Starting phenix.real_space_refine on Thu Oct 29 17:21:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29gv_57153/10_2026/29gv_57153.cif Found real_map, /net/cci-nas-00/data/ceres_data/29gv_57153/10_2026/29gv_57153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29gv_57153/10_2026/29gv_57153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29gv_57153/10_2026/29gv_57153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29gv_57153/10_2026/29gv_57153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29gv_57153/10_2026/29gv_57153.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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 144 5.16 5 C 20336 2.51 5 N 5699 2.21 5 O 6007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32186 Number of models: 1 Model: "" Number of chains: 18 Chain: "D1" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3838 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 31, 'TRANS': 479} Chain: "D2" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3838 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 31, 'TRANS': 479} Chain: "D3" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3838 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 31, 'TRANS': 479} Chain: "D4" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3838 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 31, 'TRANS': 479} Chain: "D5" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3838 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 31, 'TRANS': 479} Chain: "D6" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3838 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 31, 'TRANS': 479} Chain: "A1" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1520 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 7 Chain: "A2" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1498 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 7 Chain: "A3" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1512 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 7 Chain: "A4" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1505 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 7 Chain: "A5" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1513 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 7 Chain: "A6" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1520 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 7 Chain: "A1" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A2" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A3" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A4" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A5" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A6" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N VALA1 37 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VALA1 37 " occ=0.00 residue: pdb=" N PHEA1 38 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHEA1 38 " occ=0.00 residue: pdb=" N SERA1 39 " occ=0.00 ... (4 atoms not shown) pdb=" OG SERA1 39 " occ=0.00 residue: pdb=" N GLYA1 387 " occ=0.00 ... (2 atoms not shown) pdb=" O GLYA1 387 " occ=0.00 residue: pdb=" N VALA2 37 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VALA2 37 " occ=0.00 residue: pdb=" N PHEA2 38 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHEA2 38 " occ=0.00 residue: pdb=" N SERA2 39 " occ=0.00 ... (4 atoms not shown) pdb=" OG SERA2 39 " occ=0.00 residue: pdb=" N VALA3 37 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VALA3 37 " occ=0.00 residue: pdb=" N PHEA3 38 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHEA3 38 " occ=0.00 residue: pdb=" N SERA3 39 " occ=0.00 ... (4 atoms not shown) pdb=" OG SERA3 39 " occ=0.00 residue: pdb=" N ALAA4 36 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALAA4 36 " occ=0.00 residue: pdb=" N VALA4 37 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VALA4 37 " occ=0.00 ... (remaining 8 not shown) Time building chain proxies: 7.31, per 1000 atoms: 0.23 Number of scatterers: 32186 At special positions: 0 Unit cell: (156.268, 144.693, 174.596, 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 144 16.00 O 6007 8.00 N 5699 7.00 C 20336 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7630 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 60 sheets defined 44.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'D1' and resid 3 through 25 removed outlier: 3.950A pdb=" N GLYD1 25 " --> pdb=" O ALAD1 21 " (cutoff:3.500A) Processing helix chain 'D1' and resid 27 through 37 Processing helix chain 'D1' and resid 41 through 50 Processing helix chain 'D1' and resid 67 through 71 Processing helix chain 'D1' and resid 72 through 75 Processing helix chain 'D1' and resid 98 through 102 Processing helix chain 'D1' and resid 104 through 122 Processing helix chain 'D1' and resid 135 through 142 removed outlier: 5.587A pdb=" N ASPD1 140 " --> pdb=" O PROD1 137 " (cutoff:3.500A) Processing helix chain 'D1' and resid 150 through 162 Processing helix chain 'D1' and resid 179 through 184 Processing helix chain 'D1' and resid 201 through 210 Processing helix chain 'D1' and resid 214 through 220 Processing helix chain 'D1' and resid 220 through 227 Processing helix chain 'D1' and resid 237 through 251 removed outlier: 3.552A pdb=" N THRD1 251 " --> pdb=" O ASND1 247 " (cutoff:3.500A) Processing helix chain 'D1' and resid 271 through 273 No H-bonds generated for 'chain 'D1' and resid 271 through 273' Processing helix chain 'D1' and resid 274 through 279 removed outlier: 3.608A pdb=" N VALD1 278 " --> pdb=" O GLUD1 274 " (cutoff:3.500A) Processing helix chain 'D1' and resid 289 through 295 removed outlier: 3.703A pdb=" N ARGD1 295 " --> pdb=" O GLUD1 291 " (cutoff:3.500A) Processing helix chain 'D1' and resid 296 through 301 removed outlier: 6.970A pdb=" N GLYD1 299 " --> pdb=" O ILED1 296 " (cutoff:3.500A) Processing helix chain 'D1' and resid 335 through 352 Processing helix chain 'D1' and resid 368 through 375 Processing helix chain 'D1' and resid 375 through 390 Processing helix chain 'D1' and resid 404 through 410 removed outlier: 3.515A pdb=" N TYRD1 408 " --> pdb=" O GLYD1 404 " (cutoff:3.500A) Processing helix chain 'D1' and resid 411 through 416 removed outlier: 6.124A pdb=" N ALAD1 414 " --> pdb=" O CYSD1 411 " (cutoff:3.500A) Processing helix chain 'D1' and resid 432 through 445 Processing helix chain 'D1' and resid 449 through 468 Proline residue: D1 458 - end of helix Processing helix chain 'D1' and resid 468 through 475 removed outlier: 3.526A pdb=" N ARGD1 475 " --> pdb=" O TYRD1 471 " (cutoff:3.500A) Processing helix chain 'D1' and resid 483 through 485 No H-bonds generated for 'chain 'D1' and resid 483 through 485' Processing helix chain 'D1' and resid 486 through 499 removed outlier: 3.560A pdb=" N GLYD1 499 " --> pdb=" O LEUD1 495 " (cutoff:3.500A) Processing helix chain 'D2' and resid 4 through 24 Processing helix chain 'D2' and resid 27 through 37 Processing helix chain 'D2' and resid 41 through 50 Processing helix chain 'D2' and resid 67 through 71 Processing helix chain 'D2' and resid 72 through 75 Processing helix chain 'D2' and resid 98 through 102 Processing helix chain 'D2' and resid 104 through 122 Processing helix chain 'D2' and resid 135 through 142 removed outlier: 5.528A pdb=" N ASPD2 140 " --> pdb=" O PROD2 137 " (cutoff:3.500A) Processing helix chain 'D2' and resid 148 through 162 removed outlier: 3.896A pdb=" N ILED2 152 " --> pdb=" O HISD2 148 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHED2 153 " --> pdb=" O PHED2 149 " (cutoff:3.500A) Processing helix chain 'D2' and resid 179 through 184 Processing helix chain 'D2' and resid 201 through 210 Processing helix chain 'D2' and resid 214 through 220 Processing helix chain 'D2' and resid 220 through 227 Processing helix chain 'D2' and resid 237 through 251 removed outlier: 3.552A pdb=" N THRD2 251 " --> pdb=" O ASND2 247 " (cutoff:3.500A) Processing helix chain 'D2' and resid 271 through 273 No H-bonds generated for 'chain 'D2' and resid 271 through 273' Processing helix chain 'D2' and resid 274 through 279 removed outlier: 3.609A pdb=" N VALD2 278 " --> pdb=" O GLUD2 274 " (cutoff:3.500A) Processing helix chain 'D2' and resid 289 through 295 removed outlier: 3.706A pdb=" N ARGD2 295 " --> pdb=" O GLUD2 291 " (cutoff:3.500A) Processing helix chain 'D2' and resid 296 through 301 removed outlier: 6.988A pdb=" N GLYD2 299 " --> pdb=" O ILED2 296 " (cutoff:3.500A) Processing helix chain 'D2' and resid 335 through 352 Processing helix chain 'D2' and resid 368 through 375 Processing helix chain 'D2' and resid 375 through 390 Processing helix chain 'D2' and resid 404 through 410 Processing helix chain 'D2' and resid 411 through 416 removed outlier: 6.121A pdb=" N ALAD2 414 " --> pdb=" O CYSD2 411 " (cutoff:3.500A) Processing helix chain 'D2' and resid 432 through 445 Processing helix chain 'D2' and resid 449 through 468 Proline residue: D2 458 - end of helix Processing helix chain 'D2' and resid 468 through 475 removed outlier: 3.588A pdb=" N ARGD2 475 " --> pdb=" O TYRD2 471 " (cutoff:3.500A) Processing helix chain 'D2' and resid 483 through 485 No H-bonds generated for 'chain 'D2' and resid 483 through 485' Processing helix chain 'D2' and resid 486 through 499 removed outlier: 3.574A pdb=" N GLYD2 499 " --> pdb=" O LEUD2 495 " (cutoff:3.500A) Processing helix chain 'D3' and resid 4 through 25 removed outlier: 3.967A pdb=" N GLYD3 25 " --> pdb=" O ALAD3 21 " (cutoff:3.500A) Processing helix chain 'D3' and resid 27 through 37 Processing helix chain 'D3' and resid 41 through 50 Processing helix chain 'D3' and resid 67 through 71 Processing helix chain 'D3' and resid 72 through 75 Processing helix chain 'D3' and resid 98 through 102 Processing helix chain 'D3' and resid 104 through 122 Processing helix chain 'D3' and resid 135 through 142 removed outlier: 5.574A pdb=" N ASPD3 140 " --> pdb=" O PROD3 137 " (cutoff:3.500A) Processing helix chain 'D3' and resid 149 through 162 removed outlier: 4.253A pdb=" N PHED3 153 " --> pdb=" O PHED3 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLND3 162 " --> pdb=" O THRD3 158 " (cutoff:3.500A) Processing helix chain 'D3' and resid 179 through 184 Processing helix chain 'D3' and resid 201 through 210 Processing helix chain 'D3' and resid 214 through 220 Processing helix chain 'D3' and resid 220 through 227 Processing helix chain 'D3' and resid 237 through 251 removed outlier: 3.564A pdb=" N THRD3 251 " --> pdb=" O ASND3 247 " (cutoff:3.500A) Processing helix chain 'D3' and resid 271 through 273 No H-bonds generated for 'chain 'D3' and resid 271 through 273' Processing helix chain 'D3' and resid 274 through 279 removed outlier: 3.636A pdb=" N VALD3 278 " --> pdb=" O GLUD3 274 " (cutoff:3.500A) Processing helix chain 'D3' and resid 289 through 297 Processing helix chain 'D3' and resid 298 through 301 Processing helix chain 'D3' and resid 335 through 353 Processing helix chain 'D3' and resid 368 through 375 Processing helix chain 'D3' and resid 375 through 390 Processing helix chain 'D3' and resid 404 through 410 removed outlier: 3.509A pdb=" N TYRD3 408 " --> pdb=" O GLYD3 404 " (cutoff:3.500A) Processing helix chain 'D3' and resid 411 through 416 removed outlier: 6.082A pdb=" N ALAD3 414 " --> pdb=" O CYSD3 411 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SERD3 416 " --> pdb=" O ARGD3 413 " (cutoff:3.500A) Processing helix chain 'D3' and resid 432 through 445 Processing helix chain 'D3' and resid 448 through 468 Proline residue: D3 458 - end of helix Processing helix chain 'D3' and resid 468 through 475 removed outlier: 3.645A pdb=" N ARGD3 475 " --> pdb=" O TYRD3 471 " (cutoff:3.500A) Processing helix chain 'D3' and resid 483 through 485 No H-bonds generated for 'chain 'D3' and resid 483 through 485' Processing helix chain 'D3' and resid 486 through 499 removed outlier: 3.554A pdb=" N GLYD3 499 " --> pdb=" O LEUD3 495 " (cutoff:3.500A) Processing helix chain 'D4' and resid 4 through 25 removed outlier: 3.881A pdb=" N GLYD4 25 " --> pdb=" O ALAD4 21 " (cutoff:3.500A) Processing helix chain 'D4' and resid 27 through 37 Processing helix chain 'D4' and resid 41 through 50 Processing helix chain 'D4' and resid 67 through 71 Processing helix chain 'D4' and resid 72 through 75 Processing helix chain 'D4' and resid 98 through 102 Processing helix chain 'D4' and resid 104 through 122 Processing helix chain 'D4' and resid 135 through 142 removed outlier: 5.617A pdb=" N ASPD4 140 " --> pdb=" O PROD4 137 " (cutoff:3.500A) Processing helix chain 'D4' and resid 149 through 162 