Starting phenix.real_space_refine on Mon Nov 18 15:09:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j73_36024/11_2024/8j73_36024_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j73_36024/11_2024/8j73_36024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j73_36024/11_2024/8j73_36024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j73_36024/11_2024/8j73_36024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j73_36024/11_2024/8j73_36024_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j73_36024/11_2024/8j73_36024_neut.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 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 228 5.16 5 C 31176 2.51 5 N 8592 2.21 5 O 9156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 49152 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "H" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "I" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "J" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "K" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "L" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "M" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "N" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "O" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "P" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "Q" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Chain: "R" Number of atoms: 4096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4096 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 508} Time building chain proxies: 25.58, per 1000 atoms: 0.52 Number of scatterers: 49152 At special positions: 0 Unit cell: (161.391, 150.412, 163.587, 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 228 16.00 O 9156 8.00 N 8592 7.00 C 31176 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 - 3.00 Amino acid : True - 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: 12.11 Conformation dependent library (CDL) restraints added in 6.4 seconds 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11472 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 48 sheets defined 53.7% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain 'G' and resid 39 through 65 removed outlier: 3.650A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 114 through 117 Processing helix chain 'G' and resid 140 through 144 Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 177 through 184 removed outlier: 5.773A pdb=" N ALA G 182 " --> pdb=" O PRO G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 204 removed outlier: 4.285A pdb=" N PHE G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR G 196 " --> pdb=" O GLY G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 227 removed outlier: 3.624A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 Processing helix chain 'G' and resid 256 through 261 Processing helix chain 'G' and resid 261 through 269 removed outlier: 4.127A pdb=" N LEU G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 293 Processing helix chain 'G' and resid 316 through 322 Processing helix chain 'G' and resid 330 through 337 removed outlier: 3.886A pdb=" N VAL G 334 " --> pdb=" O ASP G 330 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG G 337 " --> pdb=" O GLU G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 removed outlier: 6.754A pdb=" N GLY G 341 " --> pdb=" O ILE G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 395 Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 417 through 432 removed outlier: 3.512A pdb=" N MET G 425 " --> pdb=" O ASP G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 452 removed outlier: 4.029A pdb=" N TYR G 450 " --> pdb=" O GLY G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 458 Processing helix chain 'G' and resid 474 through 494 Processing helix chain 'G' and resid 498 through 517 Proline residue: G 508 - end of helix Processing helix chain 'G' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG G 525 " --> pdb=" O TYR G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 549 Processing helix chain 'H' and resid 39 through 65 removed outlier: 3.659A pdb=" N LEU H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 78 Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 114 through 117 Processing helix chain 'H' and resid 140 through 144 Processing helix chain 'H' and resid 146 through 164 Processing helix chain 'H' and resid 177 through 184 removed outlier: 5.746A pdb=" N ALA H 182 " --> pdb=" O PRO H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 204 removed outlier: 4.303A pdb=" N PHE H 195 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 227 removed outlier: 3.640A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 252 Processing helix chain 'H' and resid 256 through 261 Processing helix chain 'H' and resid 261 through 269 removed outlier: 4.054A pdb=" N LEU H 265 " --> pdb=" O GLY H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 293 Processing helix chain 'H' and resid 316 through 322 Processing helix chain 'H' and resid 330 through 337 removed outlier: 3.912A pdb=" N VAL H 334 " --> pdb=" O ASP H 330 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 343 removed outlier: 6.803A pdb=" N GLY H 341 " --> pdb=" O ILE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 395 Processing helix chain 'H' and resid 410 through 416 Processing helix chain 'H' and resid 417 through 432 removed outlier: 3.532A pdb=" N MET H 425 " --> pdb=" O ASP H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 452 removed outlier: 3.989A pdb=" N TYR H 450 " --> pdb=" O GLY H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 458 Processing helix chain 'H' and resid 474 through 494 Processing helix chain 'H' and resid 498 through 517 Proline residue: H 508 - end of helix Processing helix chain 'H' and resid 518 through 525 removed outlier: 3.678A pdb=" N ARG H 525 " --> pdb=" O TYR H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 535 No H-bonds generated for 'chain 'H' and resid 533 through 535' Processing helix chain 'H' and resid 536 through 549 Processing helix chain 'I' and resid 39 through 65 removed outlier: 3.636A pdb=" N LEU I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 78 Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 114 through 117 Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'I' and resid 146 through 164 Processing helix chain 'I' and resid 177 through 184 removed outlier: 5.810A pdb=" N ALA I 182 " --> pdb=" O PRO I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE I 195 " --> pdb=" O PHE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 227 removed outlier: 3.589A pdb=" N ALA I 225 " --> pdb=" O ALA I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 243 through 252 Processing helix chain 'I' and resid 256 through 261 Processing helix chain 'I' and resid 261 through 269 removed outlier: 4.144A pdb=" N LEU I 265 " --> pdb=" O GLY I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 293 Processing helix chain 'I' and resid 316 through 322 Processing helix chain 'I' and resid 330 through 337 removed outlier: 3.926A pdb=" N VAL I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG I 337 " --> pdb=" O GLU I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 343 removed outlier: 6.671A pdb=" N GLY I 341 " --> pdb=" O ILE I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 395 Processing helix chain 'I' and resid 410 through 416 Processing helix chain 'I' and resid 417 through 432 removed outlier: 3.528A pdb=" N MET I 425 " --> pdb=" O ASP I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 452 removed outlier: 4.107A pdb=" N TYR I 450 " --> pdb=" O GLY I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 458 Processing helix chain 'I' and resid 474 through 494 Processing helix chain 'I' and resid 498 through 517 Proline residue: I 508 - end of helix Processing helix chain 'I' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG I 525 " --> pdb=" O TYR I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 533 through 535 No H-bonds generated for 'chain 'I' and resid 533 through 535' Processing helix chain 'I' and resid 536 through 549 Processing helix chain 'J' and resid 39 through 65 removed outlier: 3.637A pdb=" N LEU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 78 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 140 through 144 Processing helix chain 'J' and resid 146 through 164 Processing helix chain 'J' and resid 177 through 184 removed outlier: 5.813A pdb=" N ALA J 182 " --> pdb=" O PRO J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 204 removed outlier: 4.292A pdb=" N PHE J 195 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 227 removed outlier: 3.578A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 252 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU J 265 " --> pdb=" O GLY J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 293 Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 330 through 337 removed outlier: 3.926A pdb=" N VAL J 334 " --> pdb=" O ASP J 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG J 337 " --> pdb=" O GLU J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY J 341 " --> pdb=" O ILE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 