Starting phenix.real_space_refine on Sun Jul 5 20:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nal_24273/07_2026/7nal_24273.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nal_24273/07_2026/7nal_24273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nal_24273/07_2026/7nal_24273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nal_24273/07_2026/7nal_24273.map" model { file = "/net/cci-nas-00/data/ceres_data/7nal_24273/07_2026/7nal_24273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nal_24273/07_2026/7nal_24273.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 136 5.16 5 C 19056 2.51 5 N 5544 2.21 5 O 5656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30400 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "B" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "C" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "D" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "E" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "F" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "G" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "H" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.15, per 1000 atoms: 0.20 Number of scatterers: 30400 At special positions: 0 Unit cell: (194.394, 194.394, 70.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 8 15.00 O 5656 8.00 N 5544 7.00 C 19056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7232 Finding SS restraints... Secondary structure from input PDB file: 313 helices and 0 sheets defined 83.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 62 through 81 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.643A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 122 removed outlier: 4.368A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.764A pdb=" N GLN A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.991A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 219 through 237 Processing helix chain 'A' and resid 238 through 249 Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.605A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.679A pdb=" N ARG A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 291 through 294 removed outlier: 3.707A pdb=" N ALA A 294 " --> pdb=" O GLY A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.702A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 323 through 331 removed outlier: 3.568A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 338 through 360 removed outlier: 3.547A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.063A pdb=" N SER A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.605A pdb=" N GLU A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 4.072A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 4.320A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.552A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 543 Processing helix chain 'B' and resid 62 through 82 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 84 through 104 Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.797A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.825A pdb=" N GLN B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 3.981A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 219 through 237 Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.645A pdb=" N TRP B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 254' Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 263 through 279 removed outlier: 3.643A pdb=" N ARG B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 291 through 294 removed outlier: 3.695A pdb=" N ALA B 294 " --> pdb=" O GLY B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 294' Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.681A pdb=" N LEU B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.567A pdb=" N GLN B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 336 Processing helix chain 'B' and resid 338 through 360 removed outlier: 3.527A pdb=" N LEU B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 4.061A pdb=" N SER B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 384 through 397 Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 447 through 454 Processing helix chain 'B' and resid 459 through 476 removed outlier: 3.570A pdb=" N GLU B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.080A pdb=" N TRP B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 4.468A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.586A pdb=" N ARG B 517 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 531 through 543 Processing helix chain 'C' and resid 62 through 81 Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 84 through 104 removed outlier: 3.527A pdb=" N ALA C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 122 removed outlier: 4.312A pdb=" N LEU C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.776A pdb=" N GLN C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 removed outlier: 4.514A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 219 through 237 Processing helix chain 'C' and resid 238 through 248 Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.688A pdb=" N TRP C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 254' Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 263 through 279 removed outlier: 3.681A pdb=" N ARG C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 291 through 294 removed outlier: 3.704A pdb=" N ALA C 294 " --> pdb=" O GLY C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 294' Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.697A pdb=" N LEU C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER C 302 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 311 Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.596A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 336 Processing helix chain 'C' and resid 338 through 360 removed outlier: 3.540A pdb=" N LEU C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.030A pdb=" N SER C 366 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 380 Processing helix chain 'C' and resid 384 through 397 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 413 through 424 Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 447 through 454 Processing helix chain 'C' and resid 459 through 476 removed outlier: 3.626A pdb=" N GLU C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 495 removed outlier: 4.085A pdb=" N TRP C 490 " --> pdb=" O ASN C 486 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 