Starting phenix.real_space_refine on Fri Oct 30 13:40:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31vx_58684/10_2026/31vx_58684.cif Found real_map, /net/cci-nas-00/data/ceres_data/31vx_58684/10_2026/31vx_58684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31vx_58684/10_2026/31vx_58684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31vx_58684/10_2026/31vx_58684.map" model { file = "/net/cci-nas-00/data/ceres_data/31vx_58684/10_2026/31vx_58684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31vx_58684/10_2026/31vx_58684.cif" } resolution = 3.15 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= 0.006 sd= 0.020 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 22427 2.51 5 N 6337 2.21 5 O 6736 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: 35644 Number of models: 1 Model: "" Number of chains: 12 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: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4195 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 541} Chain breaks: 2 Chain: "A2" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4181 Classifications: {'peptide': 566} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 539} Chain breaks: 2 Chain: "A3" Number of atoms: 4195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4195 Classifications: {'peptide': 568} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 541} Chain breaks: 2 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 Residues with excluded nonbonded symmetry interactions: 74 residue: pdb=" N ARGD1 444 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARGD1 444 " occ=0.00 residue: pdb=" N GLYD1 445 " occ=0.00 ... (2 atoms not shown) pdb=" O GLYD1 445 " occ=0.00 residue: pdb=" N GLUD1 446 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLUD1 446 " occ=0.00 residue: pdb=" N METD1 447 " occ=0.00 ... (6 atoms not shown) pdb=" CE METD1 447 " occ=0.00 residue: pdb=" N THRD1 448 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THRD1 448 " occ=0.00 residue: pdb=" N ASPD1 449 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASPD1 449 " occ=0.00 residue: pdb=" N ALAD1 450 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALAD1 450 " occ=0.00 residue: pdb=" N GLUD1 451 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLUD1 451 " occ=0.00 residue: pdb=" N ALAD1 452 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALAD1 452 " occ=0.00 residue: pdb=" N GLUD1 453 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLUD1 453 " occ=0.00 residue: pdb=" N GLUD1 454 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLUD1 454 " occ=0.00 residue: pdb=" N PHED1 455 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHED1 455 " occ=0.00 ... (remaining 62 not shown) Time building chain proxies: 7.64, per 1000 atoms: 0.21 Number of scatterers: 35644 At special positions: 0 Unit cell: (157.233, 142.764, 153.375, 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 6736 8.00 N 6337 7.00 C 22427 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8504 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 43 sheets defined 45.9% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'D1' and resid 3 through 23 removed outlier: 4.333A pdb=" N GLUD1 7 " --> pdb=" O SERD1 3 " (cutoff:3.500A) Processing helix chain 'D1' and resid 27 through 37 Processing helix chain 'D1' and resid 41 through 50 removed outlier: 3.591A pdb=" N VALD1 46 " --> pdb=" O PROD1 42 " (cutoff:3.500A) 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 121 removed outlier: 3.754A pdb=" N LYSD1 109 " --> pdb=" O PROD1 105 " (cutoff:3.500A) Processing helix chain 'D1' and resid 135 through 142 removed outlier: 5.525A pdb=" N ASPD1 140 " --> pdb=" O PROD1 137 " (cutoff:3.500A) Processing helix chain 'D1' and resid 150 through 162 removed outlier: 3.677A pdb=" N TYRD1 154 " --> pdb=" O GLYD1 150 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLND1 162 " --> pdb=" O THRD1 158 " (cutoff:3.500A) Processing helix chain 'D1' and resid 179 through 185 removed outlier: 3.575A pdb=" N ALAD1 183 " --> pdb=" O ALAD1 179 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SERD1 185 " --> pdb=" O VALD1 181 " (cutoff:3.500A) 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 removed outlier: 3.502A pdb=" N LYSD1 226 " --> pdb=" O ASPD1 222 " (cutoff:3.500A) Processing helix chain 'D1' and resid 237 through 252 removed outlier: 3.519A pdb=" N THRD1 251 " --> pdb=" O ASND1 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEUD1 252 " --> pdb=" O ILED1 248 " (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: 3.557A pdb=" N VALD1 278 " --> pdb=" O GLUD1 274 " (cutoff:3.500A) Processing helix chain 'D1' and resid 289 through 297 removed outlier: 3.621A pdb=" N ARGD1 295 " --> pdb=" O GLUD1 291 " (cutoff:3.500A) Processing helix chain 'D1' and resid 298 through 301 Processing helix chain 'D1' and resid 335 through 352 Processing helix chain 'D1' and resid 368 through 374 Processing helix chain 'D1' and resid 375 through 390 Processing helix chain 'D1' and resid 404 through 410 removed outlier: 4.004A pdb=" N TYRD1 408 " --> pdb=" O GLYD1 404 " (cutoff:3.500A) Processing helix chain 'D1' and resid 412 through 416 Processing helix chain 'D1' and resid 432 through 445 removed outlier: 3.824A pdb=" N GLYD1 445 " --> pdb=" O ALAD1 441 " (cutoff:3.500A) Processing helix chain 'D1' and resid 448 through 468 Proline residue: D1 458 - end of helix Processing helix chain 'D1' and resid 468 through 474 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: 3.649A pdb=" N GLYD1 499 " --> pdb=" O LEUD1 495 " (cutoff:3.500A) Processing helix chain 'D2' and resid 4 through 25 removed outlier: 3.682A pdb=" N LEUD2 24 " --> pdb=" O ALAD2 20 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLYD2 25 " --> pdb=" O ALAD2 21 " (cutoff:3.500A) Processing helix chain 'D2' and resid 27 through 37 Processing helix chain 'D2' and resid 41 through 50 removed outlier: 3.651A pdb=" N VALD2 46 " --> pdb=" O PROD2 42 " (cutoff:3.500A) 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 removed outlier: 3.528A pdb=" N THRD2 102 " --> pdb=" O LYSD2 99 " (cutoff:3.500A) Processing helix chain 'D2' and resid 104 through 121 removed outlier: 3.880A pdb=" N LYSD2 109 " --> pdb=" O PROD2 105 " (cutoff:3.500A) Processing helix chain 'D2' and resid 135 through 142 removed outlier: 5.559A pdb=" N ASPD2 140 " --> pdb=" O PROD2 137 " (cutoff:3.500A) Processing helix chain 'D2' and resid 150 through 162 removed outlier: 3.765A pdb=" N TYRD2 154 " --> pdb=" O GLYD2 150 " (cutoff:3.500A) Processing helix chain 'D2' and resid 175 through 178 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 252 removed outlier: 3.592A pdb=" N LEUD2 252 " --> pdb=" O ILED2 248 " (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: 3.613A pdb=" N VALD2 278 " --> pdb=" O GLUD2 274 " (cutoff:3.500A) Processing helix chain 'D2' and resid 289 through 297 removed outlier: 3.712A pdb=" N ARGD2 295 " --> pdb=" O GLUD2 291 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILED2 296 " --> pdb=" O VALD2 292 " (cutoff:3.500A) Processing helix chain 'D2' and resid 298 through 301 Processing helix chain 'D2' and resid 335 through 352 Processing helix chain 'D2' and resid 368 through 374 Processing helix chain 'D2' and resid 375 through 390 Processing helix chain 'D2' and resid 404 through 410 removed outlier: 3.921A pdb=" N TYRD2 408 " --> pdb=" O GLYD2 404 " (cutoff:3.500A) Processing helix chain 'D2' and resid 412 through 416 removed outlier: 3.517A pdb=" N TYRD2 415 " --> pdb=" O GLYD2 412 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SERD2 416 " --> pdb=" O ARGD2 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D2' and resid 412 through 416' Processing helix chain 'D2' and resid 432 through 445 removed outlier: 3.540A pdb=" N ALAD2 441 " --> pdb=" O ALAD2 437 " (cutoff:3.500A) Processing helix chain 'D2' and resid 448 through 453 Processing helix chain 'D2' and resid 457 through 467 Processing helix chain 'D2' and resid 468 through 474 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 498 Processing helix chain 'D2' and resid 499 through 501 No H-bonds generated for 'chain 'D2' and resid 499 through 501' Processing helix chain 'D3' and resid 4 through 25 removed outlier: 3.652A pdb=" N LEUD3 24 " --> pdb=" O ALAD3 20 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLYD3 25 " --> pdb=" O ALAD3 21 " (cutoff:3.500A) Processing helix chain 'D3' and resid 27 through 37 removed outlier: 3.535A pdb=" N ARGD3 37 " --> pdb=" O ARGD3 33 " (cutoff:3.500A) Processing helix chain 'D3' and resid 41 through 50 removed outlier: 3.573A pdb=" N VALD3 46 " --> pdb=" O PROD3 42 " (cutoff:3.500A) 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 121 removed outlier: 3.773A pdb=" N LYSD3 109 " --> pdb=" O PROD3 105 " (cutoff:3.500A) Processing helix chain 'D3' and resid 135 through 142 removed outlier: 5.554A pdb=" N ASPD3 140 " --> pdb=" O PROD3 137 " (cutoff:3.500A) Processing helix chain 'D3' and resid 150 through 162 removed outlier: 3.687A pdb=" N TYRD3 154 " --> pdb=" O GLYD3 150 " (cutoff:3.500A) removed outlier: 3.596A 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 252 removed outlier: 3.559A pdb=" N LEUD3 252 " --> pdb=" O ILED3 248 " (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: 3.518A pdb=" N VALD3 278 " --> pdb=" O GLUD3 274 " (cutoff:3.500A) Processing helix chain 'D3' and resid 289 through 297 removed outlier: 3.648A pdb=" N ARGD3 295 " --> pdb=" O GLUD3 291 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILED3 296 " --> pdb=" O VALD3 292 " (cutoff:3.500A) 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 373 Processing helix chain 'D3' and resid 375 through 390 Processing helix chain 'D3' and resid 404 through 410 removed outlier: 3.910A pdb=" N TYRD3 408 " --> pdb=" O GLYD3 404 " (cutoff:3.500A) Processing helix chain 'D3' and resid 412 through 416 Processing helix chain 'D3' and resid 432 through 445 removed outlier: 4.142A pdb=" N GLYD3 445 " --> pdb=" O ALAD3 441 " (cutoff:3.500A) Processing helix chain 'D3' and resid 448 through 468 Proline residue: D3 458 - end of helix Processing helix chain 'D3' and resid 468 through 474 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: 3.710A pdb=" N GLYD3 499 " --> pdb=" O LEUD3 495 " (cutoff:3.500A) Processing helix chain 'D4' and resid 4 through 23 Processing helix chain 'D4' and resid 27 through 37 Processing helix chain 'D4' and resid 41 through 50 removed outlier: 3.542A pdb=" N VALD4 46 " --> pdb=" O PROD4 42 " (cutoff:3.500A) 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 121 removed outlier: 3.839A pdb=" N LYSD4 109 " --> pdb=" O PROD4 105 " (cutoff:3.500A) Processing helix chain 'D4' and resid 135 through 142 removed outlier: 5.572A pdb=" N ASPD4 140 " --> pdb=" O PROD4 137 " (cutoff:3.500A) Processing helix chain 'D4' and resid 150 through 162 removed outlier: 3.636A pdb=" N TYRD4 154 " --> pdb=" O GLYD4 150 " (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 252 removed outlier: 3.592A pdb=" N LEUD4 252 " --> pdb=" O ILED4 248 " (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: 3.669A pdb=" N VALD4 278 " --> pdb=" O GLUD4 274 " (cutoff:3.500A) Processing helix chain 'D4' and resid 289 through 297 removed outlier: 3.580A pdb=" N ARGD4 295 " --> pdb=" O GLUD4 291 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VALD4 297 " --> pdb=" O ILED4 293 " (cutoff:3.500A) Processing helix chain 'D4' and resid 298 through 301 Processing helix chain 'D4' and resid 335 through 352 Processing helix chain 'D4' and resid 368 through 374 Processing helix chain 'D4' and resid 375 through 390 Processing helix chain 'D4' and resid 404 through 410 removed outlier: 3.835A 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 448 through 468 Proline residue: D4 458 - end of helix Processing helix chain 'D4' and resid 468 through 474 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: 3.665A pdb=" N GLYD4 499 " --> pdb=" O LEUD4 495 " (cutoff:3.500A) Processing helix chain 'D5' and resid 4 through 25 removed outlier: 3.541A pdb=" N LEUD5 24 " --> pdb=" O ALAD5 20 " (cutoff:3.500A) removed outlier: 4.271A 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 removed outlier: 3.660A pdb=" N VALD5 46 " --> pdb=" O PROD5 42 " (cutoff:3.500A) 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 removed outlier: 3.502A pdb=" N THRD5 102 " --> pdb=" O LYSD5 99 " (cutoff:3.500A) Processing helix chain 'D5' and resid 104 through 121 removed outlier: 3.838A pdb=" N LYSD5 109 " --> pdb=" O PROD5 105 " (cutoff:3.500A) Processing helix chain 'D5' and resid 135 through 142 removed outlier: 5.591A pdb=" N ASPD5 140 " --> pdb=" O PROD5 137 " (cutoff:3.500A) Processing helix chain 'D5' and resid 150 through 161 removed outlier: 3.642A pdb=" N TYRD5 154 " --> pdb=" O GLYD5 150 " (cutoff:3.500A) Processing helix chain 'D5' and resid 175 through 178 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 252 removed outlier: 3.630A pdb=" N LEUD5 252 " --> pdb=" O ILED5 248 " (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: 3.585A pdb=" N VALD5 278 " --> pdb=" O GLUD5 274 " (cutoff:3.500A) Processing helix chain 'D5' and resid 289 through 297 removed outlier: 3.756A pdb=" N ARGD5 295 " --> pdb=" O GLUD5 291 " (cutoff:3.500A) 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 374 Processing helix chain 'D5' and resid 375 through 390 Processing helix chain 'D5' and resid 404 through 410 removed outlier: 3.900A pdb=" N TYRD5 408 " --> pdb=" O GLYD5 404 " (cutoff:3.500A) Processing helix chain 'D5' and resid 412 through 416 removed outlier: 3.578A pdb=" N TYRD5 415 " --> pdb=" O GLYD5 412 " (cutoff:3.500A) Processing helix chain 'D5' and resid 432 through 445 Processing helix chain 'D5' and resid 448 through 468 Proline residue: D5 458 - end of helix Processing helix chain 'D5' and resid 468 through 474 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 498 Processing helix chain 'D5' and resid 499 through 501 No H-bonds generated for 'chain 'D5' and resid 499 through 501' Processing helix chain 'D6' and resid 4 through 23 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 121 removed outlier: 3.792A pdb=" N LYSD6 109 " --> pdb=" O PROD6 105 " (cutoff:3.500A) Processing helix chain 'D6' and resid 135 through 142 removed outlier: 5.505A pdb=" N ASPD6 140 " --> pdb=" O PROD6 137 " (cutoff:3.500A) Processing helix chain 'D6' and resid 150 through 162 removed outlier: 3.694A pdb=" N TYRD6 154 " --> pdb=" O GLYD6 150 " (cutoff:3.500A) Processing helix chain 'D6' and resid 176 through 178 No H-bonds generated for 'chain 'D6' and resid 176 through 178' 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 252 removed outlier: 3.586A pdb=" N LEUD6 252 " --> pdb=" O ILED6 248 " (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: 3.648A pdb=" N VALD6 278 " --> pdb=" O GLUD6 274 " (cutoff:3.500A) Processing helix chain 'D6' and resid 289 through 297 removed outlier: 3.691A pdb=" N ARGD6 295 " --> pdb=" O GLUD6 291 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILED6 296 " --> pdb=" O VALD6 292 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VALD6 297 " --> pdb=" O ILED6 293 " (cutoff:3.500A) Processing helix chain 'D6' and resid 298 through 301 Processing helix chain 'D6' and resid 335 through 352 Processing helix chain 'D6' and resid 368 through 374 Processing helix chain 'D6' and resid 375 through 390 Processing helix chain 'D6' and resid 404 through 410 removed outlier: 4.026A pdb=" N TYRD6 408 " --> pdb=" O GLYD6 404 " (cutoff:3.500A) Processing helix chain 'D6' and resid 412 through 416 removed outlier: 3.512A pdb=" N TYRD6 415 " --> pdb=" O GLYD6 412 " (cutoff:3.500A) Processing helix chain 'D6' and resid 432 through 445 removed outlier: 3.783A pdb=" N ALAD6 441 " --> pdb=" O ALAD6 437 " (cutoff:3.500A) Processing helix chain 'D6' and resid 448 through 468 Proline residue: D6 458 - end of helix Processing helix chain 'D6' and resid 468 through 474 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: 3.707A pdb=" N GLYD6 499 " --> pdb=" O LEUD6 495 " (cutoff:3.500A) Processing helix chain 'A1' and resid 16 through 31 Processing helix chain 'A1' and resid 41 through 43 No H-bonds generated for 'chain 'A1' and resid 41 through 43' Processing helix chain 'A1' and resid 45 through 51 removed outlier: 3.951A pdb=" N THRA1 49 " --> pdb=" O ALAA1 45 " (cutoff:3.500A) Processing helix chain 'A1' and resid 68 through 79 Processing helix chain 'A1' and resid 94 through 104 Processing helix chain 'A1' and resid 112 through 120 Processing helix chain 'A1' and resid 121 through 132 removed outlier: 3.805A pdb=" N PHEA1 132 " --> pdb=" O ALAA1 128 " (cutoff:3.500A) Processing helix chain 'A1' and resid 254 through 271 Processing helix chain 'A1' and resid 304 through 313 removed outlier: 4.349A pdb=" N THRA1 308 " --> pdb=" O GLUA1 304 " (cutoff:3.500A) Processing helix chain 'A1' and resid 315 through 325 Processing helix chain 'A1' and resid 332 through 336 Processing helix chain 'A1' and resid 403 through 417 Processing helix chain 'A1' and resid 426 through 435 Processing helix chain 'A1' and resid 436 through 442 Processing helix chain 'A1' and resid 447 through 453 Processing helix chain 'A1' and resid 462 through 482 removed outlier: 3.782A pdb=" N GLYA1 482 " --> pdb=" O TRPA1 478 " (cutoff:3.500A) Processing helix chain 'A2' and resid 16 through 30 removed outlier: 3.610A pdb=" N VALA2 21 " --> pdb=" O GLYA2 17 " (cutoff:3.500A) Processing helix chain 'A2' and resid 41 through 43 No H-bonds generated for 'chain 'A2' and resid 41 through 43' Processing helix chain 'A2' and resid 45 through 51 removed outlier: 3.807A pdb=" N THRA2 49 " --> pdb=" O ALAA2 45 " (cutoff:3.500A) Processing helix chain 'A2' and resid 68 through 79 Processing helix chain 'A2' and resid 94 through 104 Processing helix chain 'A2' and resid 112 through 120 Processing helix chain 'A2' and resid 121 through 131 Processing helix chain 'A2' and resid 254 through 271 Processing helix chain 'A2' and resid 304 through 313 removed outlier: 4.240A pdb=" N THRA2 308 " --> pdb=" O GLUA2 304 " (cutoff:3.500A) Processing helix chain 'A2' and resid 315 through 325 Processing helix chain 'A2' and resid 332 through 336 Processing helix chain 'A2' and resid 403 through 417 Processing helix chain 'A2' and resid 426 through 435 Processing helix chain 'A2' and resid 436 through 442 Processing helix chain 'A2' and resid 447 through 453 Processing helix chain 'A2' and resid 462 through 482 removed outlier: 3.778A pdb=" N GLYA2 482 " --> pdb=" O TRPA2 478 " (cutoff:3.500A) Processing helix chain 'A3' and resid 16 through 31 removed outlier: 3.566A pdb=" N VALA3 21 " --> pdb=" O GLYA3 17 " (cutoff:3.500A) Processing helix chain 'A3' and resid 45 through 51 removed outlier: 3.929A pdb=" N THRA3 49 " --> pdb=" O ALAA3 45 " (cutoff:3.500A) Processing helix chain 'A3' and resid 68 through 79 Processing helix chain 'A3' and resid 94 through 104 Processing helix chain 'A3' and resid 112 through 121 removed outlier: 3.969A pdb=" N ASPA3 121 " --> pdb=" O ALAA3 117 " (cutoff:3.500A) Processing helix chain 'A3' and resid 121 through 132 Processing helix chain 'A3' and resid 254 through 272 removed outlier: 4.006A pdb=" N VALA3 272 " --> pdb=" O THRA3 268 " (cutoff:3.500A) Processing helix chain 'A3' and resid 304 through 313 removed outlier: 4.203A pdb=" N THRA3 308 " --> pdb=" O GLUA3 304 " (cutoff:3.500A) Processing helix chain 'A3' and resid 315 through 325 Processing helix chain 'A3' and resid 332 through 336 Processing helix chain 'A3' and resid 403 through 417 Processing helix chain 'A3' and resid 426 through 435 Processing helix chain 'A3' and resid 436 through 442 Processing helix chain 'A3' and resid 447 through 453 Processing helix chain 'A3' and resid 462 through 482 removed outlier: 3.890A pdb=" N GLYA3 482 " --> pdb=" O TRPA3 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D1' and resid 56 through 59 removed outlier: 4.806A pdb=" N ALAD1 79 " --> pdb=" O LEUD1 59 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYSD1 125 " --> pdb=" O ILED1 167 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALAD1 169 " --> pdb=" O CYSD1 125 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYRD1 127 " --> pdb=" O ALAD1 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VALD1 191 " --> pdb=" O VALD1 170 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALAD1 188 " --> pdb=" O HISD1 233 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ALAD1 235 " --> pdb=" O ALAD1 188 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILED1 190 " --> pdb=" O ALAD1 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D1' and resid 173 through 175 removed outlier: 6.610A pdb=" N CYSD1 174 " --> pdb=" O PHED1 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D1' and resid 303 through 304 removed outlier: 6.295A pdb=" N LEUD1 356 " --> pdb=" O LEUD1 395 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VALD1 397 " --> pdb=" O LEUD1 356 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHED1 358 " --> pdb=" O VALD1 397 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHED1 419 " --> pdb=" O LYSD1 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D1' and resid 401 through 403 removed outlier: 6.227A pdb=" N SERD1 402 " --> pdb=" O SERD1 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D2' and resid 56 through 59 removed outlier: 4.779A pdb=" N ALAD2 79 " --> pdb=" O LEUD2 59 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYSD2 125 " --> pdb=" O ILED2 167 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALAD2 169 " --> pdb=" O CYSD2 125 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYRD2 127 " --> pdb=" O ALAD2 169 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALD2 191 " --> pdb=" O VALD2 170 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALAD2 188 " --> pdb=" O HISD2 233 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALAD2 235 " --> pdb=" O ALAD2 188 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILED2 190 " --> pdb=" O ALAD2 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D2' and resid 303 through 304 removed outlier: 5.269A pdb=" N ASND2 361 " --> pdb=" O ASND2 330 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILED2 362 " --> pdb=" O ILED2 399 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLYD2 401 " --> pdb=" O ILED2 362 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHED2 419 " --> pdb=" O LYSD2 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D2' and resid 303 through 304 removed outlier: 5.269A pdb=" N ASND2 361 " --> pdb=" O ASND2 330 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILED2 362 " --> pdb=" O ILED2 399 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLYD2 401 " --> pdb=" O ILED2 362 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARGD2 427 " --> pdb=" O VALD2 398 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLYD2 400 " --> pdb=" O ARGD2 427 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N SERD2 429 " --> pdb=" O GLYD2 400 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SERD2 402 " --> pdb=" O SERD2 429 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D3' and resid 56 through 59 removed outlier: 4.809A pdb=" N ALAD3 79 " --> pdb=" O LEUD3 59 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYSD3 125 " --> pdb=" O ILED3 167 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALAD3 169 " --> pdb=" O CYSD3 125 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TYRD3 127 " --> pdb=" O ALAD3 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VALD3 191 " --> pdb=" O VALD3 170 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALAD3 188 " --> pdb=" O HISD3 233 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALAD3 235 " --> pdb=" O ALAD3 188 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILED3 190 " --> pdb=" O ALAD3 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D3' and resid 173 through 175 removed outlier: 6.552A pdb=" N CYSD3 174 " --> pdb=" O PHED3 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D3' and resid 303 through 304 removed outlier: 3.584A pdb=" N ASND3 330 " --> pdb=" O LEUD3 359 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEUD3 356 " --> pdb=" O LEUD3 395 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VALD3 397 " --> pdb=" O LEUD3 356 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHED3 358 " --> pdb=" O VALD3 397 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHED3 419 " --> pdb=" O LYSD3 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D3' and