removed outlier: 4.215A pdb=" N PHED4 153 " --> pdb=" O PHED4 149 " (cutoff:3.500A) Processing helix chain 'D4' and resid 179 through 184 Processing helix chain 'D4' and resid 201 through 210 Processing helix chain 'D4' and resid 214 through 220 Processing helix chain 'D4' and resid 220 through 227 Processing helix chain 'D4' and resid 237 through 251 removed outlier: 3.582A pdb=" N THRD4 251 " --> pdb=" O ASND4 247 " (cutoff:3.500A) Processing helix chain 'D4' and resid 271 through 273 No H-bonds generated for 'chain 'D4' and resid 271 through 273' Processing helix chain 'D4' and resid 274 through 279 removed outlier: 3.611A pdb=" N VALD4 278 " --> pdb=" O GLUD4 274 " (cutoff:3.500A) Processing helix chain 'D4' and resid 289 through 297 Processing helix chain 'D4' and resid 298 through 300 No H-bonds generated for 'chain 'D4' and resid 298 through 300' Processing helix chain 'D4' and resid 335 through 352 Processing helix chain 'D4' and resid 368 through 375 Processing helix chain 'D4' and resid 375 through 390 Processing helix chain 'D4' and resid 404 through 410 removed outlier: 3.571A pdb=" N TYRD4 408 " --> pdb=" O GLYD4 404 " (cutoff:3.500A) Processing helix chain 'D4' and resid 412 through 416 Processing helix chain 'D4' and resid 432 through 445 Processing helix chain 'D4' and resid 451 through 468 removed outlier: 3.685A pdb=" N ALAD4 457 " --> pdb=" O GLUD4 453 " (cutoff:3.500A) Proline residue: D4 458 - end of helix Processing helix chain 'D4' and resid 468 through 475 removed outlier: 3.554A pdb=" N ARGD4 475 " --> pdb=" O TYRD4 471 " (cutoff:3.500A) Processing helix chain 'D4' and resid 483 through 485 No H-bonds generated for 'chain 'D4' and resid 483 through 485' Processing helix chain 'D4' and resid 486 through 499 removed outlier: 3.560A pdb=" N GLYD4 499 " --> pdb=" O LEUD4 495 " (cutoff:3.500A) Processing helix chain 'D5' and resid 4 through 25 removed outlier: 4.015A pdb=" N GLYD5 25 " --> pdb=" O ALAD5 21 " (cutoff:3.500A) Processing helix chain 'D5' and resid 27 through 37 Processing helix chain 'D5' and resid 41 through 50 Processing helix chain 'D5' and resid 67 through 71 Processing helix chain 'D5' and resid 72 through 75 Processing helix chain 'D5' and resid 98 through 102 Processing helix chain 'D5' and resid 104 through 122 Processing helix chain 'D5' and resid 135 through 142 removed outlier: 5.571A pdb=" N ASPD5 140 " --> pdb=" O PROD5 137 " (cutoff:3.500A) Processing helix chain 'D5' and resid 149 through 162 removed outlier: 4.255A pdb=" N PHED5 153 " --> pdb=" O PHED5 149 " (cutoff:3.500A) Processing helix chain 'D5' and resid 179 through 184 Processing helix chain 'D5' and resid 201 through 210 Processing helix chain 'D5' and resid 214 through 220 Processing helix chain 'D5' and resid 220 through 227 Processing helix chain 'D5' and resid 237 through 251 removed outlier: 3.563A pdb=" N THRD5 251 " --> pdb=" O ASND5 247 " (cutoff:3.500A) Processing helix chain 'D5' and resid 271 through 273 No H-bonds generated for 'chain 'D5' and resid 271 through 273' Processing helix chain 'D5' and resid 274 through 279 removed outlier: 3.615A pdb=" N VALD5 278 " --> pdb=" O GLUD5 274 " (cutoff:3.500A) Processing helix chain 'D5' and resid 289 through 297 Processing helix chain 'D5' and resid 298 through 301 Processing helix chain 'D5' and resid 335 through 352 Processing helix chain 'D5' and resid 368 through 375 Processing helix chain 'D5' and resid 375 through 390 Processing helix chain 'D5' and resid 404 through 410 removed outlier: 3.555A pdb=" N TYRD5 408 " --> pdb=" O GLYD5 404 " (cutoff:3.500A) Processing helix chain 'D5' and resid 412 through 416 Processing helix chain 'D5' and resid 432 through 444 Processing helix chain 'D5' and resid 448 through 468 Proline residue: D5 458 - end of helix Processing helix chain 'D5' and resid 468 through 475 removed outlier: 3.655A pdb=" N ARGD5 475 " --> pdb=" O TYRD5 471 " (cutoff:3.500A) Processing helix chain 'D5' and resid 483 through 485 No H-bonds generated for 'chain 'D5' and resid 483 through 485' Processing helix chain 'D5' and resid 486 through 499 removed outlier: 3.560A pdb=" N GLYD5 499 " --> pdb=" O LEUD5 495 " (cutoff:3.500A) Processing helix chain 'D6' and resid 4 through 25 removed outlier: 3.969A pdb=" N GLYD6 25 " --> pdb=" O ALAD6 21 " (cutoff:3.500A) Processing helix chain 'D6' and resid 27 through 37 Processing helix chain 'D6' and resid 41 through 50 Processing helix chain 'D6' and resid 67 through 71 Processing helix chain 'D6' and resid 72 through 75 Processing helix chain 'D6' and resid 98 through 102 Processing helix chain 'D6' and resid 104 through 122 Processing helix chain 'D6' and resid 135 through 142 removed outlier: 5.630A pdb=" N ASPD6 140 " --> pdb=" O PROD6 137 " (cutoff:3.500A) Processing helix chain 'D6' and resid 148 through 162 removed outlier: 3.882A pdb=" N ILED6 152 " --> pdb=" O HISD6 148 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHED6 153 " --> pdb=" O PHED6 149 " (cutoff:3.500A) Processing helix chain 'D6' and resid 179 through 184 Processing helix chain 'D6' and resid 201 through 210 Processing helix chain 'D6' and resid 214 through 220 Processing helix chain 'D6' and resid 220 through 227 Processing helix chain 'D6' and resid 237 through 251 removed outlier: 3.581A pdb=" N THRD6 251 " --> pdb=" O ASND6 247 " (cutoff:3.500A) Processing helix chain 'D6' and resid 271 through 273 No H-bonds generated for 'chain 'D6' and resid 271 through 273' Processing helix chain 'D6' and resid 274 through 279 removed outlier: 3.612A pdb=" N VALD6 278 " --> pdb=" O GLUD6 274 " (cutoff:3.500A) Processing helix chain 'D6' and resid 289 through 297 Processing helix chain 'D6' and resid 298 through 300 No H-bonds generated for 'chain 'D6' and resid 298 through 300' Processing helix chain 'D6' and resid 335 through 352 Processing helix chain 'D6' and resid 368 through 375 Processing helix chain 'D6' and resid 375 through 390 Processing helix chain 'D6' and resid 404 through 410 removed outlier: 3.563A pdb=" N TYRD6 408 " --> pdb=" O GLYD6 404 " (cutoff:3.500A) Processing helix chain 'D6' and resid 412 through 416 Processing helix chain 'D6' and resid 432 through 444 Processing helix chain 'D6' and resid 448 through 468 removed outlier: 3.925A pdb=" N GLUD6 453 " --> pdb=" O ASPD6 449 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLUD6 454 " --> pdb=" O ALAD6 450 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHED6 455 " --> pdb=" O GLUD6 451 " (cutoff:3.500A) Proline residue: D6 458 - end of helix Processing helix chain 'D6' and resid 468 through 475 removed outlier: 3.546A pdb=" N ARGD6 475 " --> pdb=" O TYRD6 471 " (cutoff:3.500A) Processing helix chain 'D6' and resid 483 through 485 No H-bonds generated for 'chain 'D6' and resid 483 through 485' Processing helix chain 'D6' and resid 486 through 499 removed outlier: 3.562A pdb=" N GLYD6 499 " --> pdb=" O LEUD6 495 " (cutoff:3.500A) Processing helix chain 'A1' and resid 17 through 30 Processing helix chain 'A1' and resid 45 through 51 Processing helix chain 'A1' and resid 468 through 482 removed outlier: 3.901A pdb=" N GLYA1 482 " --> pdb=" O TRPA1 478 " (cutoff:3.500A) Processing helix chain 'A2' and resid 19 through 30 Processing helix chain 'A2' and resid 45 through 51 Processing helix chain 'A2' and resid 468 through 482 removed outlier: 3.870A pdb=" N GLYA2 482 " --> pdb=" O TRPA2 478 " (cutoff:3.500A) Processing helix chain 'A3' and resid 17 through 30 Processing helix chain 'A3' and resid 39 through 43 removed outlier: 3.735A pdb=" N ALAA3 43 " --> pdb=" O GLUA3 40 " (cutoff:3.500A) Processing helix chain 'A3' and resid 45 through 51 removed outlier: 3.764A pdb=" N THRA3 49 " --> pdb=" O ALAA3 45 " (cutoff:3.500A) Processing helix chain 'A3' and resid 468 through 482 removed outlier: 3.892A pdb=" N GLYA3 482 " --> pdb=" O TRPA3 478 " (cutoff:3.500A) Processing helix chain 'A4' and resid 17 through 30 Processing helix chain 'A4' and resid 45 through 51 removed outlier: 3.845A pdb=" N THRA4 49 " --> pdb=" O ALAA4 45 " (cutoff:3.500A) Processing helix chain 'A4' and resid 468 through 482 removed outlier: 3.877A pdb=" N GLYA4 482 " --> pdb=" O TRPA4 478 " (cutoff:3.500A) Processing helix chain 'A5' and resid 17 through 30 Processing helix chain 'A5' and resid 46 through 51 Processing helix chain 'A5' and resid 468 through 482 removed outlier: 3.897A pdb=" N GLYA5 482 " --> pdb=" O TRPA5 478 " (cutoff:3.500A) Processing helix chain 'A6' and resid 17 through 30 Processing helix chain 'A6' and resid 45 through 51 removed outlier: 4.265A pdb=" N THRA6 49 " --> pdb=" O ALAA6 45 " (cutoff:3.500A) Processing helix chain 'A6' and resid 468 through 482 removed outlier: 3.883A pdb=" N GLYA6 482 " --> pdb=" O TRPA6 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D1' and resid 56 through 59 removed outlier: 4.652A pdb=" N ALAD1 79 " --> pdb=" O LEUD1 59 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N CYSD1 125 " --> pdb=" O ILED1 167 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALAD1 169 " --> pdb=" O CYSD1 125 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYRD1 127 " --> pdb=" O ALAD1 169 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALAD1 188 " --> pdb=" O HISD1 233 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALAD1 235 " --> pdb=" O ALAD1 188 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILED1 190 " --> pdb=" O ALAD1 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D1' and resid 173 through 174 Processing sheet with id=AA3, first strand: chain 'D1' and resid 303 through 305 removed outlier: 4.537A pdb=" N THRD1 315 " --> pdb=" O PHED1 305 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASND1 361 " --> pdb=" O ASND1 330 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILED1 362 " --> pdb=" O ILED1 399 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLYD1 401 " --> pdb=" O ILED1 362 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHED1 419 " --> pdb=" O LYSD1 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D1' and resid 303 through 305 removed outlier: 4.537A pdb=" N THRD1 315 " --> pdb=" O PHED1 305 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASND1 361 " --> pdb=" O ASND1 330 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILED1 362 " --> pdb=" O ILED1 399 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLYD1 401 " --> pdb=" O ILED1 362 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARGD1 427 " --> pdb=" O VALD1 398 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLYD1 400 " --> pdb=" O ARGD1 427 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N SERD1 429 " --> pdb=" O GLYD1 400 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SERD1 402 " --> pdb=" O SERD1 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D2' and resid 56 through 59 removed outlier: 4.660A pdb=" N ALAD2 79 " --> pdb=" O LEUD2 59 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYSD2 125 " --> pdb=" O ILED2 167 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ALAD2 169 " --> pdb=" O CYSD2 125 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYRD2 127 " --> pdb=" O ALAD2 169 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALAD2 188 " --> pdb=" O HISD2 233 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALAD2 235 " --> pdb=" O ALAD2 188 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILED2 190 " --> pdb=" O ALAD2 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D2' and resid 173 through 175 removed outlier: 6.164A pdb=" N CYSD2 174 " --> pdb=" O PHED2 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D2' and resid 303 through 305 removed outlier: 4.540A pdb=" N THRD2 315 " --> pdb=" O PHED2 305 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHED2 419 " --> pdb=" O LYSD2 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D2' and resid 401 through 403 removed outlier: 6.057A pdb=" N SERD2 402 " --> pdb=" O SERD2 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D3' and resid 56 through 59 removed outlier: 4.683A pdb=" N ALAD3 79 " --> pdb=" O LEUD3 59 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYSD3 125 " --> pdb=" O ILED3 167 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ALAD3 169 " --> pdb=" O CYSD3 125 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYRD3 127 " --> pdb=" O ALAD3 169 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALAD3 188 " --> pdb=" O HISD3 233 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ALAD3 235 " --> pdb=" O ALAD3 188 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILED3 190 " --> pdb=" O