4.343A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.557A pdb=" N ARG C 517 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 531 through 543 Processing helix chain 'D' and resid 62 through 81 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 84 through 104 Processing helix chain 'D' and resid 108 through 122 removed outlier: 3.800A pdb=" N LEU D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 137 through 150 removed outlier: 3.785A pdb=" N GLN D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.971A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 219 through 237 Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.750A pdb=" N TRP D 253 " --> pdb=" O ARG D 249 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 254' Processing helix chain 'D' and resid 254 through 260 Processing helix chain 'D' and resid 263 through 279 removed outlier: 3.637A pdb=" N ARG D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 291 through 294 removed outlier: 3.699A pdb=" N ALA D 294 " --> pdb=" O GLY D 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 291 through 294' Processing helix chain 'D' and resid 295 through 301 removed outlier: 3.684A pdb=" N LEU D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 311 Processing helix chain 'D' and resid 315 through 319 removed outlier: 3.605A pdb=" N THR D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 removed outlier: 3.563A pdb=" N GLN D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 Processing helix chain 'D' and resid 338 through 360 removed outlier: 3.527A pdb=" N LEU D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 368 removed outlier: 4.063A pdb=" N SER D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 380 Processing helix chain 'D' and resid 384 through 397 Processing helix chain 'D' and resid 408 through 412 Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 426 through 428 No H-bonds generated for 'chain 'D' and resid 426 through 428' Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'D' and resid 459 through 476 removed outlier: 3.584A pdb=" N GLU D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 495 removed outlier: 4.067A pdb=" N TRP D 490 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 removed outlier: 4.416A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 507 Processing helix chain 'D' and resid 514 through 518 removed outlier: 3.589A pdb=" N ARG D 517 " --> pdb=" O LEU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 531 through 543 Processing helix chain 'E' and resid 62 through 81 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 84 through 104 removed outlier: 3.593A pdb=" N ALA E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 122 removed outlier: 4.370A pdb=" N LEU E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 137 through 150 removed outlier: 3.919A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 163 removed outlier: 3.998A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 172 Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 219 through 237 Processing helix chain 'E' and resid 238 through 249 Processing helix chain 'E' and resid 249 through 254 removed outlier: 3.572A pdb=" N LEU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 260 Processing helix chain 'E' and resid 263 through 279 removed outlier: 3.668A pdb=" N ARG E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 291 through 294 removed outlier: 3.708A pdb=" N ALA E 294 " --> pdb=" O GLY E 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.696A pdb=" N LEU E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER E 302 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 311 Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.568A pdb=" N GLN E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 336 Processing helix chain 'E' and resid 338 through 360 removed outlier: 3.553A pdb=" N LEU E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 368 removed outlier: 4.056A pdb=" N SER E 366 " --> pdb=" O THR E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 380 Processing helix chain 'E' and resid 384 through 398 Processing helix chain 'E' and resid 408 through 412 Processing helix chain 'E' and resid 413 through 424 Processing helix chain 'E' and resid 426 through 428 No H-bonds generated for 'chain 'E' and resid 426 through 428' Processing helix chain 'E' and resid 429 through 436 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 447 through 454 Processing helix chain 'E' and resid 459 through 476 removed outlier: 3.612A pdb=" N GLU E 472 " --> pdb=" O ARG E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 495 removed outlier: 4.065A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 500 removed outlier: 4.497A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.565A pdb=" N ARG E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 526 Processing helix chain 'E' and resid 531 through 543 Processing helix chain 'F' and resid 62 through 81 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 84 through 104 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 137 through 150 removed outlier: 3.833A pdb=" N GLN F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 163 removed outlier: 3.943A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 172 Processing helix chain 'F' and resid 177 through 192 Processing helix chain 'F' and resid 195 through 205 Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 219 through 237 Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 249 through 254 removed outlier: 3.597A pdb=" N TRP F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 249 through 254' Processing helix chain 'F' and resid 254 through 260 Processing helix chain 'F' and resid 263 through 279 removed outlier: 3.640A pdb=" N ARG F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 291 through 294 removed outlier: 3.700A pdb=" N ALA F 294 " --> pdb=" O GLY F 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 291 through 294' Processing helix chain 'F' and resid 295 through 301 removed outlier: 3.674A pdb=" N LEU F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 311 Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.584A pdb=" N GLN F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 336 Processing helix chain 'F' and resid 338 through 360 removed outlier: 3.527A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 368 removed outlier: 4.061A pdb=" N SER F 366 " --> pdb=" O THR F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 380 