395 Processing helix chain 'J' and resid 410 through 416 Processing helix chain 'J' and resid 417 through 432 removed outlier: 3.526A pdb=" N MET J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 452 removed outlier: 4.110A pdb=" N TYR J 450 " --> pdb=" O GLY J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 458 Processing helix chain 'J' and resid 474 through 494 Processing helix chain 'J' and resid 498 through 517 Proline residue: J 508 - end of helix Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'K' and resid 39 through 65 removed outlier: 3.655A pdb=" N LEU K 65 " --> pdb=" O GLU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 78 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 114 through 117 Processing helix chain 'K' and resid 140 through 144 Processing helix chain 'K' and resid 146 through 164 Processing helix chain 'K' and resid 177 through 184 removed outlier: 5.747A pdb=" N ALA K 182 " --> pdb=" O PRO K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 204 removed outlier: 4.302A pdb=" N PHE K 195 " --> pdb=" O PHE K 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 196 " --> pdb=" O GLY K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 227 removed outlier: 3.646A pdb=" N ALA K 225 " --> pdb=" O ALA K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 252 Processing helix chain 'K' and resid 256 through 261 Processing helix chain 'K' and resid 261 through 269 removed outlier: 4.063A pdb=" N LEU K 265 " --> pdb=" O GLY K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 293 Processing helix chain 'K' and resid 316 through 322 Processing helix chain 'K' and resid 330 through 337 removed outlier: 3.908A pdb=" N VAL K 334 " --> pdb=" O ASP K 330 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG K 337 " --> pdb=" O GLU K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 343 removed outlier: 6.799A pdb=" N GLY K 341 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 395 Processing helix chain 'K' and resid 410 through 416 Processing helix chain 'K' and resid 417 through 432 removed outlier: 3.534A pdb=" N MET K 425 " --> pdb=" O ASP K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 446 through 452 removed outlier: 3.990A pdb=" N TYR K 450 " --> pdb=" O GLY K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 454 through 458 Processing helix chain 'K' and resid 474 through 494 Processing helix chain 'K' and resid 498 through 517 Proline residue: K 508 - end of helix Processing helix chain 'K' and resid 518 through 525 removed outlier: 3.675A pdb=" N ARG K 525 " --> pdb=" O TYR K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 533 through 535 No H-bonds generated for 'chain 'K' and resid 533 through 535' Processing helix chain 'K' and resid 536 through 549 Processing helix chain 'L' and resid 39 through 65 removed outlier: 3.646A pdb=" N LEU L 65 " --> pdb=" O GLU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 78 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'L' and resid 140 through 144 Processing helix chain 'L' and resid 146 through 164 Processing helix chain 'L' and resid 177 through 184 removed outlier: 5.808A pdb=" N ALA L 182 " --> pdb=" O PRO L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 204 removed outlier: 4.286A pdb=" N PHE L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR L 196 " --> pdb=" O GLY L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 227 removed outlier: 3.634A pdb=" N ALA L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 252 Processing helix chain 'L' and resid 256 through 261 Processing helix chain 'L' and resid 261 through 269 removed outlier: 4.119A pdb=" N LEU L 265 " --> pdb=" O GLY L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 293 Processing helix chain 'L' and resid 316 through 322 Processing helix chain 'L' and resid 330 through 337 removed outlier: 3.883A pdb=" N VAL L 334 " --> pdb=" O ASP L 330 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 343 removed outlier: 6.757A pdb=" N GLY L 341 " --> pdb=" O ILE L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 395 Processing helix chain 'L' and resid 410 through 416 Processing helix chain 'L' and resid 417 through 432 removed outlier: 3.516A pdb=" N MET L 425 " --> pdb=" O ASP L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 446 through 452 removed outlier: 4.032A pdb=" N TYR L 450 " --> pdb=" O GLY L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 458 Processing helix chain 'L' and resid 474 through 494 Processing helix chain 'L' and resid 498 through 517 Proline residue: L 508 - end of helix Processing helix chain 'L' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG L 525 " --> pdb=" O TYR L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 535 No H-bonds generated for 'chain 'L' and resid 533 through 535' Processing helix chain 'L' and resid 536 through 549 Processing helix chain 'M' and resid 39 through 65 removed outlier: 3.649A pdb=" N LEU M 65 " --> pdb=" O GLU M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 78 Processing helix chain 'M' and resid 82 through 91 Processing helix chain 'M' and resid 114 through 117 Processing helix chain 'M' and resid 140 through 144 Processing helix chain 'M' and resid 146 through 164 Processing helix chain 'M' and resid 177 through 184 removed outlier: 5.773A pdb=" N ALA M 182 " --> pdb=" O PRO M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 204 removed outlier: 4.285A pdb=" N PHE M 195 " --> pdb=" O PHE M 191 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR M 196 " --> pdb=" O GLY M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 227 removed outlier: 3.623A pdb=" N ALA M 225 " --> pdb=" O ALA M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 252 Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 261 through 269 removed outlier: 4.127A pdb=" N LEU M 265 " --> pdb=" O GLY M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 293 Processing helix chain 'M' and resid 316 through 322 Processing helix chain 'M' and resid 330 through 337 removed outlier: 3.886A pdb=" N VAL M 334 " --> pdb=" O ASP M 330 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG M 337 " --> pdb=" O GLU M 333 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 343 removed outlier: 6.754A pdb=" N GLY M 341 " --> pdb=" O ILE M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 395 Processing helix chain 'M' and resid 410 through 416 Processing helix chain 'M' and resid 417 through 432 removed outlier: 3.511A pdb=" N MET M 425 " --> pdb=" O ASP M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 446 through 452 removed outlier: 4.027A pdb=" N TYR M 450 " --> pdb=" O GLY M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 458 Processing helix chain 'M' and resid 474 through 494 Processing helix chain 'M' and resid 498 through 517 Proline residue: M 508 - end of helix Processing helix chain 'M' and resid 518 through 525 removed outlier: 3.658A pdb=" N ARG M 525 " --> pdb=" O TYR M 521 " (cutoff:3.500A) Processing helix chain 'M' and resid 533 through 535 No H-bonds generated for 'chain 'M' and resid 533 through 535' Processing helix chain 'M' and resid 536 through 549 Processing helix chain 'N' and resid 39 through 65 removed outlier: 3.659A pdb=" N LEU N 65 " --> pdb=" O GLU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 78 Processing helix chain 'N' and resid 82 through 91 Processing helix chain 'N' and resid 114 through 117 Processing helix chain 'N' and resid 140 through 144 Processing helix chain 'N' and resid 146 through 164 Processing helix chain 'N' and resid 177 through 184 removed outlier: 5.747A pdb=" N ALA N 182 " --> pdb=" O PRO N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 204 removed outlier: 4.302A pdb=" N PHE N 195 " --> pdb=" O PHE N 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR N 196 " --> pdb=" O GLY N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 227 removed outlier: 3.640A pdb=" N ALA N 225 " --> pdb=" O ALA N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 252 Processing helix chain 'N' and resid 256 through 261 Processing helix chain 'N' and resid 261 through 269 removed outlier: 4.052A pdb=" N LEU N 265 " --> pdb=" O GLY N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 293 Processing helix chain 'N' and resid 316 through 322 Processing helix chain 'N' and resid 330 through 337 removed outlier: 3.911A pdb=" N VAL N 334 " --> pdb=" O ASP N 330 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG N 337 " --> pdb=" O GLU N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 343 removed outlier: 6.802A pdb=" N GLY N 341 " --> pdb=" O ILE N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 395 Processing helix chain 'N' and resid 410 through 416 Processing helix chain 'N' and resid 417 through 432 removed outlier: 3.532A pdb=" N MET N 425 " --> pdb=" O ASP N 421 " (cutoff:3.500A) Processing helix chain 'N' and resid 446 through 452 removed outlier: 3.989A pdb=" N TYR N 450 " --> pdb=" O GLY N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 458 Processing helix chain 'N' and resid 474 through 494 Processing helix chain 'N' and resid 498 through 517 Proline residue: N 508 - end of helix