resid 401 through 403 removed outlier: 6.189A pdb=" N SERD3 402 " --> pdb=" O SERD3 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D4' and resid 56 through 58 removed outlier: 6.206A pdb=" N CYSD4 125 " --> pdb=" O ILED4 167 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALAD4 169 " --> pdb=" O CYSD4 125 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYRD4 127 " --> pdb=" O ALAD4 169 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VALD4 191 " --> pdb=" O VALD4 170 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALAD4 188 " --> pdb=" O HISD4 233 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALAD4 235 " --> pdb=" O ALAD4 188 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILED4 190 " --> pdb=" O ALAD4 235 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D4' and resid 173 through 175 removed outlier: 6.747A pdb=" N CYSD4 174 " --> pdb=" O PHED4 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D4' and resid 303 through 305 removed outlier: 4.617A pdb=" N THRD4 315 " --> pdb=" O PHED4 305 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASND4 330 " --> pdb=" O LEUD4 359 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASND4 361 " --> pdb=" O ASND4 330 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILED4 362 " --> pdb=" O ILED4 399 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLYD4 401 " --> pdb=" O ILED4 362 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHED4 419 " --> pdb=" O LYSD4 394 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D4' and resid 303 through 305 removed outlier: 4.617A pdb=" N THRD4 315 " --> pdb=" O PHED4 305 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASND4 330 " --> pdb=" O LEUD4 359 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASND4 361 " --> pdb=" O ASND4 330 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILED4 362 " --> pdb=" O ILED4 399 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLYD4 401 " --> pdb=" O ILED4 362 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARGD4 427 " --> pdb=" O VALD4 398 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLYD4 400 " --> pdb=" O ARGD4 427 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N SERD4 429 " --> pdb=" O GLYD4 400 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N SERD4 402 " --> pdb=" O SERD4 429 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D5' and resid 56 through 58 removed outlier: 6.364A pdb=" N CYSD5 125 " --> pdb=" O ILED5 167 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALAD5 169 " --> pdb=" O CYSD5 125 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYRD5 127 " --> pdb=" O ALAD5 169 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VALD5 191 " --> pdb=" O VALD5 170 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALAD5 188 " --> pdb=" O HISD5 233 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALAD5 235 " --> pdb=" O ALAD5 188 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILED5 190 " --> pdb=" O ALAD5 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D5' and resid 303 through 304 removed outlier: 3.526A pdb=" N ASND5 330 " --> pdb=" O LEUD5 359 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASND5 361 " --> pdb=" O ASND5 330 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILED5 362 " --> pdb=" O ILED5 399 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLYD5 401 " --> pdb=" O ILED5 362 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHED5 419 " --> pdb=" O LYSD5 394 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D5' and resid 303 through 304 removed outlier: 3.526A pdb=" N ASND5 330 " --> pdb=" O LEUD5 359 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASND5 361 " --> pdb=" O ASND5 330 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILED5 362 " --> pdb=" O ILED5 399 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLYD5 401 " --> pdb=" O ILED5 362 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARGD5 427 " --> pdb=" O VALD5 398 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLYD5 400 " --> pdb=" O ARGD5 427 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SERD5 429 " --> pdb=" O GLYD5 400 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SERD5 402 " --> pdb=" O SERD5 429 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D6' and resid 56 through 58 removed outlier: 4.860A pdb=" N ASPD6 130 " --> pdb=" O ASND6 94 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N CYSD6 125 " --> pdb=" O ILED6 167 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALAD6 169 " --> pdb=" O CYSD6 125 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYRD6 127 " --> pdb=" O ALAD6 169 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEUD6 171 " --> pdb=" O TYRD6 127 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VALD6 129 " --> pdb=" O LEUD6 171 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SERD6 173 " --> pdb=" O VALD6 129 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLYD6 172 " --> pdb=" O VALD6 191 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALAD6 188 " --> pdb=" O HISD6 233 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALAD6 235 " --> pdb=" O ALAD6 188 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILED6 190 " --> pdb=" O ALAD6 235 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D6' and resid 303 through 304 removed outlier: 3.605A pdb=" N ASND6 330 " --> pdb=" O LEUD6 359 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASND6 361 " --> pdb=" O ASND6 330 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEUD6 356 " --> pdb=" O LEUD6 395 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VALD6 397 " --> pdb=" O LEUD6 356 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHED6 358 " --> pdb=" O VALD6 397 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILED6 399 " --> pdb=" O PHED6 358 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLND6 360 " --> pdb=" O ILED6 399 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLYD6 401 " --> pdb=" O GLND6 360 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHED6 419 " --> pdb=" O LYSD6 394 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A1' and resid 107 through 108 removed outlier: 3.521A pdb=" N ALAA1 83 " --> pdb=" O THRA1 10 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VALA1 37 " --> pdb=" O VALA1 13 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALAA1 54 " --> pdb=" O ARGA2 553 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALAA2 546 " --> pdb=" O ASPA2 537 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A1' and resid 292 through 298 removed outlier: 6.998A pdb=" N GLUA1 281 " --> pdb=" O META1 295 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N META1 297 " --> pdb=" O THRA1 279 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THRA1 279 " --> pdb=" O META1 297 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N HISA1 214 " --> pdb=" O GLUA1 234 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLUA1 234 " --> pdb=" O HISA1 214 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLUA1 216 " --> pdb=" O GLUA1 232 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLUA1 232 " --> pdb=" O GLUA1 216 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLNA1 218 " --> pdb=" O LEUA1 230 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ARGA1 233 " --> pdb=" O ALAA1 248 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALAA1 248 " --> pdb=" O ARGA1 233 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYSA1 235 " --> pdb=" O GLUA1 246 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLUA1 246 " --> pdb=" O CYSA1 235 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEUA1 237 " --> pdb=" O VALA1 244 " (cutoff:3.500A) removed outlier: 14.420A pdb=" N GLNA1 242 " --> pdb=" O TYRA1 348 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N TYRA1 348 " --> pdb=" O GLNA1 242 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VALA1 244 " --> pdb=" O ARGA1 346 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SERA1 395 " --> pdb=" O VALA1 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A1' and resid 350 through 351 removed outlier: 3.811A pdb=" N LEUA1 357 " --> pdb=" O ASPA1 351 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A1' and resid 361 through 362 Processing sheet with id=AC7, first strand: chain 'A1' and resid 365 through 367 removed outlier: 3.755A pdb=" N GLYA1 365 " --> pdb=" O LEUA1 421 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALAA1 419 " --> pdb=" O ARGA1 367 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A3' and resid 107 through 108 removed outlier: 6.593A pdb=" N THRA3 10 " --> pdb=" O ALAA3 83 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N HISA3 85 " --> pdb=" O THRA3 10 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEUA3 12 " --> pdb=" O HISA3 85 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VALA3 37 " --> pdb=" O VALA3 13 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALAA3 54 " --> pdb=" O ARGA1 553 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HISA1 505 " --> pdb=" O GLNA1 577 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALAA1 546 " --> pdb=" O ASPA1 537 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A1' and resid 594 through 597 Processing sheet with id=AD1, first strand: chain 'A1' and resid 629 through 634 removed outlier: 7.311A pdb=" N VALA1 621 " --> pdb=" O VALA1 607 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VALA1 607 " --> pdb=" O VALA1 621 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THRA1 623 " --> pdb=" O VALA1 605 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A2' and resid 107 through 108 removed outlier: 3.577A pdb=" N ALAA2 83 " --> pdb=" O THRA2 10 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VALA2 37 " --> pdb=" O VALA2 13 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALAA2 54 " --> pdb=" O ARGA3 553 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A2' and resid 293 through 298 removed outlier: 5.599A pdb=" N PHEA2 294 " --> pdb=" O ILEA2 283 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILEA2 283 " --> pdb=" O PHEA2 294 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HISA2 214 " --> pdb=" O CYSA2 235 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLYA2 231 " --> pdb=" O GLNA2 218 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEUA2 220 " --> pdb=" O HISA2 229 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N HISA2 229 " --> pdb=" O LEUA2 220 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SERA2 236 " --> pdb=" O ILEA2 245 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILEA2 245 " --> pdb=" O SERA2 236 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLNA2 238 " --> pdb=" O LYSA2 243 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYSA2 243 " --> pdb=" O GLNA2 238 " (cutoff:3.500A) removed outlier: 13.842A pdb=" N GLNA2 242 " --> pdb=" O TYRA2 348 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N TYRA2 348 " --> pdb=" O GLNA2 242 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VALA2 244 " --> pdb=" O ARGA2 346 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SERA2 395 " --> pdb=" O VALA2 347 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A2' and resid 350 through 351 removed outlier: 3.694A pdb=" N LEUA2 357 " --> pdb=" O ASPA2 351 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A2' and resid 361 through 362 removed outlier: 3.926A pdb=" N GLYA2 361 " --> pdb=" O VALA2 386 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A2' and resid 365 through 367 removed outlier: 3.563A pdb=" N GLYA2 365 " --> pdb=" O LEUA2 421 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A2' and resid 594 through 597 Processing sheet with id=AD8, first strand: chain 'A2' and resid 629 through 634 removed outlier: 3.544A pdb=" N VALA2 622 " --> pdb=" O LEUA2 633 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VALA2 621 " --> pdb=" O VALA2 607 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VALA2 607 " --> pdb=" O VALA2 621 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THRA2 623 " --> pdb=" O VALA2 605 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A3' and resid 227 through 234 removed outlier: 5.009A pdb=" N GLNA3 218 " --> pdb=" O LEUA3 230 