ALAD3 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D3' and resid 173 through 175 removed outlier: 6.190A pdb=" N CYSD3 174 " --> pdb=" O PHED3 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D3' and resid 303 through 305 removed outlier: 4.497A pdb=" N THRD3 315 " --> pdb=" O PHED3 305 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASND3 361 " --> pdb=" O ASND3 330 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILED3 362 " --> pdb=" O ILED3 399 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLYD3 401 " --> pdb=" O ILED3 362 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHED3 419 " --> pdb=" O LYSD3 394 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D3' and resid 303 through 305 removed outlier: 4.497A pdb=" N THRD3 315 " --> pdb=" O PHED3 305 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASND3 361 " --> pdb=" O ASND3 330 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILED3 362 " --> pdb=" O ILED3 399 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLYD3 401 " --> pdb=" O ILED3 362 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARGD3 427 " --> pdb=" O VALD3 398 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLYD3 400 " --> pdb=" O ARGD3 427 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SERD3 429 " --> pdb=" O GLYD3 400 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SERD3 402 " --> pdb=" O SERD3 429 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D4' and resid 56 through 59 removed outlier: 4.709A pdb=" N ALAD4 79 " --> pdb=" O LEUD4 59 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYSD4 125 " --> pdb=" O ILED4 167 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALAD4 169 " --> pdb=" O CYSD4 125 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYRD4 127 " --> pdb=" O ALAD4 169 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALAD4 188 " --> pdb=" O HISD4 233 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALAD4 235 " --> pdb=" O ALAD4 188 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILED4 190 " --> pdb=" O ALAD4 235 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D4' and resid 173 through 175 removed outlier: 6.228A pdb=" N CYSD4 174 " --> pdb=" O PHED4 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D4' and resid 302 through 305 removed outlier: 4.539A pdb=" N THRD4 315 " --> pdb=" O PHED4 305 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHED4 419 " --> pdb=" O LYSD4 394 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D4' and resid 401 through 403 removed outlier: 6.001A pdb=" N SERD4 402 " --> pdb=" O SERD4 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D5' and resid 56 through 59 removed outlier: 4.692A pdb=" N ALAD5 79 " --> pdb=" O LEUD5 59 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYSD5 125 " --> pdb=" O ILED5 167 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALAD5 169 " --> pdb=" O CYSD5 125 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYRD5 127 " --> pdb=" O ALAD5 169 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALAD5 188 " --> pdb=" O HISD5 233 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ALAD5 235 " --> pdb=" O ALAD5 188 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILED5 190 " --> pdb=" O ALAD5 235 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D5' and resid 173 through 175 removed outlier: 6.189A pdb=" N CYSD5 174 " --> pdb=" O PHED5 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D5' and resid 303 through 305 removed outlier: 4.494A pdb=" N THRD5 315 " --> pdb=" O PHED5 305 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHED5 419 " --> pdb=" O LYSD5 394 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D5' and resid 401 through 403 removed outlier: 6.029A pdb=" N SERD5 402 " --> pdb=" O SERD5 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D6' and resid 56 through 59 removed outlier: 4.715A pdb=" N ALAD6 79 " --> pdb=" O LEUD6 59 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYSD6 125 " --> pdb=" O ILED6 167 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALAD6 169 " --> pdb=" O CYSD6 125 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYRD6 127 " --> pdb=" O ALAD6 169 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALAD6 188 " --> pdb=" O HISD6 233 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALAD6 235 " --> pdb=" O ALAD6 188 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILED6 190 " --> pdb=" O ALAD6 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D6' and resid 173 through 175 removed outlier: 6.231A pdb=" N CYSD6 174 " --> pdb=" O PHED6 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D6' and resid 302 through 305 removed outlier: 4.542A pdb=" N THRD6 315 " --> pdb=" O PHED6 305 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHED6 419 " --> pdb=" O LYSD6 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D6' and resid 401 through 403 removed outlier: 6.025A pdb=" N SERD6 402 " --> pdb=" O SERD6 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A1' and resid 11 through 13 removed outlier: 3.661A pdb=" N VALA1 35 " --> pdb=" O VALA1 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A1' and resid 377 through 378 removed outlier: 3.507A pdb=" N LYSA1 396 " --> pdb=" O ASPA1 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A1' and resid 515 through 517 Processing sheet with id=AD1, first strand: chain 'A1' and resid 536 through 537 removed outlier: 3.880A pdb=" N LEUA1 549 " --> pdb=" O LEUA1 552 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A1' and resid 559 through 560 Processing sheet with id=AD3, first strand: chain 'A1' and resid 603 through 607 removed outlier: 6.871A pdb=" N THRA1 623 " --> pdb=" O VALA1 605 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VALA1 622 " --> pdb=" O LEUA1 633 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A2' and resid 11 through 13 removed outlier: 6.332A pdb=" N VALA2 11 " --> pdb=" O VALA2 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'A2' and resid 377 through 378 removed outlier: 3.513A pdb=" N ASPA2 377 " --> pdb=" O LYSA2 396 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYSA2 396 " --> pdb=" O ASPA2 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A2' and resid 515 through 517 Processing sheet with id=AD7, first strand: chain 'A2' and resid 536 through 537 removed outlier: 3.544A pdb=" N ALAA2 546 " --> pdb=" O ASPA2 537 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VALA2 547 " --> pdb=" O THRA2 554 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THRA2 554 " --> pdb=" O VALA2 547 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEUA2 549 " --> pdb=" O LEUA2 552 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A2' and resid 559 through 560 Processing sheet with id=AD9, first strand: chain 'A2' and resid 629 through 633 removed outlier: 4.099A pdb=" N VALA2 622 " --> pdb=" O LEUA2 633 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THRA2 623 " --> pdb=" O VALA2 605 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLYA2 602 " --> pdb=" O VALA2 651 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A3' and resid 11 through 13 Processing sheet with id=AE2, first strand: chain 'A3' and resid 377 through 378 Processing sheet with id=AE3, first strand: chain 'A3' and resid 515 through 518 Processing sheet with id=AE4, first strand: chain 'A3' and resid 536 through 537 removed outlier: 3.569A pdb=" N ALAA3 546 " --> pdb=" O ASPA3 537 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A3' and resid 559 through 560 Processing sheet with id=AE6, first strand: chain 'A3' and resid 629 through 632 removed outlier: 6.876A pdb=" N THRA3 623 " --> pdb=" O VALA3 605 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLYA3 602 " --> pdb=" O VALA3 651 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A4' and resid 11 through 13 Processing sheet with id=AE8, first strand: chain 'A4' and resid 377 through 378 removed outlier: 3.552A pdb=" N ASPA4 377 " --> pdb=" O LYSA4 396 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSA4 396 " --> pdb=" O ASPA4 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'A4' and resid 515 through 518 Processing sheet with id=AF1, first strand: chain 'A4' and resid 534 through 537 Processing sheet with id=AF2, first strand: chain 'A4' and resid 559 through 560 Processing sheet with id=AF3, first strand: chain 'A4' and resid 629 through 632 removed outlier: 6.920A pdb=" N THRA4 623 " --> pdb=" O VALA4 605 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A5' and resid 11 through 13 removed outlier: 6.284A pdb=" N VALA5 11 " --> pdb=" O VALA5 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'A5' and resid 377 through 378 removed outlier: 3.502A pdb=" N LYSA5 396 " --> pdb=" O ASPA5 377 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A5' and resid 515 through 517 Processing sheet with id=AF7, first strand: chain 'A5' and resid 536 through 537 removed outlier: 3.697A pdb=" N VALA5 547 " --> pdb=" O THRA5 554 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THRA5 554 " --> pdb=" O VALA5 547 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEUA5 549 " --> pdb=" O LEUA5 552 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A5' and resid 559 through 560 Processing sheet with id=AF9, first strand: chain 'A5' and resid 629 through 633 removed outlier: 4.129A pdb=" N VALA5 622 " --> pdb=" O LEUA5 633 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THRA5 623 " --> pdb=" O VALA5 605 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLYA5 602 " --> pdb=" O VALA5 651 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A6' and resid 11 through 13 removed outlier: 6.355A pdb=" N VALA6 11 " --> pdb=" O VALA6 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'A6' and resid 377 through 378 Processing sheet with id=AG3, first strand: chain 'A6' and resid 515 through 518 Processing sheet with id=AG4, first strand: chain 'A6' and resid 536 through 537 removed outlier: 3.506A pdb=" N ALAA6 546 " --> pdb=" O ASPA6 537 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A6' and resid 559 through 560 Processing sheet with id=AG6, first strand: chain 'A6' and resid 629 through 632 removed outlier: 6.883A pdb=" N THRA6 623 " --> pdb=" O VALA6 605 " (cutoff:3.500A) 1569 hydrogen bonds defined for protein. 4308 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: 6.95 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10881 1.34 - 1.47: 7403 1.47 - 1.59: 14317 1.59 - 1.71: 0 1.71 - 1.83: 246 Bond restraints: 32847 Sorted by residual: bond pdb=" C10 BTNA3 701 " pdb=" C9 BTNA3 701 " ideal model delta sigma weight residual 1.522 1.476 0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C10 BTNA6 701 " pdb=" C9 BTNA6 701 " ideal model delta sigma weight residual 1.522 1.490 0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" C10 BTNA2 701 " pdb=" C9 BTNA2 701 " ideal model delta sigma weight residual 1.522 1.491 0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C10 BTNA4 701 " pdb=" C9 BTNA4 701 " ideal model delta sigma weight residual 1.522 1.493 0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C10 BTNA5 701 " pdb=" C9 BTNA5 701 " ideal model delta sigma weight residual 1.522 1.493 0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 32842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 44045 2.13 - 4.26: 537 4.26 - 6.39: 58 6.39 - 8.52: 11 8.52 - 10.65: 2 Bond angle restraints: 44653 Sorted by residual: angle pdb=" N PHED6 143 " pdb=" CA PHED6 143 " pdb=" C PHED6 143 " ideal model delta sigma weight residual 109.81 120.30 -10.49 2.21e+00 2.05e-01 2.25e+01 angle pdb=" C VALD6 142 " pdb=" N PHED6 143 " pdb=" CA PHED6 143 " ideal model delta sigma weight residual 121.80 111.15 10.65 2.44e+00 1.68e-01 1.90e+01 angle pdb=" N PHED5 143 " pdb=" CA PHED5 143 " pdb=" C PHED5 143 " ideal model delta sigma weight residual 109.81 118.04 -8.23 2.21e+00 2.05e-01 1.39e+01 angle pdb=" N PROD2 144 " pdb=" CA PROD2 144 " pdb=" C PROD2 144 " ideal model delta sigma weight residual 112.47 120.06 -7.59 2.06e+00 2.36e-01 1.36e+01 angle pdb=" N PHED1 143 " pdb=" CA PHED1 143 " pdb=" C PHED1 143 " ideal model delta sigma weight residual 109.81 117.81 -8.00 2.21e+00 2.05e-01 1.31e+01 ... (remaining 44648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 18368 17.25 - 34.51: 817 34.51 - 51.76: 183 51.76 - 69.01: 69 69.01 - 86.27: 4 Dihedral angle restraints: 19441 sinusoidal: 7450 harmonic: 11991 Sorted by residual: dihedral pdb=" CA PHED4 143 " pdb=" C PHED4 143 " pdb=" N PROD4 144 " pdb=" CA PROD4 144 " ideal