Processing helix chain 'N' and resid 518 through 525 removed outlier: 3.679A pdb=" N ARG N 525 " --> pdb=" O TYR N 521 " (cutoff:3.500A) Processing helix chain 'N' and resid 533 through 535 No H-bonds generated for 'chain 'N' and resid 533 through 535' Processing helix chain 'N' and resid 536 through 549 Processing helix chain 'O' and resid 39 through 65 removed outlier: 3.636A pdb=" N LEU O 65 " --> pdb=" O GLU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 78 Processing helix chain 'O' and resid 82 through 91 Processing helix chain 'O' and resid 114 through 117 Processing helix chain 'O' and resid 140 through 144 Processing helix chain 'O' and resid 146 through 164 Processing helix chain 'O' and resid 177 through 184 removed outlier: 5.811A pdb=" N ALA O 182 " --> pdb=" O PRO O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 204 removed outlier: 4.289A pdb=" N PHE O 195 " --> pdb=" O PHE O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 221 through 227 removed outlier: 3.589A pdb=" N ALA O 225 " --> pdb=" O ALA O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 252 Processing helix chain 'O' and resid 256 through 261 Processing helix chain 'O' and resid 261 through 269 removed outlier: 4.144A pdb=" N LEU O 265 " --> pdb=" O GLY O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 293 Processing helix chain 'O' and resid 316 through 322 Processing helix chain 'O' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG O 337 " --> pdb=" O GLU O 333 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 343 removed outlier: 6.671A pdb=" N GLY O 341 " --> pdb=" O ILE O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 377 through 395 Processing helix chain 'O' and resid 410 through 416 Processing helix chain 'O' and resid 417 through 432 removed outlier: 3.530A pdb=" N MET O 425 " --> pdb=" O ASP O 421 " (cutoff:3.500A) Processing helix chain 'O' and resid 446 through 452 removed outlier: 4.107A pdb=" N TYR O 450 " --> pdb=" O GLY O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 458 Processing helix chain 'O' and resid 474 through 494 Processing helix chain 'O' and resid 498 through 517 Proline residue: O 508 - end of helix Processing helix chain 'O' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG O 525 " --> pdb=" O TYR O 521 " (cutoff:3.500A) Processing helix chain 'O' and resid 533 through 535 No H-bonds generated for 'chain 'O' and resid 533 through 535' Processing helix chain 'O' and resid 536 through 549 Processing helix chain 'P' and resid 39 through 65 removed outlier: 3.637A pdb=" N LEU P 65 " --> pdb=" O GLU P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 Processing helix chain 'P' and resid 82 through 91 Processing helix chain 'P' and resid 114 through 117 Processing helix chain 'P' and resid 140 through 144 Processing helix chain 'P' and resid 146 through 164 Processing helix chain 'P' and resid 177 through 184 removed outlier: 5.810A pdb=" N ALA P 182 " --> pdb=" O PRO P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE P 195 " --> pdb=" O PHE P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 227 removed outlier: 3.578A pdb=" N ALA P 225 " --> pdb=" O ALA P 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 252 Processing helix chain 'P' and resid 256 through 261 Processing helix chain 'P' and resid 261 through 269 removed outlier: 4.144A pdb=" N LEU P 265 " --> pdb=" O GLY P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 279 through 293 Processing helix chain 'P' and resid 316 through 322 Processing helix chain 'P' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL P 334 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG P 337 " --> pdb=" O GLU P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 343 removed outlier: 6.673A pdb=" N GLY P 341 " --> pdb=" O ILE P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 377 through 395 Processing helix chain 'P' and resid 410 through 416 Processing helix chain 'P' and resid 417 through 432 removed outlier: 3.527A pdb=" N MET P 425 " --> pdb=" O ASP P 421 " (cutoff:3.500A) Processing helix chain 'P' and resid 446 through 452 removed outlier: 4.109A pdb=" N TYR P 450 " --> pdb=" O GLY P 446 " (cutoff:3.500A) Processing helix chain 'P' and resid 454 through 458 Processing helix chain 'P' and resid 474 through 494 Processing helix chain 'P' and resid 498 through 517 Proline residue: P 508 - end of helix Processing helix chain 'P' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG P 525 " --> pdb=" O TYR P 521 " (cutoff:3.500A) Processing helix chain 'P' and resid 533 through 535 No H-bonds generated for 'chain 'P' and resid 533 through 535' Processing helix chain 'P' and resid 536 through 549 Processing helix chain 'Q' and resid 39 through 65 removed outlier: 3.654A pdb=" N LEU Q 65 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 78 Processing helix chain 'Q' and resid 82 through 91 Processing helix chain 'Q' and resid 114 through 117 Processing helix chain 'Q' and resid 140 through 144 Processing helix chain 'Q' and resid 146 through 164 Processing helix chain 'Q' and resid 177 through 184 removed outlier: 5.746A pdb=" N ALA Q 182 " --> pdb=" O PRO Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 204 removed outlier: 4.303A pdb=" N PHE Q 195 " --> pdb=" O PHE Q 191 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR Q 196 " --> pdb=" O GLY Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 227 removed outlier: 3.646A pdb=" N ALA Q 225 " --> pdb=" O ALA Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 243 through 252 Processing helix chain 'Q' and resid 256 through 261 Processing helix chain 'Q' and resid 261 through 269 removed outlier: 4.062A pdb=" N LEU Q 265 " --> pdb=" O GLY Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 293 Processing helix chain 'Q' and resid 316 through 322 Processing helix chain 'Q' and resid 330 through 337 removed outlier: 3.909A pdb=" N VAL Q 334 " --> pdb=" O ASP Q 330 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG Q 337 " --> pdb=" O GLU Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 343 removed outlier: 6.799A pdb=" N GLY Q 341 " --> pdb=" O ILE Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 377 through 395 Processing helix chain 'Q' and resid 410 through 416 Processing helix chain 'Q' and resid 417 through 432 removed outlier: 3.533A pdb=" N MET Q 425 " --> pdb=" O ASP Q 421 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 452 removed outlier: 3.990A pdb=" N TYR Q 450 " --> pdb=" O GLY Q 446 " (cutoff:3.500A) Processing helix chain 'Q' and resid 454 through 458 Processing helix chain 'Q' and resid 474 through 494 Processing helix chain 'Q' and resid 498 through 517 Proline residue: Q 508 - end of helix Processing helix chain 'Q' and resid 518 through 525 removed outlier: 3.675A pdb=" N ARG Q 525 " --> pdb=" O TYR Q 521 " (cutoff:3.500A) Processing helix chain 'Q' and resid 533 through 535 No H-bonds generated for 'chain 'Q' and resid 533 through 535' Processing helix chain 'Q' and resid 536 through 549 Processing helix chain 'R' and resid 39 through 65 removed outlier: 3.647A pdb=" N LEU R 65 " --> pdb=" O GLU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 78 Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 114 through 117 Processing helix chain 'R' and resid 140 through 144 Processing helix chain 'R' and resid 146 through 164 Processing helix chain 'R' and resid 177 through 184 removed outlier: 5.808A pdb=" N ALA R 182 " --> pdb=" O PRO R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 204 removed outlier: 4.286A pdb=" N PHE R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR R 196 " --> pdb=" O GLY R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 227 removed outlier: 3.634A pdb=" N ALA R 225 " --> pdb=" O ALA R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 252 Processing helix chain 'R' and resid 256 through 261 Processing helix chain 'R' and resid 261 through 269 removed outlier: 4.118A pdb=" N LEU R 265 " --> pdb=" O GLY R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 293 Processing helix chain 'R' and resid 316 through 322 Processing helix chain 'R' and resid 330 through 337 removed outlier: 3.884A pdb=" N VAL R 334 " --> pdb=" O ASP R 330 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG R 337 " --> pdb=" O GLU R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 removed outlier: 6.756A pdb=" N GLY R 341 " --> pdb=" O ILE R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 395 Processing helix chain 'R' and resid 410 through 416 Processing helix chain 'R' and resid 417 through 432 removed outlier: 3.516A pdb=" N MET R 425 " --> pdb=" O ASP R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 452 removed outlier: 4.031A pdb=" N TYR R 450 " --> pdb=" O GLY R 446 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 458 Processing helix chain 'R' and resid 474 through 494 Processing helix chain 'R' and resid 498 through 517 Proline residue: R 508 - end of helix Processing helix chain 'R' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG R 525 " --> pdb=" O TYR R 521 " (cutoff:3.500A) Processing helix chain 'R' and resid 533 through 535 No H-bonds generated for 'chain 'R' and resid 533 