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLUA3 232 " --> pdb=" O GLUA3 216 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLUA3 216 " --> pdb=" O GLUA3 232 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLUA3 234 " --> pdb=" O HISA3 214 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HISA3 214 " --> pdb=" O GLUA3 234 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILEA3 283 " --> pdb=" O PHEA3 294 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHEA3 294 " --> pdb=" O ILEA3 283 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A3' and resid 238 through 239 Processing sheet with id=AE2, first strand: chain 'A3' and resid 245 through 248 removed outlier: 3.598A pdb=" N SERA3 395 " --> pdb=" O VALA3 347 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A3' and resid 350 through 351 removed outlier: 3.648A pdb=" N LEUA3 357 " --> pdb=" O ASPA3 351 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A3' and resid 361 through 362 removed outlier: 3.549A pdb=" N GLYA3 361 " --> pdb=" O VALA3 386 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A3' and resid 365 through 367 removed outlier: 3.716A pdb=" N GLYA3 365 " --> pdb=" O LEUA3 421 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A3' and resid 594 through 597 removed outlier: 6.925A pdb=" N ALAA3 594 " --> pdb=" O ARGA3 659 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARGA3 659 " --> pdb=" O ALAA3 594 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEUA3 596 " --> pdb=" O LEUA3 657 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A3' and resid 629 through 634 removed outlier: 3.540A pdb=" N VALA3 622 " --> pdb=" O LEUA3 633 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VALA3 621 " --> pdb=" O VALA3 607 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VALA3 607 " --> pdb=" O VALA3 621 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THRA3 623 " --> pdb=" O VALA3 605 " (cutoff:3.500A) 1861 hydrogen bonds defined for protein. 5139 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: 8.40 Time building geometry restraints manager: 4.61 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: 12281 1.34 - 1.46: 7945 1.46 - 1.58: 15925 1.58 - 1.71: 0 1.71 - 1.83: 237 Bond restraints: 36388 Sorted by residual: bond pdb=" C10 BTNA1 701 " pdb=" C9 BTNA1 701 " ideal model delta sigma weight residual 1.522 1.495 0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C10 BTNA2 701 " pdb=" C9 BTNA2 701 " ideal model delta sigma weight residual 1.522 1.495 0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C10 BTNA3 701 " pdb=" C9 BTNA3 701 " ideal model delta sigma weight residual 1.522 1.495 0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C10 BTNA3 701 " pdb=" C11 BTNA3 701 " ideal model delta sigma weight residual 1.544 1.518 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C10 BTNA2 701 " pdb=" C11 BTNA2 701 " ideal model delta sigma weight residual 1.544 1.518 0.026 2.00e-02 2.50e+03 1.65e+00 ... (remaining 36383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 47938 1.35 - 2.69: 1260 2.69 - 4.04: 252 4.04 - 5.39: 47 5.39 - 6.74: 28 Bond angle restraints: 49525 Sorted by residual: angle pdb=" N PROD4 144 " pdb=" CA PROD4 144 " pdb=" C PROD4 144 " ideal model delta sigma weight residual 112.47 119.12 -6.65 2.06e+00 2.36e-01 1.04e+01 angle pdb=" N PROD5 144 " pdb=" CA PROD5 144 " pdb=" C PROD5 144 " ideal model delta sigma weight residual 112.47 118.94 -6.47 2.06e+00 2.36e-01 9.86e+00 angle pdb=" N PROD1 144 " pdb=" CA PROD1 144 " pdb=" C PROD1 144 " ideal model delta sigma weight residual 112.47 118.66 -6.19 2.06e+00 2.36e-01 9.03e+00 angle pdb=" N PHED2 143 " pdb=" CA PHED2 143 " pdb=" C PHED2 143 " ideal model delta sigma weight residual 109.81 116.03 -6.22 2.21e+00 2.05e-01 7.93e+00 angle pdb=" N PROD6 144 " pdb=" CA PROD6 144 " pdb=" C PROD6 144 " ideal model delta sigma weight residual 112.47 118.15 -5.68 2.06e+00 2.36e-01 7.59e+00 ... (remaining 49520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 20109 17.86 - 35.73: 1170 35.73 - 53.59: 219 53.59 - 71.46: 96 71.46 - 89.32: 16 Dihedral angle restraints: 21610 sinusoidal: 8227 harmonic: 13383 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 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA PHED2 143 " pdb=" C PHED2 143 " pdb=" N PROD2 144 " pdb=" CA PROD2 144 " ideal model delta harmonic sigma weight residual -180.00 -155.29 -24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA PHED6 143 " pdb=" C PHED6 143 " pdb=" N PROD6 144 " pdb=" CA PROD6 144 " ideal model delta harmonic sigma weight residual 180.00 -155.54 -24.46 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 21607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3880 0.042 - 0.083: 1235 0.083 - 0.125: 462 0.125 - 0.167: 29 0.167 - 0.208: 6 Chirality restraints: 5612 Sorted by residual: chirality pdb=" CA PROD1 144 " pdb=" N PROD1 144 " pdb=" C PROD1 144 " pdb=" CB PROD1 144 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA PROD5 144 " pdb=" N PROD5 144 " pdb=" C PROD5 144 " pdb=" CB PROD5 144 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.05e+00 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 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 5609 not shown) Planarity restraints: 6565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTNA3 701 " -0.018 2.00e-02 2.50e+03 8.90e-02 1.19e+02 pdb=" C4 BTNA3 701 " 0.131 2.00e-02 2.50e+03 pdb=" C5 BTNA3 701 " -0.015 2.00e-02 2.50e+03 pdb=" N1 BTNA3 701 " -0.039 2.00e-02 2.50e+03 pdb=" N2 BTNA3 701 " -0.145 2.00e-02 2.50e+03 pdb=" O3 BTNA3 701 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTNA2 701 " -0.008 2.00e-02 2.50e+03 8.46e-02 1.07e+02 pdb=" C4 BTNA2 701 " -0.072 2.00e-02 2.50e+03 pdb=" C5 BTNA2 701 " 0.138 2.00e-02 2.50e+03 pdb=" N1 BTNA2 701 " -0.126 2.00e-02 2.50e+03 pdb=" N2 BTNA2 701 " 0.022 2.00e-02 2.50e+03 pdb=" O3 BTNA2 701 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASPD4 222 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C ASPD4 222 " -0.045 2.00e-02 2.50e+03 pdb=" O ASPD4 222 " 0.017 2.00e-02 2.50e+03 pdb=" N LEUD4 223 " 0.015 2.00e-02 2.50e+03 ... (remaining 6562 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 22516 3.05 - 3.51: 35696 3.51 - 3.97: 58189 3.97 - 4.44: 72032 4.44 - 4.90: 111976 Nonbonded interactions: 300409 Sorted by model distance: nonbonded pdb=" O TRPA2 497 " pdb=" CA ALAA2 498 " model vdw 2.583 2.776 nonbonded pdb=" O TRPA1 497 " pdb=" CA ALAA1 498 " model vdw 2.586 2.776 nonbonded pdb=" N THRA2 79 " pdb=" OG1 THRA2 79 " model vdw 2.588 2.496 nonbonded pdb=" N VALA2 272 " pdb=" N ASPA2 273 " model vdw 2.592 2.560 nonbonded pdb=" C THRA2 7 " pdb=" OG1 THRA2 7 " model vdw 2.607 2.616 ... (remaining 300404 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 7 through 135 or resid 212 through 701)) selection = chain 'A2' selection = (chain 'A3' and (resid 7 through 135 or resid 212 through 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=0.98 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: 7.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 33.960 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 : 0.006 0.055 36391 Z= 0.241 Angle : 0.573 6.737 49525 Z= 0.297 Chirality : 0.046 0.208 5612 Planarity : 0.005 0.089 6565 Dihedral : 12.714 89.324 13106 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.87 % Allowed : 5.88 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -0.01 (0.12), residues: 4738 helix: 0.45 (0.12), residues: 1883 sheet: 0.23 (0.18), residues: 766 loop : -0.38 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGA3 659 TYR 0.021 0.002 TYRD6 415 PHE 0.021 0.002 PHED5 135 TRP 0.029 0.002 TRPA2 474 HIS 0.007 0.001 HISD6 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (36388) covalent geometry : angle 0.57268 / 0.30 (49525) hydrogen bonds : bond 0.16951 / 11.61 ( 1805) hydrogen bonds : angle 6.91010 / 4.94 ( 5139) Misc. bond : bond 0.00079 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 622 time to evaluate : 1.304 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 440 LEU cc_start: 0.4957 (OUTLIER) cc_final: 0.4664 (mt) REVERT: D3 350 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: D3 366 MET cc_start: 0.8029 (tpp) cc_final: 0.7505 (tpp) REVERT: D3 464 GLU cc_start: 0.8147 (tp30) cc_final: 0.7740 (tp30) REVERT: D4 147 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8655 (m-30) REVERT: D5 435 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: D6 435 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7167 (tm130) REVERT: A1 88 TYR cc_start: 0.8247 (p90) cc_final: 0.7988 (p90) REVERT: A1 234 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A1 348 TYR cc_start: 0.7907 (m-80) cc_final: 0.7440 (m-80) REVERT: A2 46 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6449 (ttp80) REVERT: A2 232 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8660 (pm20) REVERT: A3 57 ILE cc_start: 0.8273 (pt) cc_final: 0.8067 (tt) REVERT: A3 338 LEU cc_start: 0.8373 (mt) cc_final: 0.8144 (mp) REVERT: A3 439 VAL cc_start: 0.8523 (t) cc_final: 0.8319 (m) outliers start: 104 outliers final: 18 residues processed: 702 average time/residue: 0.2556 time to fit residues: 278.1026 Evaluate side-chains 347 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 321 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 289 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 333 VAL Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D4 residue 147 ASP Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D5 residue 59 LEU Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 435 GLN Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain A1 residue 234 GLU Chi-restraints excluded: chain A1 residue 331 ILE Chi-restraints excluded: chain A1 residue 547 VAL Chi-restraints excluded: chain A2 residue 12 LEU Chi-restraints excluded: chain A2 residue 46 ARG Chi-restraints excluded: chain A2 residue 53 VAL Chi-restraints excluded: chain A2 residue 55 VAL Chi-restraints excluded: chain A2 residue 232 GLU Chi-restraints excluded: chain A3 residue 558 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [432, 197, 388, 455, 215, 20, 132, 261, 248, 207, 470] chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.0030 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1 272 GLN D3 330 ASN D3 462 GLN D4 111 HIS D4 121 ASN D4 272 GLN D4 462 GLN D5 166 GLN D5 193 ASN D6 361 ASN D6 379 HIS D6 462 GLN A1 15 ASN A1 214 HIS A1 298 ASN A1 564 GLN A2 94 ASN A2 224 HIS A3 15 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.096238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072942 restraints weight = 78328.333| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.55 r_work: 0.2983 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36391 Z= 0.118 Angle : 0.535 7.836 49525 Z= 0.278 Chirality : 0.043 0.190 5612 Planarity : 0.005 0.046 6565 Dihedral : 5.474 83.413 5293 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.37 % Allowed : 9.82 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.34 (0.12), residues: 4738 helix: 0.91 (0.12), residues: 1925 sheet: 0.34 (0.18), residues: 777 loop : -0.37 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGD3 138 TYR 0.033 0.001 TYRD4 415 PHE 0.019 0.001 PHEA3 132 TRP 0.019 0.001 TRPA1 474 HIS 0.003 0.001 HISA3 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (36388) covalent geometry : angle 0.53494 / 0.28 (49525) hydrogen bonds : bond 0.03739 / 2.58 ( 1805) hydrogen bonds : angle 5.22749 / 3.75 ( 5139) Misc. bond : bond 0.00533 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 400 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 439 VAL cc_start: 0.7713 (t) cc_final: 0.7423 (m) REVERT: D1 440 LEU cc_start: 0.4972 (OUTLIER) cc_final: 0.4546 (mt) REVERT: D2 187 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8360 (mt-10) REVERT: D3 28 GLU cc_start: 0.8393 (tp30) cc_final: 0.8174 (tt0) REVERT: D3 32 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8106 (mm-30) REVERT: D3 206 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8438 (mppt) REVERT: D3 236 HIS cc_start: 0.8096 (m90) cc_final: 0.7707 (t70) REVERT: D3 350 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.9027 (m-30) REVERT: D3 366 MET cc_start: 0.8633 (tpp) cc_final: 0.7983 (tpp) REVERT: D3 