model delta harmonic sigma weight residual -180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHED1 143 " pdb=" C PHED1 143 " pdb=" N PROD1 144 " pdb=" CA PROD1 144 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA PHED3 143 " pdb=" C PHED3 143 " pdb=" N PROD3 144 " pdb=" CA PROD3 144 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 19438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3540 0.044 - 0.088: 1142 0.088 - 0.132: 336 0.132 - 0.175: 38 0.175 - 0.219: 4 Chirality restraints: 5060 Sorted by residual: chirality pdb=" CA PROD2 144 " pdb=" N PROD2 144 " pdb=" C PROD2 144 " pdb=" CB PROD2 144 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA PROD3 144 " pdb=" N PROD3 144 " pdb=" C PROD3 144 " pdb=" CB PROD3 144 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA PROD4 144 " pdb=" N PROD4 144 " pdb=" C PROD4 144 " pdb=" CB PROD4 144 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 5057 not shown) Planarity restraints: 5827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTNA3 701 " 0.025 2.00e-02 2.50e+03 8.13e-02 9.93e+01 pdb=" C4 BTNA3 701 " -0.066 2.00e-02 2.50e+03 pdb=" C5 BTNA3 701 " -0.063 2.00e-02 2.50e+03 pdb=" N1 BTNA3 701 " 0.101 2.00e-02 2.50e+03 pdb=" N2 BTNA3 701 " 0.103 2.00e-02 2.50e+03 pdb=" O3 BTNA3 701 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGD1 488 " 0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ARGD1 488 " -0.087 2.00e-02 2.50e+03 pdb=" O ARGD1 488 " 0.032 2.00e-02 2.50e+03 pdb=" N THRD1 489 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARGD5 488 " 0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ARGD5 488 " -0.087 2.00e-02 2.50e+03 pdb=" O ARGD5 488 " 0.032 2.00e-02 2.50e+03 pdb=" N THRD5 489 " 0.029 2.00e-02 2.50e+03 ... (remaining 5824 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 15132 2.96 - 3.44: 31613 3.44 - 3.93: 56055 3.93 - 4.41: 64697 4.41 - 4.90: 103239 Nonbonded interactions: 270736 Sorted by model distance: nonbonded pdb=" N GLYD1 150 " pdb=" N ARGD1 151 " model vdw 2.473 2.560 nonbonded pdb=" O SERA4 388 " pdb=" N TYRA4 390 " model vdw 2.535 3.120 nonbonded pdb=" O SERA2 388 " pdb=" N TYRA2 390 " model vdw 2.539 3.120 nonbonded pdb=" C SERA5 378 " pdb=" OG SERA5 378 " model vdw 2.544 2.616 nonbonded pdb=" C SERA1 378 " pdb=" OG SERA1 378 " model vdw 2.546 2.616 ... (remaining 270731 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 'A1' and (resid 10 through 609 or resid 621 through 701)) selection = chain 'A2' selection = (chain 'A3' and (resid 10 through 579 or resid 598 through 609 or resid 621 thro \ ugh 701)) selection = (chain 'A4' and (resid 10 through 579 or resid 598 through 701)) selection = (chain 'A5' and (resid 10 through 579 or resid 598 through 701)) selection = (chain 'A6' and (resid 10 through 579 or resid 598 through 609 or resid 621 thro \ ugh 701)) } ncs_group { reference = chain 'D1' selection = chain 'D2' selection = chain 'D3' selection = chain 'D4' selection = chain 'D5' selection = chain 'D6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 30.000 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32853 Z= 0.183 Angle : 0.617 10.648 44653 Z= 0.332 Chirality : 0.047 0.219 5060 Planarity : 0.006 0.081 5827 Dihedral : 11.030 86.267 11811 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.68 % Favored : 97.11 % Rotamer: Outliers : 3.90 % Allowed : 3.66 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.13), residues: 4181 helix: 1.40 (0.13), residues: 1601 sheet: 0.38 (0.22), residues: 512 loop : -0.30 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGA4 521 TYR 0.025 0.002 TYRD2 415 PHE 0.034 0.002 PHED6 143 TRP 0.012 0.002 TRPA5 574 HIS 0.007 0.001 HISD2 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (32847) covalent geometry : angle 0.61717 / 0.33 (44653) hydrogen bonds : bond 0.14743 / 9.82 ( 1529) hydrogen bonds : angle 6.58242 / 4.84 ( 4308) Misc. bond : bond 0.00503 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 417 time to evaluate : 0.963 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: D1 301 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7690 (mm-30) REVERT: D1 391 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8508 (ppt-90) REVERT: D2 222 ASP cc_start: 0.8016 (t0) cc_final: 0.7645 (t70) REVERT: D2 301 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7634 (mm-30) REVERT: D2 391 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8491 (ppt-90) REVERT: D2 475 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7897 (mtt90) REVERT: D3 67 MET cc_start: 0.8898 (mtp) cc_final: 0.8609 (mtp) REVERT: D3 77 MET cc_start: 0.9115 (ttp) cc_final: 0.8877 (ttm) REVERT: D3 222 ASP cc_start: 0.8108 (t0) cc_final: 0.7746 (m-30) REVERT: D3 301 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7546 (mm-30) REVERT: D3 350 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8483 (m-30) REVERT: D3 353 LYS cc_start: 0.8722 (mttt) cc_final: 0.8440 (mttp) REVERT: D3 461 GLU cc_start: 0.7319 (tt0) cc_final: 0.7116 (tp30) REVERT: D4 67 MET cc_start: 0.8862 (mtp) cc_final: 0.8602 (mtp) REVERT: D4 243 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7942 (ttp80) REVERT: D4 301 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7507 (mm-30) REVERT: D4 431 MET cc_start: 0.7926 (ptp) cc_final: 0.7657 (ptm) REVERT: D5 67 MET cc_start: 0.8873 (mtp) cc_final: 0.8594 (mtp) REVERT: D5 301 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7612 (mm-30) REVERT: D5 350 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: D5 353 LYS cc_start: 0.8719 (mttt) cc_final: 0.8435 (mttp) REVERT: D5 460 ARG cc_start: 0.8336 (mtt180) cc_final: 0.7964 (mtt180) REVERT: D6 29 ARG cc_start: 0.8223 (ttp-170) cc_final: 0.7543 (tpt90) REVERT: D6 67 MET cc_start: 0.8866 (mtp) cc_final: 0.8665 (mtp) REVERT: D6 143 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.4261 (p90) REVERT: D6 301 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7504 (mm-30) REVERT: D6 431 MET cc_start: 0.7714 (ptp) cc_final: 0.7442 (ptm) REVERT: D6 446 GLU cc_start: 0.4651 (OUTLIER) cc_final: 0.4327 (pt0) REVERT: D6 476 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8691 (mp) REVERT: A1 493 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.6509 (mmt90) REVERT: A1 600 MET cc_start: 0.7099 (mtm) cc_final: 0.6867 (mtp) REVERT: A2 16 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.4817 (mpt-90) REVERT: A2 493 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.6757 (mmm-85) REVERT: A3 16 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.5791 (ptp-170) REVERT: A3 493 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.6467 (mtt-85) REVERT: A5 493 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.6216 (mmt90) REVERT: A6 16 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6276 (ptp-170) REVERT: A6 493 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.6559 (mtt-85) outliers start: 128 outliers final: 20 residues processed: 526 average time/residue: 0.8692 time to fit residues: 521.2985 Evaluate side-chains 312 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 391 ARG Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 391 ARG Chi-restraints excluded: chain D2 residue 475 ARG Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 447 MET Chi-restraints excluded: chain D4 residue 222 ASP Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 446 GLU Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 549 LEU Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 547 VAL Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 49 THR Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 385 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 547 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 424, 155] chunk 197 optimal weight: 0.0050 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1 94 ASN D1 290 HIS ** D1 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 94 ASN D2 148 HIS D2 156 GLN D2 290 HIS ** D2 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 94 ASN ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 290 HIS D3 330 ASN D4 94 ASN D4 290 HIS ** D4 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D5 290 HIS D5 330 ASN D5 379 HIS D6 94 ASN D6 148 HIS D6 156 GLN D6 290 HIS D6 330 ASN A1 477 GLN A4 564 GLN A4 577 GLN A5 477 GLN ** A5 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.076891 restraints weight = 46790.639| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.83 r_work: 0.2677 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32853 Z= 0.153 Angle : 0.560 14.998 44653 Z= 0.290 Chirality : 0.044 0.195 5060 Planarity : 0.005 0.070 5827 Dihedral : 6.511 59.831 4846 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.68 % Allowed : 8.63 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4181 helix: 1.68 (0.13), residues: 1584 sheet: 0.43 (0.22), residues: 505 loop : -0.34 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGA5 28 TYR 0.017 0.001 TYRD2 415 PHE 0.020 0.001 PHED6 143 TRP 0.014 0.001 TRPA2 566 HIS 0.008 0.001 HISD2 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (32847) covalent geometry : angle 0.55973 / 0.29 (44653) hydrogen bonds : bond 0.04261 / 2.90 ( 1529) hydrogen bonds : angle 5.22213 / 3.83 ( 4308) Misc. bond : bond 0.00127 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 288 time to evaluate : 1.414 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: D1 301 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8594 (mm-30) REVERT: D2 301 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8609 (mm-30) REVERT: D2 369 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.6597 (ttp80) REVERT: D3 29 ARG cc_start: 0.8101 (tpm-80) cc_final: 0.7795 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8443 (ttp-110) cc_final: 0.8089 (mtm-85) REVERT: D3 67 MET cc_start: 0.9411 (mtp) cc_final: 0.9210 (mtp) REVERT: D3 222 ASP cc_start: 0.8637 (t0) cc_final: 0.8338 (m-30) REVERT: D3 301 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8694 (mp0) REVERT: D3 461 GLU cc_start: 0.7707 (tt0) cc_final: 0.7298 (tp30) REVERT: D4 67 MET cc_start: 0.9394 (mtp) cc_final: 0.9115 (mtp) REVERT: D4 206 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8156 (ttmt) REVERT: D4 301 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8657 (mm-30) REVERT: D4 431 MET cc_start: 0.7927 (ptp) cc_final: 0.7620 (ptm) REVERT: D4 460 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7999 (mtt90) REVERT: D5 29 ARG cc_start: 0.8084 (tpm-80) cc_final: 0.7782 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.8073 (mtm-85) REVERT: D5 67 MET cc_start: 0.9421 (mtp) cc_final: 0.9038 (mtp) REVERT: D5 284 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8299 (mtm-85) REVERT: D5 301 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8693 (mp0) REVERT: D6 29 ARG cc_start: 0.8871 (ttp-170) cc_final: 0.8084 (tpt90) REVERT: D6 67 MET cc_start: 0.9408 (mtp) cc_final: 0.9164 (mtp) REVERT: D6 143 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.4204 (p90) REVERT: D6 301 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8667 (mm-30) REVERT: D6 431 MET cc_start: 0.7868 (ptp) cc_final: 0.7536 (ptm) REVERT: D6 446 GLU cc_start: 0.3779 (OUTLIER) cc_final: 0.3566 (pt0) REVERT: D6 476 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9288 (mp) REVERT: A1 493 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.6032 (mmm-85) REVERT: A1 496 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: A2 16 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.4269 (ptp-170) REVERT: A2 564 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7406 (pt0) REVERT: A2 566 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.7331 (m-90) REVERT: A3 16 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5549 (ptp-170) REVERT: A3 28 ARG cc_start: 0.8066 (tpp-160) cc_final: 0.7365 (mmm160) REVERT: A3 493 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.6422 (mmt90) REVERT: A4 493 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.6971 (mtt-85) REVERT: A4 549 LEU cc_start: 0.7160 (tp) cc_final: 0.6907 (tp) REVERT: A5 493 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.6541 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: A6 16 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6081 (ptp-170) REVERT: A6 24 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7270 (tp) REVERT: A6 28 ARG cc_start: 0.7063 (tpp-160) cc_final: 0.6538 (mmm160) REVERT: A6 493 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.6525 (mtt-85) outliers start: 88 outliers final: 28 residues processed: 361 average time/residue: 0.8015 time