through 535' Processing helix chain 'R' and resid 536 through 549 Processing sheet with id=AA1, first strand: chain 'G' and resid 98 through 100 removed outlier: 4.689A pdb=" N THR G 121 " --> pdb=" O LEU G 100 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS G 167 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL G 211 " --> pdb=" O CYS G 167 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR G 169 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN G 230 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA G 277 " --> pdb=" O ASN G 230 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE G 232 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 215 through 217 removed outlier: 3.616A pdb=" N PHE G 240 " --> pdb=" O CYS G 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 345 through 346 removed outlier: 7.689A pdb=" N LEU G 399 " --> pdb=" O PRO G 366 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY G 368 " --> pdb=" O LEU G 399 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU G 401 " --> pdb=" O GLY G 368 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL G 370 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE G 461 " --> pdb=" O LYS G 436 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 443 through 445 removed outlier: 6.127A pdb=" N SER G 444 " --> pdb=" O SER G 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 98 through 100 removed outlier: 4.718A pdb=" N THR H 121 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS H 167 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL H 211 " --> pdb=" O CYS H 167 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR H 169 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN H 230 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA H 277 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE H 232 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 215 through 217 removed outlier: 3.666A pdb=" N PHE H 240 " --> pdb=" O CYS H 216 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 345 through 346 removed outlier: 7.633A pdb=" N LEU H 399 " --> pdb=" O PRO H 366 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU H 401 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 370 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE H 461 " --> pdb=" O LYS H 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 443 through 445 removed outlier: 6.101A pdb=" N SER H 444 " --> pdb=" O SER H 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'I' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR I 121 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS I 167 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL I 211 " --> pdb=" O CYS I 167 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR I 169 " --> pdb=" O VAL I 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN I 230 " --> pdb=" O HIS I 275 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA I 277 " --> pdb=" O ASN I 230 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE I 232 " --> pdb=" O ALA I 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 215 through 217 removed outlier: 3.655A pdb=" N PHE I 240 " --> pdb=" O CYS I 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 345 through 346 removed outlier: 7.653A pdb=" N LEU I 399 " --> pdb=" O PRO I 366 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY I 368 " --> pdb=" O LEU I 399 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU I 401 " --> pdb=" O GLY I 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL I 370 " --> pdb=" O LEU I 401 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE I 461 " --> pdb=" O LYS I 436 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 443 through 445 removed outlier: 6.116A pdb=" N SER I 444 " --> pdb=" O SER I 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR J 121 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS J 167 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL J 211 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR J 169 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 215 through 217 removed outlier: 3.655A pdb=" N PHE J 240 " --> pdb=" O CYS J 216 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 443 through 445 removed outlier: 6.112A pdb=" N SER J 444 " --> pdb=" O SER J 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 98 through 100 removed outlier: 4.718A pdb=" N THR K 121 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS K 167 " --> pdb=" O ILE K 209 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL K 211 " --> pdb=" O CYS K 167 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR K 169 " --> pdb=" O VAL K 211 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN K 230 " --> pdb=" O HIS K 275 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA K 277 " --> pdb=" O ASN K 230 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE K 232 " --> pdb=" O ALA K 277 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 215 through 217 removed outlier: 3.651A pdb=" N PHE K 240 " --> pdb=" O CYS K 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 345 through 346 removed outlier: 7.636A pdb=" N LEU K 399 " --> pdb=" O PRO K 366 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY K 368 " --> pdb=" O LEU K 399 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU K 401 " --> pdb=" O GLY K 368 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL K 370 " --> pdb=" O LEU K 401 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE K 461 " --> pdb=" O LYS K 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 443 through 445 removed outlier: 6.099A pdb=" N SER K 444 " --> pdb=" O SER K 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.691A pdb=" N THR L 121 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYS L 167 " --> pdb=" O ILE L 209 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL L 211 " --> pdb=" O CYS L 167 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR L 169 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN L 230 " --> pdb=" O HIS L 275 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 215 through 217 removed outlier: 3.624A pdb=" N PHE L 240 " --> pdb=" O CYS L 216 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 345 through 346 removed outlier: 7.690A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 443 through 445 removed outlier: 6.129A pdb=" N SER L 444 " --> pdb=" O SER L 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 98 through 100 removed outlier: 4.690A pdb=" N THR M 121 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS M 167 " --> pdb=" O ILE M 209 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL M 211 " --> pdb=" O CYS M 167 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR M 169 " --> pdb=" O VAL M 211 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN M 230 " --> pdb=" O HIS M 275 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA M 277 " --> pdb=" O ASN M 230 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE M 232 " --> pdb=" O ALA M 277 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 215 through 217 removed outlier: 3.616A pdb=" N PHE M 240 " --> pdb=" O CYS M 216 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 345 through 346 removed outlier: 7.688A pdb=" N LEU M 399 " --> pdb=" O PRO M 366 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY M 368 " --> pdb=" O LEU M 399 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU M 401 " --> pdb=" O GLY M 368 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL M 370 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE M 461 " --> pdb=" O LYS M 436 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 443 through 445 removed outlier: 6.129A pdb=" N SER M 444 " --> pdb=" O SER M 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'N' and resid 98 through 100 removed outlier: 4.718A pdb=" N THR N 121 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS N 167 " --> pdb=" O ILE N 209 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL N 211 " --> pdb=" O CYS N 167 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TYR N 169 " --> pdb=" O VAL N 211 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN N 230 " --> pdb=" O HIS N 275 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA N 277 " --> pdb=" O ASN N 230 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE N 232 " --> pdb=" O ALA N 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 215 through 217 removed outlier: 3.668A pdb=" N PHE N 240 " --> pdb=" O CYS N 216 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 345 through 346 removed outlier: 7.632A pdb=" N LEU N 399 " --> pdb=" O PRO N 366 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY N 368 " --> pdb=" O LEU N 399 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU N 401 " --> pdb=" O GLY N 368 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL N 370 " --> pdb=" O LEU N 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE N 461 " --> pdb=" O LYS N 436 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 443 through 445 removed outlier: 6.101A pdb=" N SER N 444 " --> pdb=" O SER N 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'O' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR O 121 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS O 167 " --> pdb=" O ILE O 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL O 211 " --> pdb=" O CYS O 167 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR O 169 " --> pdb=" O VAL O 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN O 230 " --> pdb=" O HIS O 275 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA O 277 " --> pdb=" O ASN O 230 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE O 232 " --> pdb=" O ALA O 277 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 215 through 217 removed outlier: 3.656A pdb=" N PHE O 240 " --> pdb=" O CYS O 216 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 345 through 346 removed outlier: 7.652A pdb=" N LEU O 399 " --> pdb=" O PRO O 366 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY O 368 " --> pdb=" O LEU O 399 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU O 401 " --> pdb=" O GLY O 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL O 370 " --> pdb=" O LEU O 401 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE O 461 " --> pdb=" O LYS O 436 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 443 through 445 removed outlier: 6.115A pdb=" N SER O 444 " --> pdb=" O SER O 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'P' and resid 98 through 100 removed outlier: 4.728A pdb=" N THR P 121 " --> pdb=" O LEU P 100 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS P 167 " --> pdb=" O ILE P 209 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL P 211 " --> pdb=" O CYS P 167 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR P 169 " --> pdb=" O VAL P 211 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN P 230 " --> pdb=" O HIS P 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA P 277 " --> pdb=" O ASN P 230 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE P 232 " --> pdb=" O ALA P 277 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 215 through 217 removed outlier: 3.656A pdb=" N PHE P 240 " --> pdb=" O CYS P 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 345 through 346 removed outlier: 7.657A pdb=" N LEU P 399 " --> pdb=" O PRO P 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY P 368 " --> pdb=" O LEU P 399 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU P 401 " --> pdb=" O GLY P 368 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL P 370 " --> pdb=" O LEU P 401 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE P 461 " --> pdb=" O LYS P 436 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 443 through 445 removed outlier: 6.112A pdb=" N SER P 444 " --> pdb=" O SER P 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'Q' and resid 98 through 100 removed outlier: 4.717A pdb=" N THR Q 121 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS Q 167 " --> pdb=" O ILE Q 209 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL Q 211 " --> pdb=" O CYS Q 167 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR Q 169 " --> pdb=" O VAL Q 211 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN Q 230 " --> pdb=" O HIS Q 275 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA Q 277 " --> pdb=" O ASN Q 230 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE Q 232 " --> pdb=" O ALA Q 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 215 through 217 removed outlier: 3.651A pdb=" N PHE Q 240 " --> pdb=" O CYS Q 216 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 345 through 346 removed outlier: 7.635A pdb=" N LEU Q 399 " --> pdb=" O PRO Q 366 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY Q 368 " --> pdb=" O LEU Q 399 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU Q 401 " --> pdb=" O GLY Q 368 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL Q 370 " --> pdb=" O LEU Q 401 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE Q 461 " --> pdb=" O LYS Q 436 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 443 through 445 removed outlier: 6.099A pdb=" N SER Q 444 " --> pdb=" O SER Q 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'R' and resid 98 through 100 removed outlier: 4.691A pdb=" N THR R 121 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS R 167 " --> pdb=" O ILE R 209 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL R 211 " --> pdb=" O CYS R 167 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR R 169 " --> pdb=" O VAL R 211 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN R 230 " --> pdb=" O HIS R 275 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA R 277 " --> pdb=" O ASN R 230 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE R 232 " --> pdb=" O ALA R 277 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R' and resid 215 through 217 removed outlier: 3.624A pdb=" N PHE R 240 " --> pdb=" O CYS R 216 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 345 through 346 removed outlier: 7.690A pdb=" N LEU R 399 " --> pdb=" O PRO R 366 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY R 368 " --> pdb=" O LEU R 399 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU R 401 " --> pdb=" O GLY R 368 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL R 370 " --> pdb=" O LEU R 401 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE R 461 " --> pdb=" O LYS R 436 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 443 through 445 removed outlier: 6.129A pdb=" N SER R 444 " --> pdb=" O SER R 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 2536 hydrogen bonds defined for protein. 7032 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: 22.56 Time building geometry restraints manager: 14.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16560 1.34 - 1.46: 9943 1.46 - 1.58: 23285 1.58 - 1.69: 0 1.69 - 1.81: 360 Bond restraints: 50148 Sorted by residual: bond pdb=" N PHE Q 240 " pdb=" CA PHE Q 240 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.16e-02 7.43e+03 7.45e+00 bond pdb=" N PHE K 240 " pdb=" CA PHE K 240 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.16e-02 7.43e+03 7.13e+00 bond pdb=" N PHE M 240 " pdb=" CA PHE M 240 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.16e-02 7.43e+03 6.93e+00 bond pdb=" N PHE G 240 " pdb=" CA PHE G 240 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.16e-02 7.43e+03 6.73e+00 bond pdb=" N MET N 49 " pdb=" CA MET N 49 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.23e-02 6.61e+03 2.65e+00 ... (remaining 50143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 66087 1.19 - 2.37: 1309 2.37 - 3.56: 327 3.56 - 4.75: 77 4.75 - 5.94: 12 Bond angle restraints: 67812 Sorted by residual: angle pdb=" C ARG I 525 " pdb=" N VAL I 526 " pdb=" CA VAL I 526 " ideal model delta sigma weight residual 121.65 117.89 3.76 9.40e-01 1.13e+00 1.60e+01 angle pdb=" C ARG O 525 " pdb=" N VAL O 526 " pdb=" CA VAL O 526 " ideal model delta sigma weight residual 121.65 117.93 3.72 9.40e-01 1.13e+00 1.57e+01 angle pdb=" C ARG G 525 " pdb=" N VAL G 526 " pdb=" CA VAL G 526 " ideal model delta sigma weight residual 121.65 117.97 3.68 9.40e-01 1.13e+00 1.53e+01 angle pdb=" C ARG P 525 " pdb=" N VAL P 526 " pdb=" CA VAL P 526 " ideal model delta sigma weight residual 121.65 117.99 3.66 9.40e-01 1.13e+00 1.51e+01 angle pdb=" C ARG M 525 " pdb=" N VAL M 526 " pdb=" CA VAL M 526 " ideal model delta sigma weight residual 121.65 118.02 3.63 9.40e-01 1.13e+00 1.49e+01 ... (remaining 67807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 27547 16.84 - 33.68: 1932 33.68 - 50.52: 397 50.52 - 67.35: 106 67.35 - 84.19: 30 Dihedral angle restraints: 30012 sinusoidal: 11904 harmonic: 18108 Sorted by residual: dihedral pdb=" CA PHE O 185 " pdb=" C PHE O 185 " pdb=" N PRO O 186 " pdb=" CA PRO O 186 " ideal model delta harmonic sigma weight residual -180.00 -153.85 -26.15 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE I 185 " pdb=" C PHE I 185 " pdb=" N PRO I 186 " pdb=" CA PRO I 186 " ideal model delta harmonic sigma weight residual -180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA PHE P 185 " pdb=" C PHE P 185 " pdb=" N PRO P 186 " pdb=" CA PRO P 186 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 30009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4778 0.027 - 0.055: 1544 0.055 - 0.082: 532 0.082 - 0.109: 424 0.109 - 0.136: 114 Chirality restraints: 7392 Sorted by residual: chirality pdb=" CA PRO L 186 " pdb=" N PRO L 186 " pdb=" C PRO L 186 " pdb=" CB PRO L 186 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA PRO H 186 " pdb=" N PRO H 186 " pdb=" C PRO H 186 " pdb=" CB PRO H 186 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PRO M 186 " pdb=" N PRO M 186 " pdb=" C PRO M 186 " pdb=" CB PRO M 186 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 7389 not shown) Planarity restraints: 8952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE L 396 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO L 397 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO L 397 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 397 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 396 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO M 397 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO M 397 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO M 397 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 396 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO G 397 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO G 397 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 397 " 0.015 5.00e-02 4.00e+02 ... (remaining 8949 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 9324 2.77 - 3.30: 47519 3.30 - 3.84: 83822 3.84 - 4.37: 105186 4.37 - 4.90: 173698 Nonbonded interactions: 419549 Sorted by model distance: nonbonded pdb=" OD1 ASP M 110 " pdb=" N ASN M 111 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASP G 110 " pdb=" N ASN G 111 " model vdw 2.241 3.120 nonbonded pdb=" OD1 ASP L 110 " pdb=" N ASN L 111 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASP R 110 " pdb=" N ASN R 111 " model vdw 2.244 3.120 nonbonded pdb=" O GLU L 69 " pdb=" OE1 GLU L 69 " model vdw 2.343 3.040 ... (remaining 419544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.730 Check model and map are aligned: 0.310 Set scattering table: 0.440 Process input model: 106.290 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.250 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4614 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 : 0.002 0.032 50148 Z= 0.132 Angle : 0.458 5.937 67812 Z= 0.262 Chirality : 0.039 0.136 7392 Planarity : 0.003 0.027 8952 Dihedral : 12.677 84.192 18540 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.20 % Allowed : 9.47 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.11), residues: 6372 helix: 2.11 (0.10), residues: 2952 sheet: 1.02 (0.16), residues: 816 loop : -0.01 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 276 HIS 0.002 0.001 HIS L 386 PHE 0.007 0.001 PHE M 240 TYR 0.008 0.001 TYR H 109 ARG 0.002 0.000 ARG I 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 905 time to evaluate : 5.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 213 MET cc_start: 0.7098 (mtp) cc_final: 0.6114 (mtt) REVERT: G 453 CYS cc_start: 0.6880 (t) cc_final: 0.6248 (t) REVERT: H 213 MET cc_start: 0.6701 (mtp) cc_final: 0.6229 (mtt) REVERT: H 453 CYS cc_start: 0.6747 (t) cc_final: 0.5972 (t) REVERT: I 213 MET cc_start: 0.6724 (mtp) cc_final: 0.5750 (mtt) REVERT: I 453 CYS cc_start: 0.6707 (t) cc_final: 0.5934 (t) REVERT: J 212 VAL cc_start: 0.5058 (t) cc_final: 0.4790 (t) REVERT: L 37 LEU cc_start: 0.6896 (mt) cc_final: 0.6606 (pp) REVERT: M 370 VAL cc_start: 0.6828 (t) cc_final: 0.6584 (t) REVERT: N 37 LEU cc_start: 0.6600 (mt) cc_final: 0.6375 (pp) REVERT: N 370 VAL cc_start: 0.6453 (t) cc_final: 0.6037 (t) REVERT: O 37 LEU cc_start: 0.6687 (mt) cc_final: 0.6220 (pp) REVERT: O 370 VAL cc_start: 0.6390 (t) cc_final: 0.6035 (t) REVERT: P 213 MET cc_start: 0.7220 (mtp) cc_final: 0.6855 (mtm) REVERT: P 453 CYS cc_start: 0.6914 (t) cc_final: 0.6186 (t) REVERT: Q 213 MET cc_start: 0.6605 (mtp) cc_final: 0.6017 (mtt) REVERT: Q 453 CYS cc_start: 0.6680 (t) cc_final: 0.5895 (t) REVERT: R 453 CYS cc_start: 0.6712 (t) cc_final: 0.5922 (t) outliers start: 10 outliers final: 8 residues processed: 915 average time/residue: 0.6974 time to fit residues: 1037.0973 Evaluate side-chains 442 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 434 time to evaluate : 5.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 537 optimal weight: 20.0000 chunk 482 optimal weight: 1.9990 chunk 267 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 325 optimal weight: 8.9990 chunk 257 optimal weight: 30.0000 chunk 498 optimal weight: 0.0970 chunk 192 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 371 optimal weight: 40.0000 chunk 577 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 282 HIS H 282 HIS ** I 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 HIS J 275 HIS J 477 GLN K 275 HIS ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 477 GLN ** M 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 GLN ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 275 HIS N 477 GLN P 282 HIS Q 282 HIS R 281 HIS R 282 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4892 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50148 Z= 0.228 Angle : 0.600 8.518 67812 Z= 0.315 Chirality : 0.045 0.175 7392 Planarity : 0.004 0.054 8952 Dihedral : 4.546 28.571 7008 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.06 % Allowed : 1.89 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.10), residues: 6372 helix: 2.01 (0.10), residues: 2952 sheet: 0.80 (0.16), residues: 852 loop : 0.03 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 276 HIS 0.009 0.001 HIS N 275 PHE 0.016 0.002 PHE M 513 TYR 0.024 0.002 TYR Q 318 ARG 0.009 0.001 ARG O 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 543 time to evaluate : 5.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 239 ILE cc_start: 0.2128 (mt) cc_final: 0.1924 (mt) REVERT: G 453 CYS cc_start: 0.6274 (t) cc_final: 0.5794 (t) REVERT: I 453 CYS cc_start: 0.6385 (t) cc_final: 0.5943 (t) REVERT: J 213 MET cc_start: 0.3845 (ptp) cc_final: 0.3118 (ptt) REVERT: J 235 LYS cc_start: 0.6584 (pttt) cc_final: 0.6183 (mmtt) REVERT: K 213 MET cc_start: 0.6015 (pmm) cc_final: 0.3913 (ptt) REVERT: L 213 MET cc_start: 0.3424 (ptp) cc_final: 0.2486 (ptp) REVERT: M 213 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.2495 (ptt) REVERT: N 213 MET cc_start: 0.3528 (ptp) cc_final: 0.2824 (ptt) REVERT: O 141 LYS cc_start: 0.6297 (mmtp) cc_final: 0.5520 (pttt) REVERT: O 213 MET cc_start: 0.4160 (ptp) cc_final: 0.3357 (ptt) REVERT: P 453 CYS cc_start: 0.6101 (t) cc_final: 0.5637 (t) REVERT: Q 236 GLN cc_start: 0.4846 (mt0) cc_final: 0.4635 (mt0) REVERT: Q 453 CYS cc_start: 0.6293 (t) cc_final: 0.5836 (t) REVERT: R 453 CYS cc_start: 0.6208 (t) cc_final: 0.5733 (t) outliers start: 3 outliers final: 2 residues processed: 545 average time/residue: 0.6068 time to fit residues: 550.8325 Evaluate side-chains 356 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 353 time to evaluate : 5.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 320 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 480 optimal weight: 9.9990 chunk 393 optimal weight: 0.7980 chunk 159 optimal weight: 40.0000 chunk 578 optimal weight: 5.9990 chunk 625 optimal weight: 9.9990 chunk 515 optimal weight: 0.5980 chunk 573 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 386 HIS ** H 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 275 HIS ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 386 HIS Q 386 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5043 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 50148 Z= 0.197 Angle : 0.574 11.645 67812 Z= 0.300 Chirality : 0.044 0.241 7392 Planarity : 0.005 0.205 8952 Dihedral : 4.580 27.582 7008 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.35 (0.10), residues: 6372 helix: 1.81 (0.09), residues: 2964 sheet: 0.77 (0.16), residues: 828 loop : -0.07 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 465 HIS 0.006 0.001 HIS M 275 PHE 0.024 0.001 PHE O 329 TYR 0.023 0.001 TYR R 318 ARG 0.012 0.001 ARG G 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 5.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 453 CYS cc_start: 0.6270 (t) cc_final: 0.5884 (t) REVERT: H 226 MET cc_start: 0.5119 (ptm) cc_final: 0.4773 (ptm) REVERT: H 453 CYS cc_start: 0.6370 (t) cc_final: 0.6027 (t) REVERT: I 49 MET cc_start: 0.4854 (tpt) cc_final: 0.4653 (tpt) REVERT: I 453 CYS cc_start: 0.6510 (t) cc_final: 0.6107 (t) REVERT: J 213 MET cc_start: 0.3365 (ptt) cc_final: 0.2644 (ptt) REVERT: J 235 LYS cc_start: 0.6659 (pttt) cc_final: 0.6290 (mmtm) REVERT: L 213 MET cc_start: 0.3144 (ptt) cc_final: 0.2477 (ptt) REVERT: M 213 MET cc_start: 0.3584 (ptt) cc_final: 0.2660 (ptt) REVERT: N 213 MET cc_start: 0.3729 (ptp) cc_final: 0.3077 (ptt) REVERT: O 141 LYS cc_start: 0.6381 (mmtp) cc_final: 0.5527 (pttt) REVERT: O 213 MET cc_start: 0.3613 (ptt) cc_final: 0.3214 (ptt) REVERT: P 453 CYS cc_start: 0.5804 (t) cc_final: 0.5524 (t) REVERT: R 408 MET cc_start: -0.3467 (tpt) cc_final: -0.3786 (mmm) REVERT: R 532 ILE cc_start: 0.4244 (mm) cc_final: 0.4042 (mm) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.6012 time to fit residues: 484.1350 Evaluate side-chains 333 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 5.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 571 optimal weight: 8.9990 chunk 435 optimal weight: 10.0000 chunk 300 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 580 optimal weight: 20.0000 chunk 614 optimal weight: 8.9990 chunk 303 optimal weight: 9.9990 chunk 550 optimal weight: 20.0000 chunk 165 optimal weight: 0.0770 overall best weight: 6.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 230 ASN ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 477 GLN ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** O 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5381 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 50148 Z= 0.304 Angle : 0.680 11.668 67812 Z= 0.355 Chirality : 0.045 0.197 7392 Planarity : 0.005 0.132 8952 Dihedral : 4.860 27.731 7008 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % 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: 0.58 (0.10), residues: 6372 helix: 1.14 (0.09), residues: 2976 sheet: 0.64 (0.16), residues: 816 loop : -0.52 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 465 HIS 0.009 0.002 HIS Q 57 PHE 0.048 0.002 PHE J 377 TYR 0.027 0.002 TYR R 318 ARG 0.013 0.001 ARG L 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 5.