369 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7911 (ttp-170) REVERT: D3 410 MET cc_start: 0.9175 (mmm) cc_final: 0.8874 (mmm) REVERT: D4 371 TYR cc_start: 0.7354 (m-80) cc_final: 0.7134 (m-80) REVERT: D5 435 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: D6 69 ASP cc_start: 0.8254 (t0) cc_final: 0.7984 (t0) REVERT: D6 256 GLU cc_start: 0.8977 (tp30) cc_final: 0.8591 (mp0) REVERT: D6 298 ASP cc_start: 0.8699 (m-30) cc_final: 0.8329 (m-30) REVERT: D6 435 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: D6 447 MET cc_start: -0.0316 (mmt) cc_final: -0.0564 (mmt) REVERT: D6 472 SER cc_start: 0.9482 (t) cc_final: 0.9187 (p) REVERT: A1 94 ASN cc_start: 0.8522 (t0) cc_final: 0.8024 (t0) REVERT: A1 234 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: A1 297 MET cc_start: 0.7888 (ttt) cc_final: 0.7686 (ttt) REVERT: A1 348 TYR cc_start: 0.8087 (m-80) cc_final: 0.7458 (m-80) REVERT: A1 367 ARG cc_start: 0.7277 (ttt180) cc_final: 0.7031 (ttp-170) REVERT: A1 432 PHE cc_start: 0.8569 (t80) cc_final: 0.8258 (t80) REVERT: A1 552 LEU cc_start: 0.8424 (tp) cc_final: 0.8085 (mt) REVERT: A1 652 LYS cc_start: 0.5930 (mttt) cc_final: 0.5715 (mptt) REVERT: A2 122 LYS cc_start: 0.7192 (ttpp) cc_final: 0.6978 (tptp) REVERT: A3 33 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.7100 (ttt-90) REVERT: A3 77 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7061 (ptp-170) REVERT: A3 213 ARG cc_start: 0.6808 (mtt180) cc_final: 0.5669 (ttm-80) REVERT: A3 234 GLU cc_start: 0.7028 (tt0) cc_final: 0.6579 (tt0) REVERT: A3 295 MET cc_start: 0.7559 (tpp) cc_final: 0.6998 (mpp) REVERT: A3 315 ASP cc_start: 0.7188 (t0) cc_final: 0.6839 (t0) REVERT: A3 327 GLU cc_start: 0.7823 (tt0) cc_final: 0.7391 (tm-30) REVERT: A3 331 ILE cc_start: 0.8355 (pt) cc_final: 0.7852 (tp) REVERT: A3 390 TYR cc_start: 0.8321 (m-80) cc_final: 0.7891 (m-80) REVERT: A3 439 VAL cc_start: 0.8718 (t) cc_final: 0.8457 (m) REVERT: A3 629 MET cc_start: 0.3056 (OUTLIER) cc_final: 0.2761 (ttp) outliers start: 86 outliers final: 38 residues processed: 468 average time/residue: 0.2312 time to fit residues: 173.5763 Evaluate side-chains 361 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 205 VAL Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 289 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 362 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 67 MET Chi-restraints excluded: chain D3 residue 204 LEU Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D3 residue 350 ASP Chi-restraints excluded: chain D3 residue 496 SER Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 376 ILE Chi-restraints excluded: chain D5 residue 435 GLN Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 204 LEU Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain D6 residue 462 GLN Chi-restraints excluded: chain A1 residue 234 GLU Chi-restraints excluded: chain A2 residue 55 VAL Chi-restraints excluded: chain A2 residue 94 ASN Chi-restraints excluded: chain A2 residue 134 VAL Chi-restraints excluded: chain A2 residue 314 ILE Chi-restraints excluded: chain A2 residue 362 ASP Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 413 ARG Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 622 VAL Chi-restraints excluded: chain A3 residue 629 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [80, 241, 305, 287, 87, 159, 441, 394, 89, 370, 225] chunk 80 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 441 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 370 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1 462 GLN D2 330 ASN D4 272 GLN D4 462 GLN ** D5 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 34 HIS A1 505 HIS A1 650 GLN A3 512 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.070329 restraints weight = 78963.499| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.50 r_work: 0.2926 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36391 Z= 0.209 Angle : 0.556 7.311 49525 Z= 0.286 Chirality : 0.044 0.199 5612 Planarity : 0.005 0.046 6565 Dihedral : 5.017 77.303 5274 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.21 % Allowed : 11.01 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.46 (0.12), residues: 4738 helix: 1.09 (0.12), residues: 1919 sheet: 0.42 (0.18), residues: 809 loop : -0.42 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD2 391 TYR 0.023 0.002 TYRD5 415 PHE 0.023 0.002 PHEA1 429 TRP 0.018 0.001 TRPA1 474 HIS 0.006 0.001 HISD6 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (36388) covalent geometry : angle 0.55636 / 0.29 (49525) hydrogen bonds : bond 0.03771 / 2.57 ( 1805) hydrogen bonds : angle 4.98220 / 3.58 ( 5139) Misc. bond : bond 0.00100 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 347 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 69 ASP cc_start: 0.8884 (t0) cc_final: 0.8624 (t0) REVERT: D1 439 VAL cc_start: 0.7552 (t) cc_final: 0.7239 (m) REVERT: D2 9 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8894 (mm) REVERT: D2 187 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8352 (mt-10) REVERT: D3 28 GLU cc_start: 0.8483 (tp30) cc_final: 0.8219 (tt0) REVERT: D3 32 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8197 (mm-30) REVERT: D3 206 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8467 (mppt) REVERT: D3 236 HIS cc_start: 0.8100 (m90) cc_final: 0.7802 (t70) REVERT: D3 366 MET cc_start: 0.8688 (tpp) cc_final: 0.7830 (tpp) REVERT: D3 369 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8110 (ttp80) REVERT: D3 410 MET cc_start: 0.9219 (mmm) cc_final: 0.8954 (mmm) REVERT: D4 34 HIS cc_start: 0.8057 (t-90) cc_final: 0.7770 (t-90) REVERT: D4 371 TYR cc_start: 0.7409 (m-80) cc_final: 0.7136 (m-80) REVERT: D5 340 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8605 (m) REVERT: D5 435 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: D6 69 ASP cc_start: 0.8354 (t0) cc_final: 0.8057 (t0) REVERT: D6 256 GLU cc_start: 0.8968 (tp30) cc_final: 0.8598 (mp0) REVERT: D6 298 ASP cc_start: 0.8700 (m-30) cc_final: 0.8354 (m-30) REVERT: D6 431 MET cc_start: 0.8392 (ptm) cc_final: 0.8060 (ptp) REVERT: D6 435 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7432 (tm130) REVERT: A1 94 ASN cc_start: 0.8485 (t0) cc_final: 0.7899 (t0) REVERT: A1 234 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: A1 247 GLU cc_start: 0.7876 (pt0) cc_final: 0.7470 (pm20) REVERT: A1 348 TYR cc_start: 0.8230 (m-80) cc_final: 0.7708 (m-80) REVERT: A1 413 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.8068 (mmp-170) REVERT: A1 552 LEU cc_start: 0.8471 (tp) cc_final: 0.8142 (mt) REVERT: A3 82 GLN cc_start: 0.6171 (mp10) cc_final: 0.5726 (mt0) REVERT: A3 213 ARG cc_start: 0.6737 (mtt180) cc_final: 0.5582 (ttm-80) REVERT: A3 234 GLU cc_start: 0.7092 (tt0) cc_final: 0.6666 (tt0) REVERT: A3 315 ASP cc_start: 0.7253 (t0) cc_final: 0.6974 (t0) REVERT: A3 327 GLU cc_start: 0.7843 (tt0) cc_final: 0.7362 (tm-30) REVERT: A3 331 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7838 (tp) REVERT: A3 390 TYR cc_start: 0.8426 (m-80) cc_final: 0.8101 (m-80) outliers start: 80 outliers final: 56 residues processed: 403 average time/residue: 0.2175 time to fit residues: 144.0185 Evaluate side-chains 370 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 205 VAL Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 289 VAL Chi-restraints excluded: chain D1 residue 422 MET Chi-restraints excluded: chain D1 residue 428 ILE Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 24 LEU Chi-restraints excluded: chain D2 residue 212 VAL Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 67 MET Chi-restraints excluded: chain D3 residue 184 MET Chi-restraints excluded: chain D3 residue 325 VAL Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D3 residue 338 SER Chi-restraints excluded: chain D3 residue 440 LEU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D4 residue 356 LEU Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 376 ILE Chi-restraints excluded: chain D5 residue 435 GLN Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 67 MET Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 325 VAL Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain A1 residue 34 SER Chi-restraints excluded: chain A1 residue 234 GLU Chi-restraints excluded: chain A1 residue 235 CYS Chi-restraints excluded: chain A1 residue 528 HIS Chi-restraints excluded: chain A2 residue 55 VAL Chi-restraints excluded: chain A2 residue 134 VAL Chi-restraints excluded: chain A2 residue 314 ILE Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 362 ASP Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A2 residue 634 THR Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 597 VAL Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [14, 417, 76, 279, 290, 15, 261, 469, 86, 170, 395] chunk 14 optimal weight: 0.9990 chunk 417 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 261 optimal weight: 0.6980 chunk 469 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 395 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D4 121 ASN ** D5 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072376 restraints weight = 79723.827| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.51 r_work: 0.2983 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36391 Z= 0.109 Angle : 0.502 11.917 49525 Z= 0.256 Chirality : 0.043 0.255 5612 Planarity : 0.004 0.047 6565 Dihedral : 4.759 74.934 5272 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.85 % Allowed : 12.00 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.59 (0.12), residues: 4738 helix: 1.27 (0.12), residues: 1923 sheet: 0.39 (0.18), residues: 777 loop : -0.38 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGD3 444 TYR 0.030 0.001 TYRD4 415 PHE 0.024 0.001 PHEA1 429 TRP 0.017 0.001 TRPA1 474 HIS 0.003 0.001 HISA3 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (36388) covalent geometry : angle 0.50187 / 0.26 (49525) hydrogen bonds : bond 0.03088 / 2.12 ( 1805) hydrogen bonds : angle 4.68417 / 3.37 ( 5139) Misc. bond : bond 0.00020 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 69 ASP cc_start: 0.8919 (t0) cc_final: 0.8618 (t0) REVERT: D2 9 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8923 (mm) REVERT: D2 187 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D3 206 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8488 (mppt) REVERT: D3 236 HIS cc_start: 0.8090 (m90) cc_final: 0.7863 (t70) REVERT: D3 366 MET cc_start: 0.8602 (tpp) cc_final: 0.7753 (tpp) REVERT: D3 369 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8086 (ttp80) REVERT: D3 410 MET cc_start: 0.9185 (mmm) cc_final: 0.8913 (mmm) REVERT: D4 34 HIS cc_start: 0.8140 (t-90) cc_final: 0.7837 (t-90) REVERT: D4 371 TYR cc_start: 0.7533 (m-80) cc_final: 0.7252 (m-80) REVERT: D5 435 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8081 (tt0) REVERT: D6 69 ASP cc_start: 0.8279 (t0) cc_final: 0.7936 (t0) REVERT: D6 139 GLN cc_start: 0.7904 (pp30) cc_final: 0.7693 (pp30) REVERT: D6 147 ASP cc_start: 0.8613 (m-30) cc_final: 0.8318 (p0) REVERT: D6 256 GLU cc_start: 0.8867 (tp30) cc_final: 0.8639 (mp0) REVERT: D6 298 ASP cc_start: 0.8581 (m-30) cc_final: 0.8298 (m-30) REVERT: D6 431 MET cc_start: 0.8288 (ptm) cc_final: 0.7571 (ptm) REVERT: D6 435 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: A1 94 ASN cc_start: 0.8550 (t0) cc_final: 0.8033 (t0) REVERT: A1 234 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: A1 247 GLU cc_start: 0.7857 (pt0) cc_final: 0.7499 (pm20) REVERT: A1 298 ASN cc_start: 0.7985 (m110) cc_final: 0.7579 (m110) REVERT: A1 348 TYR cc_start: 0.8177 (m-80) cc_final: 0.7760 (m-80) REVERT: A1 413 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.8052 (mmp-170) REVERT: A1 523 SER cc_start: 0.8933 (m) cc_final: 0.8631 (p) REVERT: A1 552 LEU cc_start: 0.8564 (tp) cc_final: 0.8281 (mt) REVERT: A2 122 LYS cc_start: 0.6770 (tptp) cc_final: 0.6137 (ttpp) REVERT: A3 82 GLN cc_start: 0.6307 (mp10) cc_final: 0.5861 (mt0) REVERT: A3 213 ARG cc_start: 0.6883 (mtt180) cc_final: 0.5681 (ttm-80) REVERT: A3 234 GLU cc_start: 0.7116 (tt0) cc_final: 0.6703 (tt0) REVERT: A3 315 ASP cc_start: 0.7254 (t0) cc_final: 0.6762 (t0) REVERT: A3 327 GLU cc_start: 0.7814 (tt0) cc_final: 0.7362 (tm-30) REVERT: A3 331 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7902 (tp) REVERT: A3 390 TYR cc_start: 0.8446 (m-80) cc_final: 0.8153 (m-80) REVERT: A3 438 ASP cc_start: 0.6911 (p0) cc_final: 0.6652 (p0) outliers start: 67 outliers final: 43 residues processed: 401 average time/residue: 0.2135 time to fit residues: 140.2145 Evaluate side-chains 362 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 289 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 67 MET Chi-restraints excluded: chain D3 residue 184 MET Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 340 VAL Chi-restraints excluded: chain D5 residue 376 ILE Chi-restraints excluded: chain D5 residue 387 VAL Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 67 MET Chi-restraints excluded: chain D6 residue 262 VAL Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain D6 residue 504 GLU Chi-restraints excluded: chain A1 residue 234 GLU Chi-restraints excluded: chain A1 residue 241 HIS Chi-restraints excluded: chain A1 residue 331 ILE Chi-restraints excluded: chain A2 residue 94 ASN Chi-restraints excluded: chain A2 residue 134 VAL Chi-restraints excluded: chain A2 residue 314 ILE Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 413 ARG Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [180, 197, 61, 454, 96, 459, 387, 473, 168, 114, 181] chunk 180 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 459 optimal weight: 0.0570 chunk 387 optimal weight: 2.9990 chunk 473 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 181 optimal weight: 0.0370 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D3 466 GLN A2 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.072298 restraints weight = 79667.011| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.48 r_work: 0.2982 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36391 Z= 0.114 Angle : 0.501 16.318 49525 Z= 0.255 Chirality : 0.043 0.184 5612 Planarity : 0.004 0.047 6565 Dihedral : 4.460 56.776 5266 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.90 % Allowed : 12.61 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.65 (0.12), residues: 4738 helix: 1.36 (0.12), residues: 1921 sheet: 0.40 (0.18), residues: 767 loop : -0.37 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGD1 33 TYR 0.017 0.001 TYRD5 415 PHE 0.014 0.001 PHEA3 97 TRP 0.015 0.001 TRPA1 474 HIS 0.003 0.000 HISA3 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (36388) covalent geometry : angle 0.50098 / 0.25 (49525) hydrogen bonds : bond 0.03048 / 2.09 ( 1805) hydrogen bonds : angle 4.57105 / 3.29 ( 5139) Misc. bond : bond 0.00026 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 335 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 69 ASP cc_start: 0.8920 (t0) cc_final: 0.8615 (t0) REVERT: D1 460 ARG cc_start: 0.8259 (ttp-170) cc_final: 0.7917 (mtp180) REVERT: D2 9 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8942 (mm) REVERT: D2 187 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8274 (mt-10) REVERT: D3 206 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8485 (mppt) REVERT: D3 236 HIS cc_start: 0.8086 (m90) cc_final: 0.7873 (t70) REVERT: D3 366 MET cc_start: 0.8603 (tpp) cc_final: 0.7776 (tpp) REVERT: D3 369 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8072 (ttp80) REVERT: D3 410 MET cc_start: 0.9206 (mmm) cc_final: 0.8921 (mmm) REVERT: D4 34 HIS cc_start: 0.8141 (t-90) cc_final: 0.7837 (t-90) REVERT: D4 198 PHE cc_start: 0.8973 (p90) cc_final: 0.8643 (p90) REVERT: D4 371 TYR cc_start: 0.7476 (m-80) cc_final: 0.7134 (m-80) REVERT: D5 435 GLN cc_start: 0.8465 (tm-30) cc_final: 0.8052 (tt0) REVERT: D6 69 ASP cc_start: 0.8287 (t0) cc_final: 0.7922 (t0) REVERT: D6 139 GLN cc_start: 0.7820 (pp30) cc_final: 0.7583 (pp30) REVERT: D6 147 ASP cc_start: 0.8610 (m-30) cc_final: 0.8314 (p0) REVERT: D6 256 GLU cc_start: 0.8867 (tp30) cc_final: 0.8631 (mp0) REVERT: D6 298 ASP cc_start: 0.8590 (m-30) cc_final: 0.8302 (m-30) REVERT: D6 435 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: A1 94 ASN cc_start: 0.8422 (t0) cc_final: 0.7816 (t0) REVERT: A1 234 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7046 (tt0) REVERT: A1 247 GLU cc_start: 0.7832 (pt0) cc_final: 0.7457 (pm20) REVERT: A1 298 ASN cc_start: 0.8007 (m110) cc_final: 0.7583 (m110) REVERT: A1 348 TYR cc_start: 0.8152 (m-80) cc_final: 0.7717 (m-80) REVERT: A1 367 ARG cc_start: 0.7242 (ttt180) cc_final: 0.6927 (ttp-170) REVERT: A1 413 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7994 (mmp-170) REVERT: A1 523 SER cc_start: 0.8919 (m) cc_final: 0.8595 (p) REVERT: A1 552 LEU cc_start: 0.8576 (tp) cc_final: 0.8309 (mt) REVERT: A2 122 LYS cc_start: 0.6802 (tptp) cc_final: 0.6050 (ttpp) REVERT: A2 391 ASP cc_start: 0.8063 (t0) cc_final: 0.7823 (t0) REVERT: A3 33 ARG cc_start: 0.7413 (ttt-90) cc_final: 0.7169 (ttt-90) REVERT: A3 82 GLN cc_start: 0.6234 (mp10) cc_final: 0.5789 (mt0) REVERT: A3 213 ARG cc_start: 0.6884 (mtt180) cc_final: 0.5687 (ttm-80) REVERT: A3 234 GLU cc_start: 0.7028 (tt0) cc_final: 0.6630 (tt0) REVERT: A3 315 ASP cc_start: 0.7003 (t0) cc_final: 0.6694 (t0) REVERT: A3 327 GLU cc_start: 0.7842 (tt0) cc_final: 0.7376 (tm-30) REVERT: A3 331 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A3 390 TYR cc_start: 0.8479 (m-80) cc_final: 0.8203 (m-80) outliers start: 69 outliers final: 48 residues processed: 389 average time/residue: 0.2170 time to fit residues: 139.1562 Evaluate side-chains 371 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 319 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 289 VAL Chi-restraints excluded: chain D1 residue 325 VAL Chi-restraints excluded: chain D1 residue 428 ILE Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 24 LEU Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 333 VAL Chi-restraints excluded: chain D2 residue 334 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 67 MET Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D3 residue 338 SER Chi-restraints excluded: chain D4 residue 59 LEU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D5 residue 158 THR Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 376 ILE Chi-restraints excluded: chain D5 residue 387 VAL Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 67 MET Chi-restraints excluded: chain D6 residue 262 VAL Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain D6 residue 504 GLU Chi-restraints excluded: chain A1 residue 234 GLU Chi-restraints excluded: chain A2 residue 134 VAL Chi-restraints excluded: chain A2 residue 314 ILE Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [134, 186, 293, 147, 162, 313, 358, 175, 355, 35, 165] chunk 134 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 293 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 358 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 355 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A2 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.094763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.072340 restraints weight = 79327.224| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.46 r_work: 0.2983 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36391 Z= 0.117 Angle : 0.494 7.954 49525 Z= 0.252 Chirality : 0.043 0.203 5612 Planarity : 0.004 0.047 6565 Dihedral : 4.366 59.896 5266 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.79 % Allowed : 12.66 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.70 (0.12), residues: 4738 helix: 1.40 (0.12), residues: 1927 sheet: 0.46 (0.18), residues: 755 loop : -0.37 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGA3 413 TYR 0.029 0.001 TYRD4 415 PHE 0.014 0.001 PHEA3 97 TRP 0.016 0.001 TRPA1 474 HIS 0.005 0.001 HISA1 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (36388) covalent geometry : angle 0.49413 / 0.25 (49525) hydrogen bonds : bond 0.02986 / 2.04 ( 1805) hydrogen bonds : angle 4.48905 / 3.23 ( 5139) Misc. bond : bond 0.00029 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 339 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 69 ASP cc_start: 0.8938 (t0) cc_final: 0.8643 (t0) REVERT: D1 460 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7914 (mtp180) REVERT: D2 9 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8930 (mm) REVERT: D2 70 ASP cc_start: 0.8175 (t0) cc_final: 0.7962 (t0) REVERT: D2 187 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8283 (mt-10) REVERT: D3 206 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8502 (mppt) REVERT: D3 236 HIS cc_start: 0.8083 (m90) cc_final: 0.7855 (t70) REVERT: D3 366 MET cc_start: 0.8606 (tpp) cc_final: 0.8335 (tpp) REVERT: D3 369 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8038 (ttp80) REVERT: D3 410 MET cc_start: 0.9198 (mmm) cc_final: 0.8920 (mmm) REVERT: D4 34 HIS cc_start: 0.8115 (t-90) cc_final: 0.7830 (t-90) REVERT: D4 371 TYR cc_start: 0.7409 (m-80) cc_final: 0.7042 (m-80) REVERT: D5 435 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8053 (tt0) REVERT: D6 69 ASP cc_start: 0.8336 (t0) cc_final: 0.7958 (t0) REVERT: D6 139 GLN cc_start: 0.7809 (pp30) cc_final: 0.7566 (pp30) REVERT: D6 147 ASP cc_start: 0.8591 (m-30) cc_final: 0.8304 (p0) REVERT: D6 256 GLU cc_start: 0.8849 (tp30) cc_final: 0.8622 (mp0) REVERT: D6 431 MET cc_start: 0.8512 (ptm) cc_final: 0.8218 (ptp) REVERT: D6 435 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7565 (tm130) REVERT: A1 94 ASN cc_start: 0.8398 (t0) cc_final: 0.7771 (t0) REVERT: A1 247 GLU cc_start: 0.7637 (pt0) cc_final: 0.7332 (pm20) REVERT: A1 273 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7286 (t0) REVERT: A1 348 TYR cc_start: 0.8178 (m-80) cc_final: 0.7750 (m-80) REVERT: A1 367 ARG cc_start: 0.7296 (ttt180) cc_final: 0.6955 (ttp-170) REVERT: A1 396 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8269 (mttt) REVERT: A1 413 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7915 (mmp-170) REVERT: A1 523 SER cc_start: 0.8877 (m) cc_final: 0.8567 (p) REVERT: A1 552 LEU cc_start: 0.8595 (tp) cc_final: 0.8342 (mt) REVERT: A2 122 LYS cc_start: 0.6881 (tptp) cc_final: 0.6154 (ttpp) REVERT: A2 391 ASP cc_start: 0.8004 (t0) cc_final: 0.7746 (t0) REVERT: A3 33 ARG cc_start: 0.7352 (ttt-90) cc_final: 0.7058 (ttt180) REVERT: A3 50 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A3 82 GLN cc_start: 0.6276 (mp10) cc_final: 0.5809 (mt0) REVERT: A3 213 ARG cc_start: 0.6787 (mtt180) cc_final: 0.5659 (ttm-80) REVERT: A3 234 GLU cc_start: 0.7057 (tt0) cc_final: 0.6626 (tt0) REVERT: A3 315 ASP cc_start: 0.6925 (t0) cc_final: 0.6580 (t0) REVERT: A3 327 GLU cc_start: 0.7877 (tt0) cc_final: 0.7471 (tm-30) REVERT: A3 331 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A3 390 TYR cc_start: 0.8518 (m-80) cc_final: 0.8295 (m-80) outliers start: 65 outliers final: 51 residues processed: 392 average time/residue: 0.2138 time to fit residues: 138.2403 Evaluate side-chains 371 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 316 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 289 VAL Chi-restraints excluded: chain D1 residue 325 VAL Chi-restraints excluded: chain D1 residue 428 ILE Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 24 LEU Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 333 VAL Chi-restraints excluded: chain D2 residue 334 LEU Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 67 MET Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D4 residue 59 LEU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D5 residue 158 THR Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 376 ILE Chi-restraints excluded: chain D5 residue 387 VAL Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 67 MET Chi-restraints excluded: chain D6 residue 262 VAL Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain D6 residue 504 GLU Chi-restraints excluded: chain A1 residue 216 GLU Chi-restraints excluded: chain A1 residue 273 ASP Chi-restraints excluded: chain A2 residue 94 ASN Chi-restraints excluded: chain A2 residue 134 VAL Chi-restraints excluded: chain A2 residue 280 VAL Chi-restraints excluded: chain A2 residue 314 ILE Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 413 ARG Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [233, 22, 138, 83, 229, 7, 326, 196, 368, 282, 81] chunk 233 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 138 optimal weight: 0.0070 chunk 83 optimal weight: 0.3980 chunk 229 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 