to fit residues: 334.9265 Evaluate side-chains 316 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 448 THR Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 369 ARG Chi-restraints excluded: chain D2 residue 513 MET Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 447 MET Chi-restraints excluded: chain D4 residue 206 LYS Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 32 GLU Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 446 GLU Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A1 residue 603 SER Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 549 LEU Chi-restraints excluded: chain A2 residue 564 GLN Chi-restraints excluded: chain A2 residue 566 TRP Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 547 VAL Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 603 SER Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 24 ILE Chi-restraints excluded: chain A6 residue 49 THR Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 547 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [12, 408, 152, 362, 142, 62, 419, 187, 372, 67, 20] chunk 12 optimal weight: 0.8980 chunk 408 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 419 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 372 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1 156 GLN ** D1 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 330 ASN D4 379 HIS D5 94 ASN D5 156 GLN A1 477 GLN ** A5 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.128220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.077464 restraints weight = 47035.873| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.83 r_work: 0.2680 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32853 Z= 0.128 Angle : 0.522 13.680 44653 Z= 0.268 Chirality : 0.044 0.187 5060 Planarity : 0.004 0.062 5827 Dihedral : 6.036 59.998 4826 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.38 % Allowed : 9.97 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.13), residues: 4181 helix: 1.77 (0.13), residues: 1590 sheet: 0.40 (0.22), residues: 505 loop : -0.28 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD4 284 TYR 0.014 0.001 TYRD5 415 PHE 0.020 0.001 PHED6 143 TRP 0.014 0.001 TRPA3 474 HIS 0.003 0.001 HISD6 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (32847) covalent geometry : angle 0.52161 / 0.27 (44653) hydrogen bonds : bond 0.03834 / 2.61 ( 1529) hydrogen bonds : angle 4.87589 / 3.58 ( 4308) Misc. bond : bond 0.00028 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 279 time to evaluate : 1.239 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: D1 301 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8649 (mp0) REVERT: D2 301 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8576 (mm-30) REVERT: D3 29 ARG cc_start: 0.8092 (tpm-80) cc_final: 0.7823 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.8045 (mtm-85) REVERT: D3 67 MET cc_start: 0.9407 (mtp) cc_final: 0.9160 (mtp) REVERT: D3 301 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8655 (mp0) REVERT: D3 350 ASP cc_start: 0.9402 (OUTLIER) cc_final: 0.9101 (m-30) REVERT: D3 461 GLU cc_start: 0.7730 (tt0) cc_final: 0.7283 (tp30) REVERT: D4 67 MET cc_start: 0.9370 (mtp) cc_final: 0.9046 (mtp) REVERT: D4 301 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8638 (mm-30) REVERT: D4 431 MET cc_start: 0.7857 (ptp) cc_final: 0.7565 (ptm) REVERT: D5 29 ARG cc_start: 0.8068 (tpm-80) cc_final: 0.7743 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.8057 (mtm-85) REVERT: D5 67 MET cc_start: 0.9421 (mtp) cc_final: 0.9182 (mtp) REVERT: D5 301 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8676 (mp0) REVERT: D5 350 ASP cc_start: 0.9402 (OUTLIER) cc_final: 0.9108 (m-30) REVERT: D6 29 ARG cc_start: 0.8854 (ttp-170) cc_final: 0.8087 (tpt90) REVERT: D6 67 MET cc_start: 0.9389 (mtp) cc_final: 0.9079 (mtp) REVERT: D6 301 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8639 (mm-30) REVERT: D6 431 MET cc_start: 0.7822 (ptp) cc_final: 0.7433 (ptm) REVERT: D6 476 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9283 (mp) REVERT: A1 28 ARG cc_start: 0.8131 (tpp-160) cc_final: 0.7343 (mmm160) REVERT: A1 493 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.6417 (mtt-85) REVERT: A1 496 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: A1 572 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7911 (ptm-80) REVERT: A1 600 MET cc_start: 0.6983 (mtm) cc_final: 0.6408 (mtp) REVERT: A2 16 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.4098 (ptp-170) REVERT: A2 493 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.6395 (mtt-85) REVERT: A2 518 ASN cc_start: 0.7739 (p0) cc_final: 0.7533 (p0) REVERT: A2 564 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: A2 566 TRP cc_start: 0.7547 (OUTLIER) cc_final: 0.7335 (m-90) REVERT: A3 16 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.5685 (ptp-170) REVERT: A3 28 ARG cc_start: 0.8096 (tpp-160) cc_final: 0.7393 (mmm160) REVERT: A3 493 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.6603 (mtt-85) REVERT: A4 493 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.6961 (mtt-85) REVERT: A5 493 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.6608 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: A6 16 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5412 (ptm160) REVERT: A6 493 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.6620 (mtt-85) REVERT: A6 566 TRP cc_start: 0.7925 (m100) cc_final: 0.7510 (m-90) outliers start: 78 outliers final: 26 residues processed: 341 average time/residue: 0.8144 time to fit residues: 320.4590 Evaluate side-chains 321 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D3 residue 447 MET Chi-restraints excluded: chain D4 residue 222 ASP Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 558 VAL Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A1 residue 603 SER Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 564 GLN Chi-restraints excluded: chain A2 residue 566 TRP Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A4 residue 597 VAL Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 547 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [96, 406, 222, 255, 293, 339, 349, 46, 178, 260, 233] chunk 96 optimal weight: 0.7980 chunk 406 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 339 optimal weight: 7.9990 chunk 349 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1 330 ASN D1 344 HIS ** D2 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 344 HIS ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3 156 GLN D3 344 HIS D4 156 GLN D4 344 HIS D5 94 ASN D6 344 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.074731 restraints weight = 46896.412| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.83 r_work: 0.2631 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 32853 Z= 0.231 Angle : 0.580 14.685 44653 Z= 0.297 Chirality : 0.046 0.198 5060 Planarity : 0.005 0.072 5827 Dihedral : 5.999 59.036 4818 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.62 % Allowed : 10.09 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4181 helix: 1.66 (0.13), residues: 1602 sheet: 0.31 (0.21), residues: 530 loop : -0.37 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGD4 295 TYR 0.021 0.002 TYRD1 415 PHE 0.022 0.002 PHED6 143 TRP 0.015 0.001 TRPA2 474 HIS 0.007 0.001 HISD2 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.23 (32847) covalent geometry : angle 0.57961 / 0.30 (44653) hydrogen bonds : bond 0.04548 / 3.09 ( 1529) hydrogen bonds : angle 4.89910 / 3.60 ( 4308) Misc. bond : bond 0.00027 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 1.131 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: D1 301 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8586 (mm-30) REVERT: D2 301 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8581 (mm-30) REVERT: D3 29 ARG cc_start: 0.8149 (tpm-80) cc_final: 0.7875 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.8031 (mtm-85) REVERT: D3 301 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8664 (mp0) REVERT: D3 350 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.9157 (m-30) REVERT: D3 461 GLU cc_start: 0.7748 (tt0) cc_final: 0.7311 (tp30) REVERT: D4 67 MET cc_start: 0.9426 (mtp) cc_final: 0.9099 (mtp) REVERT: D4 301 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8696 (mm-30) REVERT: D4 431 MET cc_start: 0.7867 (ptp) cc_final: 0.7481 (ptm) REVERT: D4 447 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6384 (mtm) REVERT: D5 33 ARG cc_start: 0.8427 (ttp-110) cc_final: 0.8095 (mtm-85) REVERT: D5 301 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8696 (mp0) REVERT: D5 350 ASP cc_start: 0.9459 (OUTLIER) cc_final: 0.9162 (m-30) REVERT: D6 29 ARG cc_start: 0.8778 (ttp-170) cc_final: 0.8176 (tpt90) REVERT: D6 67 MET cc_start: 0.9446 (mtp) cc_final: 0.9133 (mtp) REVERT: D6 143 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.4502 (p90) REVERT: D6 301 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8695 (mm-30) REVERT: D6 431 MET cc_start: 0.7904 (ptp) cc_final: 0.7518 (ptm) REVERT: D6 476 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9317 (mp) REVERT: A1 28 ARG cc_start: 0.8076 (tpp-160) cc_final: 0.7296 (mmm160) REVERT: A1 493 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.6098 (mmm-85) REVERT: A1 496 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: A1 572 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7819 (ptm-80) REVERT: A1 600 MET cc_start: 0.7093 (mtm) cc_final: 0.6551 (mtp) REVERT: A2 16 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5449 (pmt170) REVERT: A2 552 LEU cc_start: 0.5817 (pp) cc_final: 0.5521 (pt) REVERT: A2 564 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: A2 566 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.7261 (m-90) REVERT: A3 16 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5511 (ptp-170) REVERT: A3 28 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7385 (mmm160) REVERT: A3 493 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.6546 (mmt90) REVERT: A4 493 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.6956 (mtt-85) REVERT: A5 391 ASP cc_start: 0.8166 (t70) cc_final: 0.7846 (t0) REVERT: A5 493 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.6543 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: A6 16 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.5495 (ptm160) REVERT: A6 493 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.6480 (mtt-85) outliers start: 86 outliers final: 39 residues processed: 337 average time/residue: 0.7925 time to fit residues: 308.5425 Evaluate side-chains 324 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 442 THR Chi-restraints excluded: chain D1 residue 448 THR Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D3 residue 447 MET Chi-restraints excluded: chain D4 residue 32 GLU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 447 MET Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 32 GLU Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 558 VAL Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A1 residue 603 SER Chi-restraints excluded: chain A1 residue 649 ASP Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 564 GLN Chi-restraints excluded: chain A2 residue 566 TRP Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 48 VAL Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A4 residue 597 VAL Chi-restraints excluded: chain A4 residue 600 MET Chi-restraints excluded: chain A4 residue 649 ASP Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 558 VAL Chi-restraints excluded: chain A5 residue 603 SER Chi-restraints excluded: chain A5 residue 649 ASP Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 49 THR Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 547 VAL Chi-restraints excluded: chain A6 residue 558 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [139, 180, 176, 63, 150, 378, 305, 147, 216, 37, 249] chunk 139 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 378 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 249 optimal weight: 0.0010 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D2 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 94 ASN A1 477 GLN A5 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.077405 restraints weight = 46826.678| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.84 r_work: 0.2683 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32853 Z= 0.118 Angle : 0.517 15.216 44653 Z= 0.262 Chirality : 0.043 0.183 5060 Planarity : 0.004 0.061 5827 Dihedral : 5.776 59.778 4818 