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 453 CYS cc_start: 0.6631 (t) cc_final: 0.6245 (t) REVERT: G 532 ILE cc_start: 0.4667 (mm) cc_final: 0.4416 (mm) REVERT: H 226 MET cc_start: 0.5209 (ptm) cc_final: 0.4720 (ptm) REVERT: H 453 CYS cc_start: 0.6310 (t) cc_final: 0.5981 (t) REVERT: H 532 ILE cc_start: 0.4553 (mm) cc_final: 0.4348 (mm) REVERT: I 408 MET cc_start: -0.3328 (tpt) cc_final: -0.3672 (mmm) REVERT: I 453 CYS cc_start: 0.6058 (t) cc_final: 0.5762 (t) REVERT: J 213 MET cc_start: 0.3491 (ptt) cc_final: 0.2866 (ptt) REVERT: L 108 LEU cc_start: 0.6459 (tp) cc_final: 0.6029 (tp) REVERT: L 141 LYS cc_start: 0.6324 (mmtt) cc_final: 0.5835 (mmtt) REVERT: M 213 MET cc_start: 0.3616 (ptt) cc_final: 0.2797 (ptt) REVERT: N 141 LYS cc_start: 0.6330 (mmtt) cc_final: 0.5861 (mmtt) REVERT: N 213 MET cc_start: 0.4755 (ptp) cc_final: 0.3939 (ptt) REVERT: O 141 LYS cc_start: 0.6596 (mmtp) cc_final: 0.6115 (mmtp) REVERT: O 213 MET cc_start: 0.3261 (ptt) cc_final: 0.2443 (ptt) REVERT: P 236 GLN cc_start: 0.6297 (mt0) cc_final: 0.6054 (mt0) REVERT: Q 408 MET cc_start: -0.2748 (tpt) cc_final: -0.3279 (mmm) REVERT: Q 453 CYS cc_start: 0.6043 (t) cc_final: 0.5810 (t) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.6004 time to fit residues: 449.1160 Evaluate side-chains 302 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 5.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 511 optimal weight: 6.9990 chunk 348 optimal weight: 20.0000 chunk 8 optimal weight: 0.2980 chunk 457 optimal weight: 0.7980 chunk 253 optimal weight: 20.0000 chunk 524 optimal weight: 7.9990 chunk 424 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 313 optimal weight: 0.6980 chunk 551 optimal weight: 0.0770 chunk 155 optimal weight: 6.9990 overall best weight: 1.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 GLN I 386 HIS J 48 GLN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 GLN ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 386 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5285 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 50148 Z= 0.163 Angle : 0.549 12.298 67812 Z= 0.287 Chirality : 0.044 0.200 7392 Planarity : 0.004 0.075 8952 Dihedral : 4.546 26.950 7008 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.88 % 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: 0.90 (0.10), residues: 6372 helix: 1.60 (0.09), residues: 2904 sheet: 0.71 (0.17), residues: 816 loop : -0.54 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 276 HIS 0.008 0.001 HIS H 57 PHE 0.017 0.001 PHE I 387 TYR 0.029 0.001 TYR I 318 ARG 0.013 0.000 ARG J 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 425 time to evaluate : 5.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 226 MET cc_start: 0.4408 (ptt) cc_final: 0.4053 (ptm) REVERT: G 408 MET cc_start: -0.1319 (ttm) cc_final: -0.1552 (ptm) REVERT: G 453 CYS cc_start: 0.6316 (t) cc_final: 0.6002 (t) REVERT: G 532 ILE cc_start: 0.4551 (mm) cc_final: 0.4316 (mm) REVERT: H 49 MET cc_start: 0.5769 (tpt) cc_final: 0.5546 (tpt) REVERT: H 226 MET cc_start: 0.5484 (ptm) cc_final: 0.5055 (ptm) REVERT: I 236 GLN cc_start: 0.5255 (mt0) cc_final: 0.5050 (mt0) REVERT: I 408 MET cc_start: -0.3302 (tpt) cc_final: -0.3624 (mmm) REVERT: I 453 CYS cc_start: 0.6576 (t) cc_final: 0.6310 (t) REVERT: J 213 MET cc_start: 0.3428 (ptt) cc_final: 0.2821 (ptt) REVERT: K 213 MET cc_start: 0.5803 (pmm) cc_final: 0.4273 (ptp) REVERT: L 108 LEU cc_start: 0.6282 (tp) cc_final: 0.5974 (tp) REVERT: L 141 LYS cc_start: 0.6699 (mmtt) cc_final: 0.6395 (mmtt) REVERT: L 213 MET cc_start: 0.3678 (ptt) cc_final: 0.2615 (ptt) REVERT: M 213 MET cc_start: 0.3644 (ptt) cc_final: 0.2775 (ptt) REVERT: N 108 LEU cc_start: 0.4932 (tp) cc_final: 0.4625 (tp) REVERT: N 141 LYS cc_start: 0.6763 (mmtt) cc_final: 0.6492 (mmtt) REVERT: N 213 MET cc_start: 0.5139 (ptp) cc_final: 0.4525 (ptt) REVERT: O 213 MET cc_start: 0.3193 (ptt) cc_final: 0.2432 (ptt) REVERT: Q 408 MET cc_start: -0.2715 (tpt) cc_final: -0.3130 (mmm) REVERT: R 408 MET cc_start: -0.3464 (tpt) cc_final: -0.3719 (mmm) REVERT: R 453 CYS cc_start: 0.6288 (t) cc_final: 0.6032 (t) outliers start: 2 outliers final: 2 residues processed: 427 average time/residue: 0.6111 time to fit residues: 438.7031 Evaluate side-chains 309 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 307 time to evaluate : 5.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 206 optimal weight: 4.9990 chunk 553 optimal weight: 40.0000 chunk 121 optimal weight: 10.0000 chunk 360 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 615 optimal weight: 20.0000 chunk 510 optimal weight: 8.9990 chunk 284 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 203 optimal weight: 40.0000 chunk 323 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 386 HIS ** K 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 386 HIS ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 GLN ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 50148 Z= 0.234 Angle : 0.593 9.870 67812 Z= 0.312 Chirality : 0.044 0.183 7392 Planarity : 0.005 0.168 8952 Dihedral : 4.659 27.114 7008 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 6372 helix: 1.27 (0.09), residues: 2976 sheet: 0.64 (0.17), residues: 816 loop : -0.62 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 465 HIS 0.007 0.001 HIS P 57 PHE 0.025 0.002 PHE G 195 TYR 0.021 0.002 TYR I 318 ARG 0.011 0.001 ARG L 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 5.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 226 MET cc_start: 0.4281 (ptt) cc_final: 0.3758 (ptm) REVERT: G 408 MET cc_start: -0.0821 (ttm) cc_final: -0.1195 (ptm) REVERT: G 453 CYS cc_start: 0.6666 (t) cc_final: 0.6375 (t) REVERT: H 226 MET cc_start: 0.5562 (ptm) cc_final: 0.5149 (ptm) REVERT: H 453 CYS cc_start: 0.6123 (t) cc_final: 0.5824 (t) REVERT: I 408 MET cc_start: -0.3065 (tpt) cc_final: -0.3468 (mmm) REVERT: I 453 CYS cc_start: 0.6197 (t) cc_final: 0.5963 (t) REVERT: J 213 MET cc_start: 0.3605 (ptt) cc_final: 0.2891 (ptt) REVERT: K 213 MET cc_start: 0.6194 (pmm) cc_final: 0.4841 (ptt) REVERT: L 132 MET cc_start: 0.7037 (tpp) cc_final: 0.6799 (tpp) REVERT: L 141 LYS cc_start: 0.6843 (mmtt) cc_final: 0.6564 (mmtp) REVERT: L 213 MET cc_start: 0.4068 (ptt) cc_final: 0.3036 (ptt) REVERT: M 213 MET cc_start: 0.3974 (ptt) cc_final: 0.3101 (ptt) REVERT: N 132 MET cc_start: 0.7036 (tpp) cc_final: 0.6726 (tpp) REVERT: N 141 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6845 (mmtp) REVERT: N 213 MET cc_start: 0.5625 (ptp) cc_final: 0.5185 (ptt) REVERT: P 408 MET cc_start: -0.2653 (ttm) cc_final: -0.3311 (ptm) REVERT: Q 110 ASP cc_start: 0.7044 (p0) cc_final: 0.6838 (p0) REVERT: R 453 CYS cc_start: 0.6465 (t) cc_final: 0.6233 (t) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.6163 time to fit residues: 406.5009 Evaluate side-chains 296 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 593 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 449 optimal weight: 20.0000 chunk 348 optimal weight: 0.2980 chunk 518 optimal weight: 30.0000 chunk 343 optimal weight: 7.9990 chunk 613 optimal weight: 0.0030 chunk 383 optimal weight: 6.9990 chunk 373 optimal weight: 0.9990 chunk 283 optimal weight: 50.0000 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 386 HIS ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 50148 Z= 0.147 Angle : 0.536 9.390 67812 Z= 0.282 Chirality : 0.043 0.178 7392 Planarity : 0.004 0.105 8952 Dihedral : 4.473 26.482 7008 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.02 % Allowed : 0.83 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 6372 helix: 1.47 (0.10), residues: 2976 sheet: 0.69 (0.17), residues: 816 loop : -0.58 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 276 HIS 0.004 0.001 HIS K 75 PHE 0.014 0.001 PHE G 387 TYR 0.032 0.001 TYR Q 413 ARG 0.008 0.000 ARG Q 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 5.