: 0.8966 (mtm) cc_final: 0.8706 (mtp) REVERT: I 307 MET cc_start: 0.8582 (pmm) cc_final: 0.8336 (pmm) REVERT: I 389 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8472 (tmt) REVERT: J 233 MET cc_start: 0.8769 (pmm) cc_final: 0.8520 (pmm) REVERT: K 44 PHE cc_start: 0.8060 (m-80) cc_final: 0.7850 (m-10) REVERT: K 111 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8440 (mtt) REVERT: L 138 CYS cc_start: 0.8004 (t) cc_final: 0.7752 (t) REVERT: M 307 MET cc_start: 0.8471 (tpt) cc_final: 0.8261 (tpt) REVERT: N 389 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8217 (tmt) outliers start: 42 outliers final: 6 residues processed: 335 average time/residue: 1.3903 time to fit residues: 584.8554 Evaluate side-chains 319 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 308 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain N residue 389 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 550 optimal weight: 6.9990 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 20.0000 chunk 662 optimal weight: 20.0000 chunk 715 optimal weight: 6.9990 chunk 589 optimal weight: 7.9990 chunk 656 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 531 optimal weight: 2.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 479 ASN ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54362 Z= 0.264 Angle : 0.508 7.558 73402 Z= 0.271 Chirality : 0.040 0.165 8932 Planarity : 0.003 0.027 9618 Dihedral : 3.757 18.267 7728 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.88 % Allowed : 7.94 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.10), residues: 7308 helix: 2.34 (0.08), residues: 4242 sheet: 0.66 (0.15), residues: 1064 loop : -0.19 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.013 0.001 PHE B 204 TYR 0.011 0.001 TYR F 199 ARG 0.007 0.000 ARG H 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 321 time to evaluate : 4.572 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: A 111 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8132 (mtt) REVERT: A 114 MET cc_start: 0.8126 (mmm) cc_final: 0.7804 (mmm) REVERT: A 193 MET cc_start: 0.8663 (ptp) cc_final: 0.8320 (ptt) REVERT: A 352 GLN cc_start: 0.9336 (mm110) cc_final: 0.9115 (mm110) REVERT: A 488 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8417 (mmm) REVERT: B 389 MET cc_start: 0.8665 (tmm) cc_final: 0.7817 (tmm) REVERT: C 166 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8238 (mtt) REVERT: C 389 MET cc_start: 0.9004 (tmm) cc_final: 0.8584 (tmm) REVERT: D 144 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9150 (mp) REVERT: D 221 LEU cc_start: 0.9388 (tp) cc_final: 0.9168 (tm) REVERT: D 389 MET cc_start: 0.8781 (tmm) cc_final: 0.8179 (tmt) REVERT: E 16 MET cc_start: 0.8510 (mtm) cc_final: 0.8232 (mtt) REVERT: E 111 MET cc_start: 0.8741 (mpp) cc_final: 0.8338 (mpt) REVERT: F 59 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8465 (mm-30) REVERT: F 114 MET cc_start: 0.8579 (mmm) cc_final: 0.8318 (mmm) REVERT: F 204 PHE cc_start: 0.8130 (m-80) cc_final: 0.7847 (m-80) REVERT: F 233 MET cc_start: 0.8406 (pmt) cc_final: 0.7733 (ppp) REVERT: G 389 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6388 (tmt) REVERT: G 397 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8540 (mm-30) REVERT: H 193 MET cc_start: 0.8628 (ttm) cc_final: 0.8328 (ttm) REVERT: H 307 MET cc_start: 0.8854 (pmt) cc_final: 0.8524 (pmm) REVERT: I 307 MET cc_start: 0.8583 (pmm) cc_final: 0.8331 (pmm) REVERT: I 389 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8532 (tmt) REVERT: J 233 MET cc_start: 0.8770 (pmm) cc_final: 0.8522 (pmm) REVERT: J 389 MET cc_start: 0.8805 (tmt) cc_final: 0.8603 (tmt) REVERT: K 44 PHE cc_start: 0.8051 (m-80) cc_final: 0.7846 (m-10) REVERT: L 138 CYS cc_start: 0.8076 (t) cc_final: 0.7790 (t) REVERT: L 146 GLN cc_start: 0.9445 (OUTLIER) cc_final: 0.9149 (tm-30) REVERT: L 366 GLN cc_start: 0.9537 (mm110) cc_final: 0.9271 (mm110) outliers start: 50 outliers final: 15 residues processed: 338 average time/residue: 1.4391 time to fit residues: 606.5026 Evaluate side-chains 331 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 309 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 166 MET Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 354 GLU Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 9.9990 chunk 497 optimal weight: 8.9990 chunk 343 optimal weight: 0.0040 chunk 73 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 444 optimal weight: 20.0000 chunk 664 optimal weight: 5.9990 chunk 703 optimal weight: 9.9990 chunk 347 optimal weight: 40.0000 chunk 629 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 GLN ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 467 ASN L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 54362 Z= 0.209 Angle : 0.484 8.263 73402 Z= 0.258 Chirality : 0.039 0.163 8932 Planarity : 0.003 0.027 9618 Dihedral : 3.736 16.546 7728 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.83 % Allowed : 9.64 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4256 sheet: 0.56 (0.15), residues: 1064 loop : -0.20 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.015 0.001 PHE B 204 TYR 0.015 0.001 TYR B 360 ARG 0.005 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 335 time to evaluate : 5.330 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: A 73 MET cc_start: 0.8102 (mtm) cc_final: 0.7785 (mtp) REVERT: A 114 MET cc_start: 0.8099 (mmm) cc_final: 0.7784 (mmm) REVERT: A 193 MET cc_start: 0.8653 (ptp) cc_final: 0.8322 (ptt) REVERT: A 488 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8419 (mmm) REVERT: B 267 MET cc_start: 0.8446 (mmm) cc_final: 0.8016 (mtp) REVERT: B 389 MET cc_start: 0.8673 (tmm) cc_final: 0.7800 (tmm) REVERT: C 16 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8250 (mtt) REVERT: C 389 MET cc_start: 0.9025 (tmm) cc_final: 0.8607 (tmm) REVERT: D 111 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8224 (mpm) REVERT: D 144 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9100 (mp) REVERT: D 221 LEU cc_start: 0.9380 (tp) cc_final: 0.9164 (tm) REVERT: E 76 GLU cc_start: 0.8513 (tp30) cc_final: 0.8311 (tp30) REVERT: F 59 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8470 (mm-30) REVERT: F 114 MET cc_start: 0.8575 (mmm) cc_final: 0.8307 (mmm) REVERT: F 204 PHE cc_start: 0.8184 (m-80) cc_final: 0.7853 (m-80) REVERT: G 397 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8552 (mm-30) REVERT: H 193 MET cc_start: 0.8592 (ttm) cc_final: 0.8304 (ttm) REVERT: I 307 MET cc_start: 0.8595 (pmm) cc_final: 0.8348 (pmm) REVERT: I 389 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8438 (tmt) REVERT: J 233 MET cc_start: 0.8808 (pmm) cc_final: 0.8540 (pmm) REVERT: J 250 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8313 (pp) REVERT: K 44 PHE cc_start: 0.8036 (m-80) cc_final: 0.7830 (m-10) REVERT: K 307 MET cc_start: 0.8985 (mpm) cc_final: 0.8710 (mpm) REVERT: L 138 CYS cc_start: 0.8100 (t) cc_final: 0.7800 (t) REVERT: L 146 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9195 (tm-30) REVERT: L 307 MET cc_start: 0.8845 (pmm) cc_final: 0.8554 (pmm) REVERT: L 366 GLN cc_start: 0.9538 (mm110) cc_final: 0.9272 (mm110) REVERT: N 389 MET cc_start: 0.8468 (tmt) cc_final: 0.8210 (tmt) outliers start: 47 outliers final: 13 residues processed: 353 average time/residue: 1.4152 time to fit residues: 626.5077 Evaluate side-chains 331 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 311 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 5.9990 chunk 399 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 523 optimal weight: 0.7980 chunk 290 optimal weight: 10.0000 chunk 600 optimal weight: 30.0000 chunk 486 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 