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.62 % Allowed : 10.55 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.13), residues: 4181 helix: 1.82 (0.13), residues: 1602 sheet: 0.19 (0.23), residues: 470 loop : -0.29 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA1 572 TYR 0.014 0.001 TYRD5 415 PHE 0.020 0.001 PHED6 143 TRP 0.016 0.001 TRPA2 474 HIS 0.003 0.001 HISD4 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (32847) covalent geometry : angle 0.51677 / 0.26 (44653) hydrogen bonds : bond 0.03514 / 2.40 ( 1529) hydrogen bonds : angle 4.65544 / 3.41 ( 4308) Misc. bond : bond 0.00014 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 282 time to evaluate : 1.171 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: D1 301 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8529 (mm-30) REVERT: D2 301 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8572 (mm-30) REVERT: D3 29 ARG cc_start: 0.8146 (tpm-80) cc_final: 0.7867 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8003 (mtm-85) REVERT: D3 301 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8645 (mp0) REVERT: D3 461 GLU cc_start: 0.7752 (tt0) cc_final: 0.7351 (tp30) REVERT: D4 67 MET cc_start: 0.9402 (mtp) cc_final: 0.9053 (mtp) REVERT: D4 301 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8661 (mm-30) REVERT: D4 431 MET cc_start: 0.7826 (ptp) cc_final: 0.7504 (ptm) REVERT: D5 29 ARG cc_start: 0.8099 (tpm-80) cc_final: 0.7818 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8061 (mtm-85) REVERT: D5 301 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8679 (mp0) REVERT: D6 29 ARG cc_start: 0.8791 (ttp-170) cc_final: 0.8231 (tpt90) REVERT: D6 67 MET cc_start: 0.9418 (mtp) cc_final: 0.9084 (mtp) REVERT: D6 301 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8667 (mm-30) REVERT: D6 476 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9283 (mp) REVERT: A1 28 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7280 (mmm160) REVERT: A1 493 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.6114 (mmm-85) REVERT: A1 496 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: A1 572 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7848 (ptm-80) REVERT: A1 600 MET cc_start: 0.6919 (mtm) cc_final: 0.6453 (mtp) REVERT: A2 16 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.4063 (ptp-170) REVERT: A2 552 LEU cc_start: 0.5765 (pp) cc_final: 0.5423 (pt) REVERT: A2 564 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: A2 566 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.7218 (m-90) REVERT: A3 16 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.5646 (ptp-170) REVERT: A3 28 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7398 (mmm160) REVERT: A3 493 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.6620 (mtt-85) REVERT: A4 16 ARG cc_start: 0.3840 (ptp-170) cc_final: 0.2650 (ptp-170) REVERT: A4 493 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.6965 (mtt-85) REVERT: A4 496 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A4 545 PHE cc_start: 0.8499 (t80) cc_final: 0.7786 (t80) REVERT: A4 549 LEU cc_start: 0.6654 (tp) cc_final: 0.6411 (tt) REVERT: A5 30 MET cc_start: 0.7196 (ttp) cc_final: 0.6238 (tmm) REVERT: A5 391 ASP cc_start: 0.8070 (t70) cc_final: 0.7766 (t0) REVERT: A5 493 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.6497 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: A6 16 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5551 (ptm160) REVERT: A6 24 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7179 (tp) REVERT: A6 28 ARG cc_start: 0.7091 (tpp-160) cc_final: 0.6586 (mmm160) REVERT: A6 493 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.6571 (mtt-85) REVERT: A6 543 ASP cc_start: 0.8545 (t70) cc_final: 0.8068 (t0) REVERT: A6 564 GLN cc_start: 0.7648 (pt0) cc_final: 0.7364 (pt0) outliers start: 86 outliers final: 34 residues processed: 348 average time/residue: 0.7878 time to fit residues: 316.7177 Evaluate side-chains 334 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 442 THR Chi-restraints excluded: chain D1 residue 448 THR Chi-restraints excluded: chain D2 residue 171 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 447 MET Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D3 residue 447 MET Chi-restraints excluded: chain D4 residue 32 GLU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 32 GLU Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 558 VAL Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 564 GLN Chi-restraints excluded: chain A2 residue 566 TRP Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 48 VAL Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 496 GLU Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 558 VAL Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 24 ILE Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 547 VAL Chi-restraints excluded: chain A6 residue 558 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [401, 291, 261, 247, 168, 269, 347, 329, 150, 11, 147] chunk 401 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 chunk 347 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 150 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D2 330 ASN ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.076953 restraints weight = 46763.575| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.84 r_work: 0.2678 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32853 Z= 0.132 Angle : 0.526 15.484 44653 Z= 0.265 Chirality : 0.044 0.185 5060 Planarity : 0.004 0.061 5827 Dihedral : 5.722 59.829 4818 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.53 % Allowed : 11.09 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.13), residues: 4181 helix: 1.86 (0.13), residues: 1602 sheet: 0.29 (0.23), residues: 479 loop : -0.27 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD6 284 TYR 0.017 0.001 TYRA3 556 PHE 0.019 0.001 PHED6 143 TRP 0.017 0.001 TRPA4 474 HIS 0.003 0.001 HISD4 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (32847) covalent geometry : angle 0.52573 / 0.27 (44653) hydrogen bonds : bond 0.03623 / 2.47 ( 1529) hydrogen bonds : angle 4.60032 / 3.38 ( 4308) Misc. bond : bond 0.00015 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 289 time to evaluate : 0.879 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: D1 301 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8547 (mm-30) REVERT: D2 301 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8567 (mm-30) REVERT: D3 29 ARG cc_start: 0.8147 (tpm-80) cc_final: 0.7872 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.8006 (mtm-85) REVERT: D3 59 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9211 (tp) REVERT: D3 301 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8641 (mp0) REVERT: D3 350 ASP cc_start: 0.9451 (OUTLIER) cc_final: 0.9196 (m-30) REVERT: D3 461 GLU cc_start: 0.7738 (tt0) cc_final: 0.7259 (tp30) REVERT: D4 67 MET cc_start: 0.9419 (mtp) cc_final: 0.9089 (mtp) REVERT: D4 301 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8672 (mm-30) REVERT: D4 369 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7792 (tmt170) REVERT: D4 431 MET cc_start: 0.7798 (ptp) cc_final: 0.7484 (ptm) REVERT: D4 446 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5511 (pp20) REVERT: D5 29 ARG cc_start: 0.8113 (tpm-80) cc_final: 0.7822 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8062 (mtm-85) REVERT: D5 59 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9214 (tp) REVERT: D5 301 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8678 (mp0) REVERT: D5 350 ASP cc_start: 0.9448 (OUTLIER) cc_final: 0.9205 (m-30) REVERT: D6 29 ARG cc_start: 0.8765 (ttp-170) cc_final: 0.8243 (tpt90) REVERT: D6 67 MET cc_start: 0.9429 (mtp) cc_final: 0.9052 (mtp) REVERT: D6 301 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8680 (mm-30) REVERT: D6 476 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9298 (mp) REVERT: A1 493 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.6410 (mtt-85) REVERT: A1 496 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: A1 572 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7839 (ptm-80) REVERT: A1 600 MET cc_start: 0.6978 (mtm) cc_final: 0.6504 (mtp) REVERT: A2 16 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.4103 (ptp-170) REVERT: A2 496 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: A2 552 LEU cc_start: 0.5638 (pp) cc_final: 0.5310 (pt) REVERT: A2 564 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7774 (tt0) REVERT: A3 16 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.5631 (ptp-170) REVERT: A3 28 ARG cc_start: 0.8130 (tpp-160) cc_final: 0.7398 (mmm160) REVERT: A3 493 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.6629 (mtt-85) REVERT: A4 493 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.6904 (mtt-85) REVERT: A4 545 PHE cc_start: 0.8420 (t80) cc_final: 0.7857 (t80) REVERT: A5 30 MET cc_start: 0.7140 (ttp) cc_final: 0.6182 (tmm) REVERT: A5 42 ASP cc_start: 0.7728 (t70) cc_final: 0.7477 (t0) REVERT: A5 52 ASP cc_start: 0.8663 (m-30) cc_final: 0.8190 (m-30) REVERT: A5 391 ASP cc_start: 0.8070 (t70) cc_final: 0.7788 (t0) REVERT: A5 493 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.6590 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A5 543 ASP cc_start: 0.8696 (t0) cc_final: 0.8155 (t70) REVERT: A5 627 MET cc_start: 0.8325 (mpt) cc_final: 0.7825 (mpp) REVERT: A6 16 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.5595 (ptm160) REVERT: A6 18 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5936 (pp20) REVERT: A6 493 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.6621 (mtt-85) REVERT: A6 543 ASP cc_start: 0.8520 (t70) cc_final: 0.8071 (t0) REVERT: A6 564 GLN cc_start: 0.7624 (pt0) cc_final: 0.7283 (pt0) outliers start: 83 outliers final: 37 residues processed: 353 average time/residue: 0.7735 time to fit residues: 317.0709 Evaluate side-chains 332 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 429 SER Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 442 THR Chi-restraints excluded: chain D1 residue 448 THR Chi-restraints excluded: chain D2 residue 171 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 447 MET Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 429 SER Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D4 residue 32 GLU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 446 GLU Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 59 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 32 GLU Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 429 SER Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 558 VAL Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 496 GLU Chi-restraints excluded: chain A2 residue 564 GLN Chi-restraints excluded: chain A2 residue 572 ARG Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 48 VAL Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A4 residue 600 MET Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 558 VAL Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 18 GLU Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 558 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [30, 176, 88, 62, 359, 357, 258, 169, 219, 312, 322] chunk 30 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 88 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 359 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 258 optimal weight: 0.5980 chunk 169 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 312 optimal weight: 0.3980 chunk 322 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 94 ASN A1 477 GLN A5 477 GLN A5 564 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.077735 restraints weight = 47015.095| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.85 r_work: 0.2694 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32853 Z= 0.112 Angle : 0.517 14.107 44653 Z= 0.260 Chirality : 0.043 0.179 5060 Planarity : 0.004 0.058 5827 Dihedral : 5.601 59.883 4814 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.38 % Allowed : 11.31 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.13), residues: 4181 helix: 1.91 (0.13), residues: 1602 sheet: 0.34 (0.23), residues: 477 loop : -0.24 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGD4 284 TYR 0.016 0.001 TYRD4 408 PHE 0.019 0.001 PHED6 143 TRP 0.018 0.001 TRPA2 474 HIS 0.003 0.001 HISD3 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (32847) covalent geometry : angle 0.51730 / 0.26 (44653) hydrogen bonds : bond 0.03356 / 2.29 ( 1529) hydrogen bonds : angle 4.51688 / 3.31 ( 4308) Misc. bond : bond 0.00015 