chunk 196 optimal weight: 0.6980 chunk 368 optimal weight: 2.9990 chunk 282 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.094711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.072051 restraints weight = 80078.367| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.49 r_work: 0.2978 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36391 Z= 0.126 Angle : 0.500 7.625 49525 Z= 0.255 Chirality : 0.043 0.193 5612 Planarity : 0.004 0.047 6565 Dihedral : 4.247 59.891 5262 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.93 % Allowed : 12.83 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.70 (0.12), residues: 4738 helix: 1.43 (0.12), residues: 1933 sheet: 0.36 (0.18), residues: 781 loop : -0.36 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGD1 33 TYR 0.016 0.001 TYRD5 415 PHE 0.013 0.001 PHEA1 356 TRP 0.015 0.001 TRPA2 474 HIS 0.004 0.001 HISA3 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (36388) covalent geometry : angle 0.49957 / 0.26 (49525) hydrogen bonds : bond 0.02992 / 2.04 ( 1805) hydrogen bonds : angle 4.45723 / 3.21 ( 5139) Misc. bond : bond 0.00031 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 329 time to evaluate : 1.046 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 69 ASP cc_start: 0.8928 (t0) cc_final: 0.8677 (t0) REVERT: D1 460 ARG cc_start: 0.8275 (ttp-170) cc_final: 0.7905 (mtp180) REVERT: D2 9 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8937 (mm) REVERT: D2 70 ASP cc_start: 0.8239 (t0) cc_final: 0.8033 (t0) REVERT: D2 77 MET cc_start: 0.9575 (OUTLIER) cc_final: 0.9314 (ttm) REVERT: D2 187 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8262 (mt-10) REVERT: D3 206 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8504 (mppt) REVERT: D3 366 MET cc_start: 0.8582 (tpp) cc_final: 0.7718 (tpp) REVERT: D3 369 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8051 (ttp80) REVERT: D3 410 MET cc_start: 0.9198 (mmm) cc_final: 0.8929 (mmm) REVERT: D4 34 HIS cc_start: 0.8165 (t-90) cc_final: 0.7860 (t-90) REVERT: D4 198 PHE cc_start: 0.8947 (p90) cc_final: 0.8636 (p90) REVERT: D5 312 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8896 (p) REVERT: D5 435 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8060 (tt0) REVERT: D5 508 TYR cc_start: 0.8957 (m-80) cc_final: 0.8752 (m-80) REVERT: D6 69 ASP cc_start: 0.8331 (t0) cc_final: 0.7958 (t0) REVERT: D6 139 GLN cc_start: 0.7737 (pp30) cc_final: 0.7496 (pp30) REVERT: D6 147 ASP cc_start: 0.8609 (m-30) cc_final: 0.8330 (p0) REVERT: D6 435 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: A1 94 ASN cc_start: 0.8359 (t0) cc_final: 0.7750 (t0) REVERT: A1 247 GLU cc_start: 0.7618 (pt0) cc_final: 0.7381 (pm20) REVERT: A1 273 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7285 (t0) REVERT: A1 348 TYR cc_start: 0.8211 (m-80) cc_final: 0.7788 (m-80) REVERT: A1 367 ARG cc_start: 0.7319 (ttt180) cc_final: 0.6999 (ttp-170) REVERT: A1 413 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7933 (mmp-170) REVERT: A1 523 SER cc_start: 0.8879 (m) cc_final: 0.8587 (p) REVERT: A1 552 LEU cc_start: 0.8619 (tp) cc_final: 0.8373 (mt) REVERT: A2 122 LYS cc_start: 0.6913 (tptp) cc_final: 0.6172 (ttpp) REVERT: A2 391 ASP cc_start: 0.7968 (t0) cc_final: 0.7605 (t0) REVERT: A3 33 ARG cc_start: 0.7239 (ttt-90) cc_final: 0.7002 (ttt180) REVERT: A3 82 GLN cc_start: 0.6317 (mp10) cc_final: 0.5850 (mt0) REVERT: A3 315 ASP cc_start: 0.6881 (t0) cc_final: 0.6529 (t0) REVERT: A3 327 GLU cc_start: 0.7876 (tt0) cc_final: 0.7473 (tm-30) REVERT: A3 331 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A3 334 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.6995 (t0) REVERT: A3 390 TYR cc_start: 0.8552 (m-80) cc_final: 0.8345 (m-80) outliers start: 70 outliers final: 53 residues processed: 382 average time/residue: 0.2116 time to fit residues: 133.9846 Evaluate side-chains 373 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 187 GLU Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 325 VAL Chi-restraints excluded: chain D1 residue 428 ILE Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 24 LEU Chi-restraints excluded: chain D2 residue 77 MET Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 333 VAL Chi-restraints excluded: chain D2 residue 334 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 67 MET Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D3 residue 338 SER Chi-restraints excluded: chain D4 residue 59 LEU Chi-restraints excluded: chain D4 residue 340 VAL Chi-restraints excluded: chain D5 residue 158 THR Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 312 THR Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 387 VAL Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 67 MET Chi-restraints excluded: chain D6 residue 262 VAL Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 429 SER Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain D6 residue 504 GLU Chi-restraints excluded: chain A1 residue 34 SER Chi-restraints excluded: chain A1 residue 273 ASP Chi-restraints excluded: chain A1 residue 434 LEU Chi-restraints excluded: chain A2 residue 134 VAL Chi-restraints excluded: chain A2 residue 280 VAL Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A2 residue 634 THR Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 334 ASP Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [2, 179, 172, 13, 121, 249, 368, 226, 49, 193, 241] chunk 2 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 172 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 368 optimal weight: 3.9990 chunk 226 optimal weight: 0.0050 chunk 49 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D6 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1 298 ASN A3 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072738 restraints weight = 79426.398| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.52 r_work: 0.2994 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36391 Z= 0.104 Angle : 0.489 7.841 49525 Z= 0.249 Chirality : 0.043 0.185 5612 Planarity : 0.004 0.047 6565 Dihedral : 4.140 56.420 5261 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.85 % Allowed : 12.94 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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 (0.12), residues: 4738 helix: 1.50 (0.12), residues: 1933 sheet: 0.41 (0.18), residues: 781 loop : -0.34 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGD3 138 TYR 0.026 0.001 TYRD4 415 PHE 0.017 0.001 PHEA1 432 TRP 0.016 0.001 TRPA1 474 HIS 0.003 0.000 HISA3 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (36388) covalent geometry : angle 0.48948 / 0.25 (49525) hydrogen bonds : bond 0.02858 / 1.95 ( 1805) hydrogen bonds : angle 4.37594 / 3.15 ( 5139) Misc. bond : bond 0.00021 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 338 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 187 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: D1 460 ARG cc_start: 0.8276 (ttp-170) cc_final: 0.7917 (mtp180) REVERT: D2 9 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8926 (mm) REVERT: D2 70 ASP cc_start: 0.8359 (t0) cc_final: 0.8102 (t0) REVERT: D2 103 TYR cc_start: 0.9200 (m-80) cc_final: 0.8936 (m-80) REVERT: D2 187 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8261 (mt-10) REVERT: D3 206 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8504 (mppt) REVERT: D3 366 MET cc_start: 0.8596 (tpp) cc_final: 0.7752 (tpp) REVERT: D4 34 HIS cc_start: 0.8127 (t-90) cc_final: 0.7801 (t-90) REVERT: D4 198 PHE cc_start: 0.8952 (p90) cc_final: 0.8621 (p90) REVERT: D4 410 MET cc_start: 0.8887 (mmm) cc_final: 0.8149 (mmm) REVERT: D5 312 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8899 (p) REVERT: D5 435 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: D6 69 ASP cc_start: 0.8346 (t0) cc_final: 0.7953 (t0) REVERT: D6 139 GLN cc_start: 0.7816 (pp30) cc_final: 0.7590 (pp30) REVERT: D6 147 ASP cc_start: 0.8591 (m-30) cc_final: 0.8315 (p0) REVERT: D6 271 ASP cc_start: 0.7947 (t0) cc_final: 0.7727 (t0) REVERT: D6 435 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: A1 94 ASN cc_start: 0.8322 (t0) cc_final: 0.7695 (t0) REVERT: A1 247 GLU cc_start: 0.7823 (pt0) cc_final: 0.7379 (pm20) REVERT: A1 348 TYR cc_start: 0.8261 (m-80) cc_final: 0.7853 (m-80) REVERT: A1 367 ARG cc_start: 0.7332 (ttt180) cc_final: 0.6995 (ttp-170) REVERT: A1 393 MET cc_start: 0.8468 (tpp) cc_final: 0.8252 (tpt) REVERT: A1 396 LYS cc_start: 0.8509 (mttt) cc_final: 0.8296 (mttm) REVERT: A1 413 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7924 (mmp-170) REVERT: A1 523 SER cc_start: 0.8855 (m) cc_final: 0.8544 (p) REVERT: A1 552 LEU cc_start: 0.8586 (tp) cc_final: 0.8345 (mt) REVERT: A2 122 LYS cc_start: 0.6904 (tptp) cc_final: 0.6164 (ttpp) REVERT: A2 391 ASP cc_start: 0.8073 (t0) cc_final: 0.7731 (t0) REVERT: A3 28 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7727 (tpp-160) REVERT: A3 33 ARG cc_start: 0.7170 (ttt-90) cc_final: 0.6968 (ttt180) REVERT: A3 50 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A3 77 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7040 (ptp-170) REVERT: A3 82 GLN cc_start: 0.6248 (mp10) cc_final: 0.5750 (mt0) REVERT: A3 315 ASP cc_start: 0.6842 (t0) cc_final: 0.6487 (t0) REVERT: A3 327 GLU cc_start: 0.7963 (tt0) cc_final: 0.7528 (tm-30) REVERT: A3 331 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7964 (tp) outliers start: 67 outliers final: 46 residues processed: 388 average time/residue: 0.2068 time to fit residues: 132.3275 Evaluate side-chains 364 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 187 GLU Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 325 VAL Chi-restraints excluded: chain D1 residue 428 ILE Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 24 LEU Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 333 VAL Chi-restraints excluded: chain D2 residue 334 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 362 ILE Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D3 residue 338 SER Chi-restraints excluded: chain D4 residue 59 LEU Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 312 THR Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 387 VAL Chi-restraints excluded: chain D5 residue 435 GLN Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 262 VAL Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 325 VAL Chi-restraints excluded: chain D6 residue 429 SER Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain D6 residue 504 GLU Chi-restraints excluded: chain A1 residue 434 LEU Chi-restraints excluded: chain A2 residue 280 VAL Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A2 residue 634 THR Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [221, 417, 330, 331, 1, 55, 312, 184, 321, 178, 392] chunk 221 optimal weight: 4.9990 chunk 417 optimal weight: 20.0000 chunk 330 optimal weight: 2.9990 chunk 331 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 312 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 178 optimal weight: 0.3980 chunk 392 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D2 330 ASN ** D3 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D6 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2 650 GLN A3 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.093489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.070940 restraints weight = 79975.627| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.48 r_work: 0.2955 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36391 Z= 0.173 Angle : 0.532 8.589 49525 Z= 0.272 Chirality : 0.044 0.192 5612 Planarity : 0.004 0.046 6565 Dihedral : 4.230 56.004 5257 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.63 % Allowed : 13.21 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.73 (0.12), residues: 4738 helix: 1.44 (0.12), residues: 1933 sheet: 0.38 (0.18), residues: 804 loop : -0.35 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGA3 233 TYR 0.021 0.001 TYRD5 415 PHE 0.018 0.001 PHEA1 432 TRP 0.013 0.001 TRPA1 474 HIS 0.003 0.001 HISD5 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (36388) covalent geometry : angle 0.53217 / 0.27 (49525) hydrogen bonds : bond 0.03242 / 2.20 ( 1805) hydrogen bonds : angle 4.49695 / 3.23 ( 5139) Misc. bond : bond 0.00071 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 321 