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 226 MET cc_start: 0.4288 (ptt) cc_final: 0.3876 (ptm) REVERT: G 453 CYS cc_start: 0.6374 (t) cc_final: 0.6132 (t) REVERT: H 226 MET cc_start: 0.5565 (ptm) cc_final: 0.5121 (ptm) REVERT: H 453 CYS cc_start: 0.6121 (t) cc_final: 0.5882 (t) REVERT: I 408 MET cc_start: -0.3161 (tpt) cc_final: -0.3535 (mmm) REVERT: I 453 CYS cc_start: 0.6404 (t) cc_final: 0.6156 (t) REVERT: J 141 LYS cc_start: 0.6200 (mmtp) cc_final: 0.5969 (mmtm) REVERT: J 213 MET cc_start: 0.3650 (ptt) cc_final: 0.2974 (ptt) REVERT: K 213 MET cc_start: 0.6078 (pmm) cc_final: 0.4906 (ptt) REVERT: L 213 MET cc_start: 0.3923 (ptt) cc_final: 0.3094 (ptt) REVERT: M 213 MET cc_start: 0.3691 (ptt) cc_final: 0.3260 (ptt) REVERT: N 213 MET cc_start: 0.5594 (ptp) cc_final: 0.5209 (ptt) REVERT: P 408 MET cc_start: -0.2085 (ttm) cc_final: -0.2834 (ptm) REVERT: Q 49 MET cc_start: 0.5172 (tpt) cc_final: 0.4952 (mtp) REVERT: Q 110 ASP cc_start: 0.7034 (p0) cc_final: 0.6816 (p0) REVERT: Q 213 MET cc_start: 0.7093 (ptt) cc_final: 0.6622 (ptt) REVERT: Q 408 MET cc_start: -0.1931 (ttt) cc_final: -0.3015 (ptt) REVERT: R 292 ARG cc_start: 0.6907 (ptt90) cc_final: 0.6552 (ptt90) outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.6075 time to fit residues: 408.8044 Evaluate side-chains 297 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 379 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 389 optimal weight: 7.9990 chunk 417 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 481 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 236 GLN ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 ASN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 386 HIS ** M 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 386 HIS ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 GLN ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5493 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 50148 Z= 0.218 Angle : 0.597 12.516 67812 Z= 0.312 Chirality : 0.043 0.169 7392 Planarity : 0.005 0.086 8952 Dihedral : 4.646 30.359 7008 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: 0.58 (0.10), residues: 6372 helix: 1.26 (0.09), residues: 2976 sheet: 0.70 (0.17), residues: 816 loop : -0.71 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 465 HIS 0.009 0.001 HIS H 57 PHE 0.023 0.002 PHE Q 195 TYR 0.016 0.002 TYR J 109 ARG 0.010 0.001 ARG Q 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 226 MET cc_start: 0.4325 (ptt) cc_final: 0.4019 (ptm) REVERT: G 453 CYS cc_start: 0.6537 (t) cc_final: 0.6306 (t) REVERT: H 226 MET cc_start: 0.5658 (ptm) cc_final: 0.5123 (ptm) REVERT: H 532 ILE cc_start: 0.4653 (mm) cc_final: 0.4450 (mm) REVERT: I 213 MET cc_start: 0.7358 (pmm) cc_final: 0.6841 (pmm) REVERT: J 213 MET cc_start: 0.4242 (ptt) cc_final: 0.3622 (ptt) REVERT: L 213 MET cc_start: 0.4327 (ptt) cc_final: 0.3448 (ptt) REVERT: N 213 MET cc_start: 0.5815 (ptp) cc_final: 0.5363 (ptt) REVERT: O 226 MET cc_start: 0.5690 (ppp) cc_final: 0.5426 (ptm) REVERT: P 408 MET cc_start: -0.1941 (ttm) cc_final: -0.2735 (ptm) REVERT: Q 110 ASP cc_start: 0.7221 (p0) cc_final: 0.6973 (p0) REVERT: Q 213 MET cc_start: 0.7296 (ptt) cc_final: 0.7068 (ptt) REVERT: Q 408 MET cc_start: -0.1789 (ttt) cc_final: -0.2892 (ptt) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.6405 time to fit residues: 409.3295 Evaluate side-chains 283 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 5.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 557 optimal weight: 6.9990 chunk 587 optimal weight: 3.9990 chunk 535 optimal weight: 7.9990 chunk 571 optimal weight: 30.0000 chunk 343 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 448 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 516 optimal weight: 5.9990 chunk 540 optimal weight: 8.9990 chunk 569 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 389 GLN ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 GLN I 389 GLN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 477 GLN ** K 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 386 HIS ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 197 ASN R 236 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 50148 Z= 0.269 Angle : 0.654 14.570 67812 Z= 0.346 Chirality : 0.045 0.289 7392 Planarity : 0.005 0.150 8952 Dihedral : 4.994 45.905 7008 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.17 (0.10), residues: 6372 helix: 0.90 (0.09), residues: 2988 sheet: 0.65 (0.17), residues: 816 loop : -0.96 (0.11), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 276 HIS 0.023 0.002 HIS L 190 PHE 0.030 0.002 PHE Q 363 TYR 0.073 0.002 TYR I 413 ARG 0.010 0.001 ARG I 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 5.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 213 MET cc_start: 0.6553 (ptt) cc_final: 0.6033 (ptp) REVERT: G 226 MET cc_start: 0.4216 (ptt) cc_final: 0.3776 (ptm) REVERT: G 453 CYS cc_start: 0.6793 (t) cc_final: 0.6523 (t) REVERT: H 213 MET cc_start: 0.6695 (ptt) cc_final: 0.6214 (ptp) REVERT: H 226 MET cc_start: 0.5441 (ptm) cc_final: 0.5020 (ptm) REVERT: I 408 MET cc_start: -0.2688 (ttt) cc_final: -0.3262 (ptt) REVERT: J 37 LEU cc_start: 0.8027 (pt) cc_final: 0.7734 (pp) REVERT: J 235 LYS cc_start: 0.6592 (pttt) cc_final: 0.6331 (mmtt) REVERT: L 213 MET cc_start: 0.4732 (ptt) cc_final: 0.3889 (ptt) REVERT: M 213 MET cc_start: 0.3902 (ptt) cc_final: 0.3685 (ptp) REVERT: N 213 MET cc_start: 0.6016 (ptp) cc_final: 0.5564 (ptt) REVERT: O 226 MET cc_start: 0.5838 (ppp) cc_final: 0.5503 (ptm) REVERT: Q 110 ASP cc_start: 0.7400 (p0) cc_final: 0.7106 (p0) REVERT: Q 213 MET cc_start: 0.7139 (ptt) cc_final: 0.6900 (ptt) REVERT: Q 408 MET cc_start: -0.2018 (ttt) cc_final: -0.2788 (ptm) REVERT: R 49 MET cc_start: 0.6953 (mtt) cc_final: 0.6192 (tpp) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.6173 time to fit residues: 391.0024 Evaluate side-chains 281 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 5.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 375 optimal weight: 20.0000 chunk 604 optimal weight: 8.9990 chunk 368 optimal weight: 5.9990 chunk 286 optimal weight: 0.0370 chunk 419 optimal weight: 4.9990 chunk 633 optimal weight: 6.9990 chunk 583 optimal weight: 0.0370 chunk 504 optimal weight: 6.9990 chunk 52 optimal weight: 0.1980 chunk 389 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 overall best weight: 2.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 GLN ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 386 HIS ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 GLN N 295 ASN N 372 ASN ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 389 GLN ** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.6997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 50148 Z= 0.170 Angle : 0.574 12.497 67812 Z= 0.301 Chirality : 0.044 0.207 7392 Planarity : 0.004 0.051 8952 Dihedral : 4.679 29.902 7008 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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: 0.40 (0.10), residues: 6372 helix: 1.14 (0.09), residues: 2988 sheet: 0.44 (0.17), residues: 852 loop : -0.80 (0.11), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 276 HIS 0.006 0.001 HIS N 190 PHE 0.022 0.001 PHE M 561 TYR 0.028 0.001 TYR R 365 ARG 0.009 0.001 ARG P 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12744 Ramachandran restraints generated. 6372 Oldfield, 0 Emsley, 6372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 5.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 213 MET cc_start: 0.6446 (ptt) cc_final: 0.5959 (ptp) REVERT: G 226 MET cc_start: 0.4019 (ptt) cc_final: 0.3700 (ptm) REVERT: G 453 CYS cc_start: 0.6512 (t) cc_final: 0.6252 (t) REVERT: H 213 MET cc_start: 0.6526 (ptt) cc_final: 0.6161 (ptp) REVERT: I 213 MET cc_start: 0.7473 (pmm) cc_final: 0.7005 (pmm) REVERT: J 37 LEU cc_start: 0.8007 (pt) cc_final: 0.7707 (pp) REVERT: J 213 MET cc_start: 0.3745 (ptt) cc_final: 0.3458 (ptt) REVERT: L 213 MET cc_start: 0.4705 (ptt) cc_final: 0.4027 (ptt) REVERT: L 226 MET cc_start: 0.5652 (ptt) cc_final: 0.5311 (ptt) REVERT: M 213 MET cc_start: 0.3849 (ptt) cc_final: 0.3590 (ptp) REVERT: N 213 MET cc_start: 0.5664 (ptp) cc_final: 0.5402 (ptt) REVERT: O 226 MET cc_start: 0.5710 (ppp) cc_final: 0.5340 (ptt) REVERT: P 292 ARG cc_start: 0.7082 (ptt90) cc_final: 0.6394 (ptt90) REVERT: Q 110 ASP cc_start: 0.7330 (p0) cc_final: 0.7074 (p0) REVERT: Q 213 MET cc_start: 0.7043 (ptt) cc_final: 0.6811 (ptt) REVERT: Q 408 MET cc_start: -0.1935 (ttt) cc_final: -0.2910 (ptt) REVERT: R 49 MET cc_start: 0.6948 (mtt) cc_final: 0.6089 (tpt) REVERT: R 110 ASP cc_start: 0.7372 (p0) cc_final: 0.7131 (p0) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.6127 time to fit residues: 382.9960 Evaluate side-chains 273 residues out of total 5088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 636 random chunks: chunk 400 optimal weight: 1.9990 chunk 537 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 465 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 505 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 518 optimal weight: 0.0670 chunk 63 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN ** I 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 ASN N 208 GLN ** O 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 236 GLN ** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.105599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4030 r_free = 0.4030 target = 0.079974 restraints weight = 361073.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.080432 restraints weight = 320553.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.080433 restraints weight = 299647.861| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 50148 Z= 0.168 Angle : 0.569 14.655 67812 Z= 0.297 Chirality : 0.043 0.176 7392 Planarity : 0.005 0.171 8952 Dihedral : 4.589 34.478 7008 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.48 (0.10), residues: 6372 helix: 1.19 (0.09), residues: 2988 sheet: 0.54 (0.17), residues: 852 loop : -0.77 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 465 HIS 0.007 0.001 HIS O 285 PHE 0.021 0.001 PHE G 387 TYR 0.014 0.001 TYR J 109 ARG 0.006 0.000 ARG L 525 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10012.86 seconds wall clock time: 180 minutes 39.56 seconds (10839.56 seconds total)