631 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 ASN ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 54362 Z= 0.229 Angle : 0.496 8.813 73402 Z= 0.264 Chirality : 0.039 0.172 8932 Planarity : 0.003 0.027 9618 Dihedral : 3.741 15.977 7728 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.81 % Allowed : 10.73 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4256 sheet: 0.50 (0.15), residues: 1064 loop : -0.21 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.016 0.001 PHE B 204 TYR 0.010 0.001 TYR L 360 ARG 0.007 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 321 time to evaluate : 4.656 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: A 69 MET cc_start: 0.7697 (mtt) cc_final: 0.7257 (mtt) REVERT: A 73 MET cc_start: 0.8123 (mtm) cc_final: 0.7794 (mtp) REVERT: A 114 MET cc_start: 0.8078 (mmm) cc_final: 0.7762 (mmm) REVERT: A 193 MET cc_start: 0.8634 (ptp) cc_final: 0.8248 (ptt) REVERT: A 488 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8432 (mmm) REVERT: B 267 MET cc_start: 0.8414 (mmm) cc_final: 0.7968 (mtp) REVERT: B 389 MET cc_start: 0.8659 (tmm) cc_final: 0.7803 (tmm) REVERT: C 389 MET cc_start: 0.9028 (tmm) cc_final: 0.8642 (tmm) REVERT: D 111 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8184 (mpm) REVERT: D 144 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9078 (mp) REVERT: D 221 LEU cc_start: 0.9436 (tp) cc_final: 0.9212 (tm) REVERT: F 59 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8482 (mm-30) REVERT: F 114 MET cc_start: 0.8573 (mmm) cc_final: 0.8304 (mmm) REVERT: F 204 PHE cc_start: 0.8190 (m-80) cc_final: 0.7787 (m-80) REVERT: F 233 MET cc_start: 0.8392 (pmt) cc_final: 0.7862 (ppp) REVERT: F 520 MET cc_start: 0.8568 (mtp) cc_final: 0.8335 (mtp) REVERT: G 397 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8556 (mm-30) REVERT: H 193 MET cc_start: 0.8581 (ttm) cc_final: 0.8280 (ttm) REVERT: H 447 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8665 (mmt) REVERT: I 307 MET cc_start: 0.8588 (pmm) cc_final: 0.8376 (pmm) REVERT: I 389 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8451 (tmt) REVERT: J 233 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8488 (pmm) REVERT: J 389 MET cc_start: 0.8832 (tmt) cc_final: 0.8572 (tmt) REVERT: K 44 PHE cc_start: 0.8046 (m-80) cc_final: 0.7825 (m-10) REVERT: K 307 MET cc_start: 0.8972 (mpm) cc_final: 0.8678 (mpm) REVERT: L 138 CYS cc_start: 0.8110 (t) cc_final: 0.7859 (t) REVERT: L 146 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9185 (tm-30) REVERT: L 307 MET cc_start: 0.8736 (pmm) cc_final: 0.8433 (pmm) REVERT: L 366 GLN cc_start: 0.9547 (mm110) cc_final: 0.9270 (mm110) REVERT: N 389 MET cc_start: 0.8487 (tmt) cc_final: 0.8213 (tmt) outliers start: 46 outliers final: 17 residues processed: 338 average time/residue: 1.4177 time to fit residues: 602.1099 Evaluate side-chains 335 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 16 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 359 ASP Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 5.9990 chunk 633 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 413 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 704 optimal weight: 6.9990 chunk 584 optimal weight: 10.0000 chunk 326 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 505 GLN ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN L 348 GLN ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54362 Z= 0.237 Angle : 0.498 9.029 73402 Z= 0.265 Chirality : 0.040 0.156 8932 Planarity : 0.003 0.027 9618 Dihedral : 3.741 16.263 7728 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.94 % Allowed : 11.47 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4256 sheet: 0.46 (0.15), residues: 1064 loop : -0.21 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.018 0.001 PHE B 204 TYR 0.017 0.001 TYR B 360 