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 290 time to evaluate : 1.127 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: D1 211 GLU cc_start: 0.7331 (tt0) cc_final: 0.6606 (pt0) REVERT: D1 301 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8599 (mp0) REVERT: D2 214 THR cc_start: 0.8623 (p) cc_final: 0.8398 (t) REVERT: D2 301 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8566 (mm-30) REVERT: D3 29 ARG cc_start: 0.8131 (tpm-80) cc_final: 0.7845 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8373 (ttp-110) cc_final: 0.7978 (mtm-85) REVERT: D3 301 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8636 (mp0) REVERT: D3 350 ASP cc_start: 0.9430 (OUTLIER) cc_final: 0.9192 (m-30) REVERT: D3 461 GLU cc_start: 0.7747 (tt0) cc_final: 0.7217 (tp30) REVERT: D4 67 MET cc_start: 0.9408 (mtp) cc_final: 0.9016 (mtp) REVERT: D4 211 GLU cc_start: 0.7228 (tt0) cc_final: 0.6588 (pt0) REVERT: D4 301 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8694 (mm-30) REVERT: D4 369 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7727 (tmt170) REVERT: D4 431 MET cc_start: 0.7786 (ptp) cc_final: 0.7478 (ptm) REVERT: D4 446 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5326 (pp20) REVERT: D5 29 ARG cc_start: 0.8115 (tpm-80) cc_final: 0.7811 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8049 (mtm-85) REVERT: D5 301 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8672 (mp0) REVERT: D5 350 ASP cc_start: 0.9426 (OUTLIER) cc_final: 0.9173 (m-30) REVERT: D6 29 ARG cc_start: 0.8811 (ttp-170) cc_final: 0.8230 (tpt90) REVERT: D6 67 MET cc_start: 0.9419 (mtp) cc_final: 0.9042 (mtp) REVERT: D6 301 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8699 (mm-30) REVERT: D6 476 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9300 (mp) REVERT: A1 493 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.6432 (mtt-85) REVERT: A1 496 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A1 572 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7849 (ptm-80) REVERT: A1 600 MET cc_start: 0.6802 (mtm) cc_final: 0.6310 (mtp) REVERT: A2 16 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.4066 (ptp-170) REVERT: A2 493 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.6335 (mmm-85) REVERT: A2 496 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: A2 518 ASN cc_start: 0.7729 (p0) cc_final: 0.7514 (p0) REVERT: A3 16 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.5666 (ptp-170) REVERT: A3 28 ARG cc_start: 0.8151 (tpp-160) cc_final: 0.7407 (mmm160) REVERT: A3 493 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.6629 (mtt-85) REVERT: A3 627 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7473 (mtp) REVERT: A4 16 ARG cc_start: 0.3785 (ptp-170) cc_final: 0.2469 (ptp-170) REVERT: A4 493 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.6762 (mtt-85) REVERT: A4 496 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A5 30 MET cc_start: 0.7146 (ttp) cc_final: 0.6180 (tmm) REVERT: A5 493 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.6426 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: A5 627 MET cc_start: 0.8312 (mpt) cc_final: 0.7849 (mpp) REVERT: A6 16 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.5813 (ptm160) REVERT: A6 52 ASP cc_start: 0.7963 (m-30) cc_final: 0.7438 (m-30) REVERT: A6 391 ASP cc_start: 0.8534 (t70) cc_final: 0.8192 (t0) REVERT: A6 493 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.6627 (mtt-85) REVERT: A6 537 ASP cc_start: 0.8692 (t0) cc_final: 0.8037 (p0) REVERT: A6 543 ASP cc_start: 0.8534 (t70) cc_final: 0.8077 (t0) REVERT: A6 566 TRP cc_start: 0.7785 (m100) cc_final: 0.7373 (m-90) outliers start: 78 outliers final: 33 residues processed: 353 average time/residue: 0.7832 time to fit residues: 320.9171 Evaluate side-chains 324 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 442 THR Chi-restraints excluded: chain D1 residue 448 THR Chi-restraints excluded: chain D2 residue 59 LEU Chi-restraints excluded: chain D2 residue 171 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 447 MET Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D4 residue 32 GLU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 446 GLU Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 558 VAL Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 496 GLU Chi-restraints excluded: chain A2 residue 572 ARG Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 48 VAL Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 627 MET Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 496 GLU Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A4 residue 597 VAL Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 558 VAL Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 49 THR Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 558 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [344, 115, 53, 296, 335, 100, 153, 48, 203, 420, 142] chunk 344 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 335 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 420 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 94 ASN A1 477 GLN A6 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.077461 restraints weight = 46991.728| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.85 r_work: 0.2689 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32853 Z= 0.125 Angle : 0.523 13.921 44653 Z= 0.264 Chirality : 0.043 0.181 5060 Planarity : 0.004 0.058 5827 Dihedral : 5.599 59.854 4814 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.10 % Allowed : 11.67 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4181 helix: 1.92 (0.13), residues: 1602 sheet: 0.42 (0.24), residues: 465 loop : -0.23 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD6 284 TYR 0.015 0.001 TYRA3 556 PHE 0.019 0.001 PHED6 143 TRP 0.019 0.001 TRPA2 474 HIS 0.003 0.001 HISD2 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (32847) covalent geometry : angle 0.52254 / 0.26 (44653) hydrogen bonds : bond 0.03470 / 2.36 ( 1529) hydrogen bonds : angle 4.51330 / 3.31 ( 4308) Misc. bond : bond 0.00015 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 211 GLU cc_start: 0.7347 (tt0) cc_final: 0.6621 (pt0) REVERT: D1 301 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8581 (mp0) REVERT: D2 214 THR cc_start: 0.8643 (p) cc_final: 0.8421 (t) REVERT: D2 301 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8576 (mm-30) REVERT: D3 29 ARG cc_start: 0.8148 (tpm-80) cc_final: 0.7865 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.7998 (mtm-85) REVERT: D3 59 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9217 (tp) REVERT: D3 301 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8654 (mp0) REVERT: D3 350 ASP cc_start: 0.9447 (OUTLIER) cc_final: 0.9213 (m-30) REVERT: D3 461 GLU cc_start: 0.7734 (tt0) cc_final: 0.7187 (tp30) REVERT: D4 67 MET cc_start: 0.9440 (mtp) cc_final: 0.9062 (mtp) REVERT: D4 211 GLU cc_start: 0.7252 (tt0) cc_final: 0.6616 (pt0) REVERT: D4 301 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8696 (mm-30) REVERT: D4 369 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7733 (tmt170) REVERT: D4 431 MET cc_start: 0.7751 (ptp) cc_final: 0.7440 (ptm) REVERT: D4 446 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5124 (pp20) REVERT: D5 29 ARG cc_start: 0.8139 (tpm-80) cc_final: 0.7834 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.8040 (mtm-85) REVERT: D5 59 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9217 (tp) REVERT: D5 301 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8683 (mp0) REVERT: D5 350 ASP cc_start: 0.9440 (OUTLIER) cc_final: 0.9195 (m-30) REVERT: D6 29 ARG cc_start: 0.8814 (ttp-170) cc_final: 0.8246 (tpt90) REVERT: D6 67 MET cc_start: 0.9427 (mtp) cc_final: 0.9059 (mtp) REVERT: D6 301 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8702 (mm-30) REVERT: D6 476 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9295 (mp) REVERT: A1 493 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.6467 (mtt-85) REVERT: A1 496 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: A1 572 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7874 (ptm-80) REVERT: A1 600 MET cc_start: 0.6802 (mtm) cc_final: 0.6322 (mtp) REVERT: A2 16 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5372 (pmt170) REVERT: A2 496 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: A3 16 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5709 (ptp-170) REVERT: A3 493 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.6647 (mtt-85) REVERT: A3 567 LEU cc_start: 0.7382 (mm) cc_final: 0.7096 (tm) REVERT: A3 627 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7541 (mtp) REVERT: A4 16 ARG cc_start: 0.3714 (ptp-170) cc_final: 0.2413 (ptp-170) REVERT: A4 493 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.6832 (mtt180) REVERT: A4 496 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A5 30 MET cc_start: 0.7175 (ttp) cc_final: 0.6187 (tmm) REVERT: A5 493 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.6448 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A5 627 MET cc_start: 0.8309 (mpt) cc_final: 0.7891 (mpp) REVERT: A6 16 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5900 (ptm160) REVERT: A6 391 ASP cc_start: 0.8483 (t70) cc_final: 0.8164 (t0) REVERT: A6 493 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.6656 (mtt-85) REVERT: A6 543 ASP cc_start: 0.8543 (t70) cc_final: 0.8089 (t0) REVERT: A6 566 TRP cc_start: 0.7809 (m100) cc_final: 0.7389 (m-90) outliers start: 69 outliers final: 35 residues processed: 332 average time/residue: 0.7734 time to fit residues: 298.1924 Evaluate side-chains 332 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 442 THR Chi-restraints excluded: chain D1 residue 448 THR Chi-restraints excluded: chain D2 residue 59 LEU Chi-restraints excluded: chain D2 residue 171 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 447 MET Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 429 SER Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 446 GLU Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 59 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 558 VAL Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A2 residue 496 GLU Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 48 VAL Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 627 MET Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 496 GLU Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A4 residue 597 VAL Chi-restraints excluded: chain A4 residue 600 MET Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 558 VAL Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 49 THR Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 558 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [242, 148, 170, 288, 400, 341, 41, 396, 333, 393, 303] chunk 242 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 400 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 396 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 393 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 94 ASN A3 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.076608 restraints weight = 46620.670| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.85 r_work: 0.2671 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32853 Z= 0.149 Angle : 0.540 13.832 44653 Z= 0.272 Chirality : 0.044 0.185 5060 Planarity : 0.004 0.060 5827 Dihedral : 5.647 59.990 4814 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.04 % Allowed : 11.83 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.13), residues: 4181 helix: 1.88 (0.13), residues: 1602 sheet: 0.51 (0.22), residues: 537 loop : -0.23 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD6 284 TYR 0.016 0.001 TYRD1 415 PHE 0.019 0.001 PHED6 143 TRP 0.019 0.001 TRPA2 474 HIS 0.004 0.001 HISD2 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (32847) covalent geometry : angle 0.54023 / 0.27 (44653) hydrogen bonds : bond 0.03724 / 2.53 ( 1529) hydrogen bonds : angle 4.55943 / 3.35 ( 4308) Misc. bond : bond 0.00019 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 283 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 211 GLU cc_start: 0.7330 (tt0) cc_final: 0.6661 (pt0) REVERT: D1 301 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8537 (mm-30) REVERT: D2 301 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8558 (mm-30) REVERT: D3 29 ARG cc_start: 0.8160 (tpm-80) cc_final: 0.7882 (tpm-80) REVERT: D3 33 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.8000 (mtm-85) REVERT: D3 59 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9229 (tp) REVERT: D3 301 