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 187 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: D1 440 LEU cc_start: 0.4726 (OUTLIER) cc_final: 0.4437 (mt) REVERT: D2 9 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8986 (mm) REVERT: D2 70 ASP cc_start: 0.8463 (t0) cc_final: 0.8224 (t0) REVERT: D2 187 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8298 (mt-10) REVERT: D3 88 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7295 (mm-30) REVERT: D3 206 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8518 (mppt) REVERT: D3 366 MET cc_start: 0.8659 (tpp) cc_final: 0.7814 (tpp) REVERT: D3 410 MET cc_start: 0.9112 (mmm) cc_final: 0.8849 (mmm) REVERT: D4 34 HIS cc_start: 0.8143 (t-90) cc_final: 0.7835 (t-90) REVERT: D5 312 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8910 (p) REVERT: D5 435 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: D6 69 ASP cc_start: 0.8398 (t0) cc_final: 0.8017 (t0) REVERT: D6 139 GLN cc_start: 0.7748 (pp30) cc_final: 0.7486 (pp30) REVERT: D6 147 ASP cc_start: 0.8613 (m-30) cc_final: 0.8334 (p0) REVERT: D6 435 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: A1 94 ASN cc_start: 0.8346 (t0) cc_final: 0.7729 (t0) REVERT: A1 245 ILE cc_start: 0.9213 (mt) cc_final: 0.9011 (mm) REVERT: A1 247 GLU cc_start: 0.7812 (pt0) cc_final: 0.7360 (pm20) REVERT: A1 273 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7347 (t0) REVERT: A1 298 ASN cc_start: 0.7962 (m110) cc_final: 0.7740 (m110) REVERT: A1 348 TYR cc_start: 0.8376 (m-80) cc_final: 0.7809 (m-80) REVERT: A1 367 ARG cc_start: 0.7403 (ttt180) cc_final: 0.7154 (ttp-170) REVERT: A1 413 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7965 (mmp-170) REVERT: A1 523 SER cc_start: 0.8941 (m) cc_final: 0.8625 (p) REVERT: A1 552 LEU cc_start: 0.8621 (tp) cc_final: 0.8359 (mt) REVERT: A1 631 HIS cc_start: 0.6845 (t70) cc_final: 0.6392 (t70) REVERT: A2 122 LYS cc_start: 0.6880 (tptp) cc_final: 0.6184 (ttpp) REVERT: A2 391 ASP cc_start: 0.8072 (t0) cc_final: 0.7731 (t0) REVERT: A3 33 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.7005 (ttt180) REVERT: A3 77 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7354 (mtm-85) REVERT: A3 82 GLN cc_start: 0.6281 (mp10) cc_final: 0.5816 (mt0) REVERT: A3 315 ASP cc_start: 0.6881 (t0) cc_final: 0.6380 (t0) REVERT: A3 327 GLU cc_start: 0.7915 (tt0) cc_final: 0.7500 (tm-30) REVERT: A3 331 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7927 (tp) outliers start: 59 outliers final: 48 residues processed: 369 average time/residue: 0.2188 time to fit residues: 132.8199 Evaluate side-chains 362 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 187 GLU Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 428 ILE Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 24 LEU Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 333 VAL Chi-restraints excluded: chain D2 residue 334 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 362 ILE Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D4 residue 59 LEU Chi-restraints excluded: chain D5 residue 158 THR Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 312 THR Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 387 VAL Chi-restraints excluded: chain D5 residue 435 GLN Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 262 VAL Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 325 VAL Chi-restraints excluded: chain D6 residue 429 SER Chi-restraints excluded: chain D6 residue 435 GLN Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain D6 residue 504 GLU Chi-restraints excluded: chain A1 residue 273 ASP Chi-restraints excluded: chain A1 residue 434 LEU Chi-restraints excluded: chain A2 residue 280 VAL Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A2 residue 634 THR Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 334 ASP Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 413 ARG Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [332, 348, 364, 380, 43, 206, 191, 205, 147, 354, 430] chunk 332 optimal weight: 0.3980 chunk 348 optimal weight: 6.9990 chunk 364 optimal weight: 0.2980 chunk 380 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 206 optimal weight: 0.0030 chunk 191 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 354 optimal weight: 0.6980 chunk 430 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D3 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D6 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.095187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072739 restraints weight = 79802.604| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.50 r_work: 0.2994 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 36391 Z= 0.097 Angle : 0.497 9.122 49525 Z= 0.254 Chirality : 0.043 0.181 5612 Planarity : 0.004 0.047 6565 Dihedral : 4.121 54.103 5257 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.46 % Allowed : 13.66 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.84 (0.12), residues: 4738 helix: 1.56 (0.12), residues: 1933 sheet: 0.40 (0.18), residues: 800 loop : -0.30 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGA2 63 TYR 0.025 0.001 TYRD4 415 PHE 0.019 0.001 PHEA1 432 TRP 0.017 0.001 TRPA1 474 HIS 0.003 0.000 HISA3 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (36388) covalent geometry : angle 0.49689 / 0.25 (49525) hydrogen bonds : bond 0.02855 / 1.95 ( 1805) hydrogen bonds : angle 4.35138 / 3.14 ( 5139) Misc. bond : bond 0.00014 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9476 Ramachandran restraints generated. 4738 Oldfield, 0 Emsley, 4738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 325 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D1 187 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: D1 440 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4391 (mt) REVERT: D2 9 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8926 (mm) REVERT: D2 70 ASP cc_start: 0.8503 (t0) cc_final: 0.8265 (t0) REVERT: D2 187 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D3 88 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D3 206 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8506 (mppt) REVERT: D3 366 MET cc_start: 0.8626 (tpp) cc_final: 0.7774 (tpp) REVERT: D3 410 MET cc_start: 0.9070 (mmm) cc_final: 0.8780 (mmm) REVERT: D4 34 HIS cc_start: 0.8100 (t-90) cc_final: 0.7775 (t-90) REVERT: D4 198 PHE cc_start: 0.8912 (p90) cc_final: 0.8673 (p90) REVERT: D4 410 MET cc_start: 0.8862 (mmm) cc_final: 0.8134 (mmm) REVERT: D5 312 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8909 (p) REVERT: D5 435 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7957 (tt0) REVERT: D6 69 ASP cc_start: 0.8405 (t0) cc_final: 0.8018 (t0) REVERT: D6 139 GLN cc_start: 0.7954 (pp30) cc_final: 0.7737 (pp30) REVERT: D6 147 ASP cc_start: 0.8585 (m-30) cc_final: 0.8263 (p0) REVERT: D6 435 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A1 94 ASN cc_start: 0.8318 (t0) cc_final: 0.7688 (t0) REVERT: A1 247 GLU cc_start: 0.7737 (pt0) cc_final: 0.7335 (pm20) REVERT: A1 298 ASN cc_start: 0.7908 (m110) cc_final: 0.7677 (m110) REVERT: A1 348 TYR cc_start: 0.8247 (m-80) cc_final: 0.7793 (m-80) REVERT: A1 367 ARG cc_start: 0.7333 (ttt180) cc_final: 0.7094 (ttp-170) REVERT: A1 396 LYS cc_start: 0.8515 (mttt) cc_final: 0.8241 (mttm) REVERT: A1 413 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7926 (mmp-170) REVERT: A1 523 SER cc_start: 0.8889 (m) cc_final: 0.8559 (p) REVERT: A1 552 LEU cc_start: 0.8574 (tp) cc_final: 0.8327 (mt) REVERT: A1 631 HIS cc_start: 0.6838 (t70) cc_final: 0.6374 (t70) REVERT: A2 122 LYS cc_start: 0.6722 (tptp) cc_final: 0.6022 (ttpp) REVERT: A2 391 ASP cc_start: 0.8064 (t0) cc_final: 0.7724 (t0) REVERT: A3 28 ARG cc_start: 0.8155 (ttm170) cc_final: 0.7731 (tpp-160) REVERT: A3 77 ARG cc_start: 0.7980 (tpp80) cc_final: 0.7306 (mtm-85) REVERT: A3 82 GLN cc_start: 0.6225 (mp10) cc_final: 0.5727 (mt0) REVERT: A3 315 ASP cc_start: 0.6842 (t0) cc_final: 0.6364 (t0) REVERT: A3 327 GLU cc_start: 0.7995 (tt0) cc_final: 0.7560 (tm-30) REVERT: A3 331 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A3 427 ILE cc_start: 0.8649 (mm) cc_final: 0.8401 (mm) outliers start: 53 outliers final: 46 residues processed: 367 average time/residue: 0.2158 time to fit residues: 131.0134 Evaluate side-chains 365 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D1 residue 7 GLU Chi-restraints excluded: chain D1 residue 59 LEU Chi-restraints excluded: chain D1 residue 187 GLU Chi-restraints excluded: chain D1 residue 269 ILE Chi-restraints excluded: chain D1 residue 325 VAL Chi-restraints excluded: chain D1 residue 440 LEU Chi-restraints excluded: chain D2 residue 9 LEU Chi-restraints excluded: chain D2 residue 24 LEU Chi-restraints excluded: chain D2 residue 261 GLN Chi-restraints excluded: chain D2 residue 269 ILE Chi-restraints excluded: chain D2 residue 289 VAL Chi-restraints excluded: chain D2 residue 333 VAL Chi-restraints excluded: chain D2 residue 334 LEU Chi-restraints excluded: chain D2 residue 340 VAL Chi-restraints excluded: chain D2 residue 362 ILE Chi-restraints excluded: chain D2 residue 428 ILE Chi-restraints excluded: chain D2 residue 440 LEU Chi-restraints excluded: chain D2 residue 489 THR Chi-restraints excluded: chain D3 residue 59 LEU Chi-restraints excluded: chain D3 residue 333 VAL Chi-restraints excluded: chain D4 residue 59 LEU Chi-restraints excluded: chain D5 residue 175 THR Chi-restraints excluded: chain D5 residue 289 VAL Chi-restraints excluded: chain D5 residue 312 THR Chi-restraints excluded: chain D5 residue 333 VAL Chi-restraints excluded: chain D5 residue 376 ILE Chi-restraints excluded: chain D5 residue 387 VAL Chi-restraints excluded: chain D5 residue 442 THR Chi-restraints excluded: chain D6 residue 59 LEU Chi-restraints excluded: chain D6 residue 262 VAL Chi-restraints excluded: chain D6 residue 289 VAL Chi-restraints excluded: chain D6 residue 429 SER Chi-restraints excluded: chain D6 residue 476 LEU Chi-restraints excluded: chain D6 residue 504 GLU Chi-restraints excluded: chain A1 residue 434 LEU Chi-restraints excluded: chain A2 residue 280 VAL Chi-restraints excluded: chain A2 residue 331 ILE Chi-restraints excluded: chain A2 residue 516 THR Chi-restraints excluded: chain A2 residue 530 ASP Chi-restraints excluded: chain A2 residue 634 THR Chi-restraints excluded: chain A3 residue 10 THR Chi-restraints excluded: chain A3 residue 30 MET Chi-restraints excluded: chain A3 residue 130 SER Chi-restraints excluded: chain A3 residue 308 THR Chi-restraints excluded: chain A3 residue 331 ILE Chi-restraints excluded: chain A3 residue 334 ASP Chi-restraints excluded: chain A3 residue 341 HIS Chi-restraints excluded: chain A3 residue 505 HIS Chi-restraints excluded: chain A3 residue 516 THR Chi-restraints excluded: chain A3 residue 558 VAL Chi-restraints excluded: chain A3 residue 622 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: [290, 366, 256, 75, 354, 283, 49, 300, 34, 55, 464] chunk 290 optimal weight: 0.9980 chunk 366 optimal weight: 0.8980 chunk 256 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 283 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 464 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D3 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.072564 restraints weight = 79298.005| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.49 r_work: 0.2991 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36391 Z= 0.112 Angle : 0.499 9.055 49525 Z= 0.255 Chirality : 0.043 0.178 5612 Planarity : 0.004 0.047 6565 Dihedral : 3.995 37.621 5254 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.54 % Allowed : 13.68 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.88 (0.12), residues: 4738 helix: 1.58 (0.12), residues: 1936 sheet: 0.47 (0.18), residues: 786 loop : -0.30 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGA3 33 TYR 0.021 0.001 TYRD1 415 PHE 0.019 0.001 PHEA1 432 TRP 0.016 0.001 TRPA1 474 HIS 0.003 0.000 HISA3 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (36388) covalent geometry : angle 0.49950 / 0.25 (49525) hydrogen bonds : bond 0.02888 / 1.97 ( 1805) hydrogen bonds : angle 4.33358 / 3.12 ( 5139) Misc. bond : bond 0.00024 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9996.98 seconds wall clock time: 171 minutes 10.82 seconds (10270.82 seconds total)