ARG 0.006 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 325 time to evaluate : 4.761 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: A 166 MET cc_start: 0.8595 (mmm) cc_final: 0.8184 (tpt) REVERT: A 193 MET cc_start: 0.8621 (ptp) cc_final: 0.8335 (ptt) REVERT: B 250 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8303 (pp) REVERT: C 389 MET cc_start: 0.9040 (tmm) cc_final: 0.8644 (tmm) REVERT: D 111 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8238 (mpm) REVERT: D 144 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9057 (mp) REVERT: D 164 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: D 221 LEU cc_start: 0.9474 (tp) cc_final: 0.9253 (tm) REVERT: F 59 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8485 (mm-30) REVERT: F 114 MET cc_start: 0.8578 (mmm) cc_final: 0.8313 (mmm) REVERT: F 204 PHE cc_start: 0.8204 (m-80) cc_final: 0.7757 (m-80) REVERT: F 233 MET cc_start: 0.8386 (pmt) cc_final: 0.7775 (ppp) REVERT: G 397 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8509 (mm-30) REVERT: H 193 MET cc_start: 0.8587 (ttm) cc_final: 0.8290 (ttm) REVERT: I 389 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8471 (tmt) REVERT: I 520 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8257 (mtt) REVERT: J 233 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8538 (pmm) REVERT: J 250 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8248 (pp) REVERT: J 288 MET cc_start: 0.8543 (mtm) cc_final: 0.8104 (ptp) REVERT: J 389 MET cc_start: 0.8847 (tmt) cc_final: 0.8600 (tmt) REVERT: J 488 MET cc_start: 0.9204 (mmm) cc_final: 0.8902 (mmm) REVERT: K 44 PHE cc_start: 0.8083 (m-80) cc_final: 0.7841 (m-10) REVERT: K 307 MET cc_start: 0.8957 (mpm) cc_final: 0.8658 (mpm) REVERT: K 389 MET cc_start: 0.8626 (tmt) cc_final: 0.8120 (tmt) REVERT: L 138 CYS cc_start: 0.8107 (t) cc_final: 0.7880 (t) REVERT: L 146 GLN cc_start: 0.9454 (OUTLIER) cc_final: 0.9183 (tm-30) REVERT: L 307 MET cc_start: 0.8716 (pmm) cc_final: 0.8495 (pmm) REVERT: L 366 GLN cc_start: 0.9557 (mm110) cc_final: 0.9282 (mm110) REVERT: M 473 ASP cc_start: 0.8751 (p0) cc_final: 0.8539 (p0) REVERT: N 389 MET cc_start: 0.8470 (tmt) cc_final: 0.8199 (tmt) outliers start: 53 outliers final: 17 residues processed: 353 average time/residue: 1.4050 time to fit residues: 625.1868 Evaluate side-chains 339 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 313 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 401 optimal weight: 20.0000 chunk 514 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 chunk 592 optimal weight: 5.9990 chunk 393 optimal weight: 8.9990 chunk 701 optimal weight: 40.0000 chunk 439 optimal weight: 7.9990 chunk 427 optimal weight: 0.9980 chunk 323 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 GLN L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54362 Z= 0.225 Angle : 0.507 10.478 73402 Z= 0.268 Chirality : 0.040 0.195 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.748 18.819 7728 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.85 % Allowed : 12.27 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4256 sheet: 0.43 (0.15), residues: 1064 loop : -0.21 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.018 0.001 PHE B 204 TYR 0.011 0.001 TYR L 360 ARG 0.005 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 321 time to evaluate : 4.644 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: A 166 MET cc_start: 0.8589 (mmm) cc_final: 0.8187 (tpt) REVERT: A 193 MET cc_start: 0.8592 (ptp) cc_final: 0.8196 (ptt) REVERT: B 250 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8306 (pp) REVERT: B 267 MET cc_start: 0.8445 (mmm) cc_final: 0.8075 (mtp) REVERT: C 389 MET cc_start: 0.9054 (tmm) cc_final: 0.8650 (tmm) REVERT: D 111 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8188 (mpm) REVERT: D 144 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9047 (mp) REVERT: D 164 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: D 267 MET cc_start: 0.8590 (mmm) cc_final: 0.8297 (mpp) REVERT: F 59 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8479 (mm-30) REVERT: F 114 MET cc_start: 0.8575 (mmm) cc_final: 0.8314 (mmm) REVERT: F 204 PHE cc_start: 0.8191 (m-80) cc_final: 0.7715 (m-80) REVERT: F 233 MET cc_start: 0.8432 (pmt) cc_final: 0.7821 (ppp) REVERT: G 69 MET cc_start: 0.8665 (mtt) cc_final: 0.8418 (mtt) REVERT: G 397 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8511 (mm-30) REVERT: H 193 MET cc_start: 0.8554 (ttm) cc_final: 0.8257 (ttm) REVERT: I 307 MET cc_start: 0.8489 (pmm) cc_final: 0.8230 (pmm) REVERT: I 389 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8480 (tmt) REVERT: I 520 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: J 233 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8528 (pmm) REVERT: J 250 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8223 (pp) REVERT: J 307 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7855 (ppp) REVERT: J 389 MET cc_start: 0.8871 (tmt) cc_final: 0.8599 (tmt) REVERT: J 488 MET cc_start: 0.9209 (mmm) cc_final: 0.8906 (mmm) REVERT: K 44 PHE cc_start: 0.8090 (m-80) cc_final: 0.7847 (m-10) REVERT: K 307 MET cc_start: 0.8961 (mpm) cc_final: 0.8665 (mpm) REVERT: K 389 MET cc_start: 0.8631 (tmt) cc_final: 0.8133 (tmt) REVERT: L 138 CYS cc_start: 0.8111 (t) cc_final: 0.7875 (t) REVERT: L 146 GLN cc_start: 0.9457 (OUTLIER) cc_final: 0.9180 (tm-30) REVERT: L 366 GLN cc_start: 0.9556 (mm110) cc_final: 0.9280 (mm110) REVERT: M 307 MET cc_start: 0.8297 (tpt) cc_final: 0.7930 (tpp) REVERT: M 473 ASP cc_start: 0.8774 (p0) cc_final: 0.8548 (p0) REVERT: N 166 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8768 (mtp) REVERT: N 389 MET cc_start: 0.8481 (tmt) cc_final: 0.8205 (tmt) REVERT: N 447 MET cc_start: 0.8737 (mtt) cc_final: 0.8488 (mtt) outliers start: 48 outliers final: 22 residues processed: 349 average time/residue: 1.4304 time to fit residues: 624.7129 Evaluate side-chains 347 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 314 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain J residue 288 MET Chi-restraints excluded: chain J residue 307 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 514 MET Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 359 ASP Chi-restraints excluded: chain N residue 166 MET Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 419 optimal weight: 0.0770 chunk 211 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 40.0000 chunk 446 optimal weight: 10.0000 chunk 478 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 551 optimal weight: 30.0000 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 54362 Z= 0.331 Angle : 0.551 10.556 73402 Z= 0.288 Chirality : 0.041 0.162 8932 Planarity : 0.003 0.027 9618 Dihedral : 3.800 16.493 7728 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.81 % Allowed : 12.82 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.10), residues: 7308 helix: 2.31 (0.08), residues: 4242 sheet: 0.38 (0.15), residues: 1064 loop : -0.23 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS K 401 PHE 0.020 0.001 PHE B 204 TYR 0.010 0.001 TYR N 476 ARG 0.008 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 319 time to evaluate : 4.650 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: A 166 MET cc_start: 0.8650 (mmm) cc_final: 0.8166 (tpt) REVERT: A 193 MET cc_start: 0.8566 (ptp) cc_final: 0.8224 (ptt) REVERT: A 520 MET cc_start: 0.9025 (ptp) cc_final: 0.8637 (mtm) REVERT: B 250 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8326 (pp) REVERT: B 267 MET cc_start: 0.8446 (mmm) cc_final: 0.8043 (mtp) REVERT: B 520 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.5684 (mpt) REVERT: C 111 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7686 (mtm) REVERT: C 389 MET cc_start: 0.9055 (tmm) cc_final: 0.8658 (tmm) REVERT: D 111 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8291 (mpm) REVERT: D 144 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9043 (mp) REVERT: D 164 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: F 59 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8498 (mm-30) REVERT: F 114 MET cc_start: 0.8596 (mmm) cc_final: 0.8327 (mmm) REVERT: F 204 PHE cc_start: 0.8212 (m-80) cc_final: 0.7710 (m-80) REVERT: F 233 MET cc_start: 0.8448 (pmt) cc_final: 0.7862 (ppp) REVERT: H 193 MET cc_start: 0.8553 (ttm) cc_final: 0.8263 (ttm) REVERT: H 362 ARG cc_start: 0.8955 (ptp90) cc_final: 0.8589 (ptp90) REVERT: I 16 MET cc_start: 0.8359 (mmm) cc_final: 0.8134 (mtp) REVERT: I 307 MET cc_start: 0.8524 (pmm) cc_final: 0.8274 (pmm) REVERT: I 389 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8485 (tmt) REVERT: I 520 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8448 (mtt) REVERT: J 233 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8538 (pmm) REVERT: J 250 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8244 (pp) REVERT: J 389 MET cc_start: 0.8890 (tmt) cc_final: 0.8626 (tmt) REVERT: K 44 PHE cc_start: 0.8080 (m-80) cc_final: 0.7842 (m-10) REVERT: K 307 MET cc_start: 0.8938 (mpm) cc_final: 0.8633 (mpm) REVERT: L 138 CYS cc_start: 0.8137 (t) cc_final: 0.7882 (t) REVERT: L 146 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9191 (tm-30) REVERT: L 307 MET cc_start: 0.8507 (pmm) cc_final: 0.8261 (pmm) REVERT: M 473 ASP cc_start: 0.8801 (p0) cc_final: 0.8566 (p0) REVERT: N 166 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8785 (mtp) REVERT: N 389 MET cc_start: 0.8499 (tmt) cc_final: 0.8225 (tmt) REVERT: N 447 MET cc_start: 0.8863 (mtt) cc_final: 0.8596 (mtt) outliers start: 46 outliers final: 25 residues processed: 350 average time/residue: 1.4069 time to fit residues: 620.0596 Evaluate side-chains 347 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 310 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 520 MET Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 514 MET Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 359 ASP Chi-restraints excluded: chain N residue 166 MET Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 20.0000 chunk 672 optimal weight: 3.9990 chunk 613 optimal weight: 0.9990 chunk 653 optimal weight: 30.0000 chunk 393 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 chunk 513 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 590 optimal weight: 8.9990 chunk 618 optimal weight: 6.9990 chunk 651 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54362 Z= 0.199 Angle : 0.519 12.193 73402 Z= 0.272 Chirality : 0.039 0.155 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.771 17.936 7728 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.65 % Allowed : 13.22 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4228 sheet: 0.37 (0.15), residues: 1064 loop : -0.24 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.021 0.001 PHE B 204 TYR 0.020 0.001 TYR G 360 ARG 0.004 0.000 ARG H 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 322 time to evaluate : 4.625 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: A 160 LYS cc_start: 0.9512 (tppt) cc_final: 0.9302 (tppt) REVERT: A 166 MET cc_start: 0.8633 (mmm) cc_final: 0.8153 (tpt) REVERT: A 193 MET cc_start: 0.8581 (ptp) cc_final: 0.8287 (ptt) REVERT: A 520 MET cc_start: 0.8991 (ptp) cc_final: 0.8561 (mtm) REVERT: B 267 MET cc_start: 0.8437 (mmm) cc_final: 0.7975 (mtp) REVERT: C 111 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7730 (mtm) REVERT: C 389 MET cc_start: 0.9065 (tmm) cc_final: 0.8662 (tmm) REVERT: D 111 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8252 (mpm) REVERT: D 144 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9053 (mp) REVERT: D 164 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: D 267 MET cc_start: 0.8629 (mmm) cc_final: 0.8319 (mpp) REVERT: E 199 TYR cc_start: 0.8004 (p90) cc_final: 0.7615 (p90) REVERT: F 59 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8463 (mm-30) REVERT: F 114 MET cc_start: 0.8566 (mmm) cc_final: 0.8306 (mmm) REVERT: F 204 PHE cc_start: 0.8208 (m-80) cc_final: 0.7685 (m-80) REVERT: F 233 MET cc_start: 0.8476 (pmt) cc_final: 0.7866 (ppp) REVERT: F 520 MET cc_start: 0.8557 (mtp) cc_final: 0.8344 (mtp) REVERT: H 193 MET cc_start: 0.8534 (ttm) cc_final: 0.8251 (ttm) REVERT: I 16 MET cc_start: 0.8320 (mmm) cc_final: 0.8003 (mtp) REVERT: I 111 MET cc_start: 0.8528 (mpp) cc_final: 0.8171 (mtm) REVERT: I 307 MET cc_start: 0.8554 (pmm) cc_final: 0.8296 (pmm) REVERT: I 389 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8509 (tmt) REVERT: I 520 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8327 (mtp) REVERT: J 233 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8553 (pmm) REVERT: J 250 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8208 (pp) REVERT: J 389 MET cc_start: 0.8898 (tmt) cc_final: 0.8625 (tmt) REVERT: J 488 MET cc_start: 0.9205 (mmm) cc_final: 0.8809 (mmm) REVERT: K 44 PHE cc_start: 0.8051 (m-80) cc_final: 0.7824 (m-10) REVERT: K 160 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9281 (tmmm) REVERT: K 307 MET cc_start: 0.8933 (mpm) cc_final: 0.8625 (mpm) REVERT: L 138 CYS cc_start: 0.8085 (t) cc_final: 0.7831 (t) REVERT: L 146 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9176 (tm-30) REVERT: L 307 MET cc_start: 0.8510 (pmm) cc_final: 0.8244 (pmm) REVERT: M 193 MET cc_start: 0.8351 (ptm) cc_final: 0.7310 (ppp) REVERT: N 166 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8761 (mtp) REVERT: N 389 MET cc_start: 0.8510 (tmt) cc_final: 0.8245 (tmt) REVERT: N 447 MET cc_start: 0.8737 (mtt) cc_final: 0.8522 (mtt) REVERT: N 488 MET cc_start: 0.9184 (tpt) cc_final: 0.8898 (tpp) outliers start: 37 outliers final: 22 residues processed: 344 average time/residue: 1.4388 time to fit residues: 620.5143 Evaluate side-chains 347 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 314 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 514 MET Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 359 ASP Chi-restraints excluded: chain N residue 166 MET Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 0.7980 chunk 691 optimal weight: 0.9980 chunk 422 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 480 optimal weight: 5.9990 chunk 725 optimal weight: 0.0170 chunk 667 optimal weight: 9.9990 chunk 577 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 446 optimal weight: 30.0000 chunk 354 optimal weight: 7.9990 overall best weight: 2.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54362 Z= 0.188 Angle : 0.531 14.316 73402 Z= 0.275 Chirality : 0.040 0.160 8932 Planarity : 0.003 0.033 9618 Dihedral : 3.745 16.594 7728 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.60 % Allowed : 13.38 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4242 sheet: 0.36 (0.16), residues: 1064 loop : -0.25 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.021 0.001 PHE G 44 TYR 0.012 0.001 TYR C 203 ARG 0.010 0.000 ARG H 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 4.636 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: A 160 LYS cc_start: 0.9518 (tppt) cc_final: 0.9284 (tppt) REVERT: A 166 MET cc_start: 0.8625 (mmm) cc_final: 0.8149 (tpt) REVERT: A 193 MET cc_start: 0.8572 (ptp) cc_final: 0.8275 (ptt) REVERT: B 267 MET cc_start: 0.8402 (mmm) cc_final: 0.7959 (mtp) REVERT: C 111 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: C 389 MET cc_start: 0.9068 (tmm) cc_final: 0.8664 (tmm) REVERT: D 69 MET cc_start: 0.8665 (mtt) cc_final: 0.8413 (mtt) REVERT: D 144 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9046 (mp) REVERT: D 164 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8534 (pm20) REVERT: D 267 MET cc_start: 0.8609 (mmm) cc_final: 0.8313 (mpp) REVERT: F 59 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8429 (mm-30) REVERT: F 114 MET cc_start: 0.8573 (mmm) cc_final: 0.8312 (mmm) REVERT: F 204 PHE cc_start: 0.8198 (m-80) cc_final: 0.7590 (m-80) REVERT: F 233 MET cc_start: 0.8478 (pmt) cc_final: 0.7901 (ppp) REVERT: F 520 MET cc_start: 0.8575 (mtp) cc_final: 0.8361 (mtp) REVERT: H 193 MET cc_start: 0.8534 (ttm) cc_final: 0.8240 (ttm) REVERT: I 16 MET cc_start: 0.8277 (mmm) cc_final: 0.8075 (mtp) REVERT: I 111 MET cc_start: 0.8531 (mpp) cc_final: 0.8169 (mtm) REVERT: I 307 MET cc_start: 0.8513 (pmm) cc_final: 0.8245 (pmm) REVERT: I 389 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8509 (tmt) REVERT: I 520 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8405 (mtp) REVERT: J 233 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8556 (pmm) REVERT: J 250 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8215 (pp) REVERT: J 389 MET cc_start: 0.8902 (tmt) cc_final: 0.8625 (tmt) REVERT: J 488 MET cc_start: 0.9192 (mmm) cc_final: 0.8896 (mmm) REVERT: K 44 PHE cc_start: 0.8089 (m-80) cc_final: 0.7846 (m-10) REVERT: K 160 LYS cc_start: 0.9498 (OUTLIER) cc_final: 0.9281 (tmmm) REVERT: K 307 MET cc_start: 0.8931 (mpm) cc_final: 0.8640 (mpm) REVERT: K 389 MET cc_start: 0.8616 (tmt) cc_final: 0.8199 (tmt) REVERT: L 138 CYS cc_start: 0.8101 (t) cc_final: 0.7848 (t) REVERT: L 146 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.9178 (tm-30) REVERT: L 307 MET cc_start: 0.8514 (pmm) cc_final: 0.8274 (pmm) REVERT: M 193 MET cc_start: 0.8364 (ptm) cc_final: 0.7320 (ppp) REVERT: N 166 MET cc_start: 0.9111 (mtt) cc_final: 0.8786 (mtp) REVERT: N 389 MET cc_start: 0.8507 (tmt) cc_final: 0.8237 (tmt) REVERT: N 488 MET cc_start: 0.9192 (tpt) cc_final: 0.8910 (tpp) outliers start: 34 outliers final: 21 residues processed: 343 average time/residue: 1.4112 time to fit residues: 607.9685 Evaluate side-chains 344 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 314 time to evaluate : 4.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 250 ILE Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 160 LYS Chi-restraints excluded: chain K residue 514 MET Chi-restraints excluded: chain K residue 517 THR Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 359 ASP Chi-restraints excluded: chain M residue 473 ASP Chi-restraints excluded: chain M residue 517 THR Chi-restraints excluded: chain N residue 352 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 3.9990 chunk 615 optimal weight: 10.0000 chunk 176 optimal weight: 0.0060 chunk 532 optimal weight: 2.9990 chunk 85 optimal weight: 40.0000 chunk 160 optimal weight: 8.9990 chunk 578 optimal weight: 2.9990 chunk 242 optimal weight: 30.0000 chunk 593 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN ** L 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.090332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062120 restraints weight = 155027.717| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.27 r_work: 0.3059 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 54362 Z= 0.185 Angle : 0.568 35.522 73402 Z= 0.291 Chirality : 0.040 0.193 8932 Planarity : 0.003 0.116 9618 Dihedral : 3.746 16.858 7728 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.62 % Allowed : 13.45 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.10), residues: 7308 helix: 2.44 (0.08), residues: 4242 sheet: 0.36 (0.16), residues: 1064 loop : -0.25 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 401 PHE 0.024 0.001 PHE D 204 TYR 0.017 0.001 TYR B 360 ARG 0.011 0.000 ARG H 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12067.60 seconds wall clock time: 213 minutes 19.51 seconds (12799.51 seconds total)