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8648 (mp0) REVERT: D3 350 ASP cc_start: 0.9471 (OUTLIER) cc_final: 0.9221 (m-30) REVERT: D3 461 GLU cc_start: 0.7741 (tt0) cc_final: 0.7174 (tp30) REVERT: D4 67 MET cc_start: 0.9437 (mtp) cc_final: 0.9066 (mtp) REVERT: D4 211 GLU cc_start: 0.7248 (tt0) cc_final: 0.6617 (pt0) REVERT: D4 301 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8698 (mm-30) REVERT: D4 369 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7745 (tmt170) REVERT: D4 431 MET cc_start: 0.7787 (ptp) cc_final: 0.7463 (ptm) REVERT: D5 29 ARG cc_start: 0.8152 (tpm-80) cc_final: 0.7848 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8408 (ttp-110) cc_final: 0.8032 (mtm-85) REVERT: D5 59 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9231 (tp) REVERT: D5 301 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8665 (mp0) REVERT: D5 350 ASP cc_start: 0.9464 (OUTLIER) cc_final: 0.9227 (m-30) REVERT: D6 29 ARG cc_start: 0.8808 (ttp-170) cc_final: 0.8263 (tpt90) REVERT: D6 67 MET cc_start: 0.9449 (mtp) cc_final: 0.9095 (mtp) REVERT: D6 301 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8701 (mm-30) REVERT: D6 476 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9301 (mp) REVERT: A1 493 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.6417 (mtt-85) REVERT: A1 496 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A1 572 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7870 (ptm-80) REVERT: A1 600 MET cc_start: 0.6947 (mtm) cc_final: 0.6460 (mtp) REVERT: A2 16 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.5275 (pmt170) REVERT: A3 16 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.5792 (ptp-170) REVERT: A3 493 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.6561 (mtt-85) REVERT: A3 567 LEU cc_start: 0.7445 (mm) cc_final: 0.7166 (mm) REVERT: A4 493 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.6358 (mmm-85) REVERT: A5 493 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.6594 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: A5 562 ASP cc_start: 0.8409 (p0) cc_final: 0.8209 (p0) REVERT: A5 627 MET cc_start: 0.8337 (mpt) cc_final: 0.7938 (mpp) REVERT: A6 16 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.5958 (ptm160) REVERT: A6 52 ASP cc_start: 0.7888 (m-30) cc_final: 0.7389 (m-30) REVERT: A6 391 ASP cc_start: 0.8479 (t70) cc_final: 0.8157 (t0) REVERT: A6 493 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.6561 (mtt-85) REVERT: A6 537 ASP cc_start: 0.8687 (t0) cc_final: 0.8005 (p0) REVERT: A6 543 ASP cc_start: 0.8542 (t70) cc_final: 0.8085 (t0) REVERT: A6 566 TRP cc_start: 0.7810 (m100) cc_final: 0.7426 (m-90) outliers start: 67 outliers final: 35 residues processed: 336 average time/residue: 0.7753 time to fit residues: 302.8684 Evaluate side-chains 318 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 442 THR Chi-restraints excluded: chain D2 residue 171 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 447 MET Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 429 SER Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D4 residue 32 GLU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 59 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 48 VAL Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A4 residue 48 VAL Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A4 residue 597 VAL Chi-restraints excluded: chain A4 residue 600 MET Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 558 VAL Chi-restraints excluded: chain A5 residue 620 VAL Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 49 THR Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [208, 186, 361, 239, 330, 256, 341, 230, 144, 289, 46] chunk 208 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 361 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 330 optimal weight: 20.0000 chunk 256 optimal weight: 0.5980 chunk 341 optimal weight: 0.2980 chunk 230 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 94 ASN ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D5 94 ASN A1 477 GLN A5 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.077805 restraints weight = 46994.539| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.85 r_work: 0.2698 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32853 Z= 0.114 Angle : 0.528 13.019 44653 Z= 0.264 Chirality : 0.043 0.179 5060 Planarity : 0.004 0.057 5827 Dihedral : 5.564 59.666 4814 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.65 % Allowed : 12.47 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4181 helix: 1.95 (0.13), residues: 1602 sheet: 0.47 (0.24), residues: 465 loop : -0.19 (0.14), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD4 284 TYR 0.014 0.001 TYRA3 556 PHE 0.019 0.001 PHED6 143 TRP 0.020 0.001 TRPA2 474 HIS 0.003 0.001 HISD1 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (32847) covalent geometry : angle 0.52827 / 0.26 (44653) hydrogen bonds : bond 0.03349 / 2.27 ( 1529) hydrogen bonds : angle 4.49205 / 3.30 ( 4308) Misc. bond : bond 0.00020 / 0.01 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8362 Ramachandran restraints generated. 4181 Oldfield, 0 Emsley, 4181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 279 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 211 GLU cc_start: 0.7399 (tt0) cc_final: 0.6708 (pt0) REVERT: D1 301 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8528 (mm-30) REVERT: D2 32 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8121 (mm-30) REVERT: D2 211 GLU cc_start: 0.7389 (tt0) cc_final: 0.6553 (pt0) REVERT: D2 301 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8552 (mm-30) REVERT: D3 33 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.8042 (mtm-85) REVERT: D3 59 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9207 (tp) REVERT: D3 301 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8634 (mp0) REVERT: D3 350 ASP cc_start: 0.9433 (OUTLIER) cc_final: 0.9195 (m-30) REVERT: D3 461 GLU cc_start: 0.7741 (tt0) cc_final: 0.7158 (tp30) REVERT: D4 67 MET cc_start: 0.9439 (mtp) cc_final: 0.9065 (mtp) REVERT: D4 211 GLU cc_start: 0.7263 (tt0) cc_final: 0.6638 (pt0) REVERT: D4 301 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8677 (mm-30) REVERT: D4 369 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7744 (tmt170) REVERT: D4 431 MET cc_start: 0.7781 (ptp) cc_final: 0.7477 (ptm) REVERT: D4 446 GLU cc_start: 0.5513 (OUTLIER) cc_final: 0.4749 (pp20) REVERT: D5 29 ARG cc_start: 0.8161 (tpm-80) cc_final: 0.7860 (tpm-80) REVERT: D5 33 ARG cc_start: 0.8403 (ttp-110) cc_final: 0.8057 (mtm-85) REVERT: D5 59 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9212 (tp) REVERT: D5 301 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8657 (mp0) REVERT: D5 350 ASP cc_start: 0.9425 (OUTLIER) cc_final: 0.9171 (m-30) REVERT: D6 29 ARG cc_start: 0.8814 (ttp-170) cc_final: 0.8252 (tpt90) REVERT: D6 67 MET cc_start: 0.9438 (mtp) cc_final: 0.9077 (mtp) REVERT: D6 211 GLU cc_start: 0.7314 (tt0) cc_final: 0.6608 (pt0) REVERT: D6 301 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8682 (mm-30) REVERT: D6 476 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9310 (mp) REVERT: A1 472 TYR cc_start: 0.8689 (t80) cc_final: 0.8474 (t80) REVERT: A1 493 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.6388 (mtt-85) REVERT: A1 496 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: A1 572 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7896 (ptm-80) REVERT: A1 600 MET cc_start: 0.6860 (mtm) cc_final: 0.6352 (mtp) REVERT: A2 16 ARG cc_start: 0.5638 (OUTLIER) cc_final: 0.5212 (pmt170) REVERT: A3 16 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5885 (ptp-170) REVERT: A3 493 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.6632 (mtt-85) REVERT: A3 567 LEU cc_start: 0.7437 (mm) cc_final: 0.7169 (mm) REVERT: A4 16 ARG cc_start: 0.3685 (ptp-170) cc_final: 0.2369 (ptp-170) REVERT: A4 493 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.6784 (mtt-85) REVERT: A5 493 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.6392 (mtt-85) REVERT: A5 496 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: A5 562 ASP cc_start: 0.8418 (p0) cc_final: 0.8209 (p0) REVERT: A5 627 MET cc_start: 0.8317 (mpt) cc_final: 0.7931 (mpp) REVERT: A6 16 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6057 (ptm160) REVERT: A6 52 ASP cc_start: 0.8005 (m-30) cc_final: 0.7495 (m-30) REVERT: A6 391 ASP cc_start: 0.8464 (t70) cc_final: 0.8138 (t0) REVERT: A6 493 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.6660 (mtt-85) REVERT: A6 537 ASP cc_start: 0.8659 (t0) cc_final: 0.8003 (p0) REVERT: A6 543 ASP cc_start: 0.8538 (t70) cc_final: 0.8079 (t0) REVERT: A6 566 TRP cc_start: 0.7797 (m100) cc_final: 0.7434 (m-90) outliers start: 54 outliers final: 31 residues processed: 326 average time/residue: 0.7714 time to fit residues: 292.2950 Evaluate side-chains 320 residues out of total 3281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 340 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D1 residue 442 THR Chi-restraints excluded: chain D2 residue 171 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 447 MET Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 340 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 391 ARG Chi-restraints excluded: chain D3 residue 442 THR Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 446 GLU Chi-restraints excluded: chain D4 residue 476 LEU Chi-restraints excluded: chain D5 residue 59 LEU Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 350 ASP Chi-restraints excluded: chain D5 residue 391 ARG Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 143 PHE Chi-restraints excluded: chain D6 residue 340 VAL Chi-restraints excluded: chain D6 residue 442 THR Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain A1 residue 13 VAL Chi-restraints excluded: chain A1 residue 385 VAL Chi-restraints excluded: chain A1 residue 493 ARG Chi-restraints excluded: chain A1 residue 496 GLU Chi-restraints excluded: chain A1 residue 572 ARG Chi-restraints excluded: chain A2 residue 16 ARG Chi-restraints excluded: chain A2 residue 385 VAL Chi-restraints excluded: chain A2 residue 493 ARG Chi-restraints excluded: chain A3 residue 16 ARG Chi-restraints excluded: chain A3 residue 493 ARG Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A4 residue 493 ARG Chi-restraints excluded: chain A4 residue 549 LEU Chi-restraints excluded: chain A4 residue 558 VAL Chi-restraints excluded: chain A4 residue 597 VAL Chi-restraints excluded: chain A4 residue 600 MET Chi-restraints excluded: chain A5 residue 49 THR Chi-restraints excluded: chain A5 residue 493 ARG Chi-restraints excluded: chain A5 residue 496 GLU Chi-restraints excluded: chain A5 residue 558 VAL Chi-restraints excluded: chain A6 residue 16 ARG Chi-restraints excluded: chain A6 residue 49 THR Chi-restraints excluded: chain A6 residue 376 VAL Chi-restraints excluded: chain A6 residue 493 ARG Chi-restraints excluded: chain A6 residue 558 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [300, 420, 239, 143, 271, 274, 250, 75, 157, 405, 375] chunk 300 optimal weight: 1.9990 chunk 420 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 143 optimal weight: 0.0370 chunk 271 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 chunk 405 optimal weight: 10.0000 chunk 375 optimal weight: 0.0020 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 94 ASN ** D3 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4 162 GLN D5 94 ASN A5 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.078148 restraints weight = 46740.241| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.85 r_work: 0.2706 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32853 Z= 0.106 Angle : 0.523 12.736 44653 Z= 0.261 Chirality : 0.043 0.175 5060 Planarity : 0.004 0.056 5827 Dihedral : 5.519 59.594 4814 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.62 % Allowed : 12.62 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.13), residues: 4181 helix: 2.13 (0.13), residues: 1566 sheet: 0.46 (0.24), residues: 477 loop : -0.07 (0.14), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD4 284 TYR 0.013 0.001 TYRA1 556 PHE 0.019 0.001 PHED6 143 TRP 0.021 0.001 TRPA2 474 HIS 0.003 0.001 HISD3 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (32847) covalent geometry : angle 0.52329 / 0.26 (44653) hydrogen bonds : bond 0.03254 / 2.21 ( 1529) hydrogen bonds : angle 4.45199 / 3.27 ( 4308) Misc. bond : bond 0.00017 / 0.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14076.85 seconds wall clock time: 239 minutes 0.36 seconds (14340.36 seconds total)