Processing helix chain 'F' and resid 384 through 397 Processing helix chain 'F' and resid 408 through 412 Processing helix chain 'F' and resid 413 through 425 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 429 through 437 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 447 through 454 Processing helix chain 'F' and resid 459 through 476 removed outlier: 3.562A pdb=" N GLU F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 486 through 495 removed outlier: 4.087A pdb=" N TRP F 490 " --> pdb=" O ASN F 486 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 4.379A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.591A pdb=" N ARG F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 526 Processing helix chain 'F' and resid 531 through 543 Processing helix chain 'G' and resid 62 through 81 Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 84 through 104 removed outlier: 3.600A pdb=" N ALA G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 removed outlier: 4.315A pdb=" N LEU G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 134 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.876A pdb=" N GLN G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 removed outlier: 4.106A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL G 160 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 172 Processing helix chain 'G' and resid 177 through 192 Processing helix chain 'G' and resid 195 through 205 Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 219 through 237 Processing helix chain 'G' and resid 238 through 248 Processing helix chain 'G' and resid 249 through 254 removed outlier: 3.574A pdb=" N LEU G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 260 Processing helix chain 'G' and resid 263 through 279 removed outlier: 3.659A pdb=" N ARG G 267 " --> pdb=" O ASP G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 282 No H-bonds generated for 'chain 'G' and resid 280 through 282' Processing helix chain 'G' and resid 283 through 290 Processing helix chain 'G' and resid 291 through 294 removed outlier: 3.762A pdb=" N ALA G 294 " --> pdb=" O GLY G 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 291 through 294' Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.697A pdb=" N LEU G 299 " --> pdb=" O LEU G 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER G 302 " --> pdb=" O PRO G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 311 Processing helix chain 'G' and resid 323 through 331 removed outlier: 3.622A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 336 Processing helix chain 'G' and resid 338 through 360 removed outlier: 3.547A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 368 removed outlier: 4.004A pdb=" N SER G 366 " --> pdb=" O THR G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 380 Processing helix chain 'G' and resid 384 through 397 Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 413 through 424 Processing helix chain 'G' and resid 426 through 428 No H-bonds generated for 'chain 'G' and resid 426 through 428' Processing helix chain 'G' and resid 429 through 436 Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 447 through 454 Processing helix chain 'G' and resid 459 through 476 removed outlier: 3.600A pdb=" N GLU G 472 " --> pdb=" O ARG G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 495 removed outlier: 4.072A pdb=" N TRP G 490 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 500 removed outlier: 4.436A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 507 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.553A pdb=" N ARG G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 526 Processing helix chain 'G' and resid 531 through 543 Processing helix chain 'H' and resid 62 through 82 Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 84 through 104 Processing helix chain 'H' and resid 108 through 122 removed outlier: 3.695A pdb=" N LEU H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 134 Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.794A pdb=" N GLN H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 163 removed outlier: 4.018A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 172 Processing helix chain 'H' and resid 177 through 192 Processing helix chain 'H' and resid 195 through 205 Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 219 through 237 Processing helix chain 'H' and resid 238 through 248 Processing helix chain 'H' and resid 249 through 254 removed outlier: 3.617A pdb=" N TRP H 253 " --> pdb=" O ARG H 249 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU H 254 " --> pdb=" O ALA H 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 249 through 254' Processing helix chain 'H' and resid 254 through 260 Processing helix chain 'H' and resid 263 through 279 removed outlier: 3.637A pdb=" N ARG H 267 " --> pdb=" O ASP H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 282 No H-bonds generated for 'chain 'H' and resid 280 through 282' Processing helix chain 'H' and resid 283 through 290 Processing helix chain 'H' and resid 291 through 294 removed outlier: 3.693A pdb=" N ALA H 294 " --> pdb=" O GLY H 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 291 through 294' Processing helix chain 'H' and resid 295 through 303 removed outlier: 3.679A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER H 302 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 311 Processing helix chain 'H' and resid 323 through 329 removed outlier: 3.594A pdb=" N GLN H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 336 Processing helix chain 'H' and resid 338 through 360 removed outlier: 3.528A pdb=" N LEU H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 368 removed outlier: 4.051A pdb=" N SER H 366 " --> pdb=" O THR H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 380 Processing helix chain 'H' and resid 384 through 397 Processing helix chain 'H' and resid 408 through 412 Processing helix chain 'H' and resid 413 through 425 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 429 through 436 Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 459 through 476 removed outlier: 3.572A pdb=" N GLU H 472 " --> pdb=" O ARG H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 495 removed outlier: 4.065A pdb=" N TRP H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 4.414A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 507 Processing helix chain 'H' and resid 514 through 518 removed outlier: 3.586A pdb=" N ARG H 517 " --> pdb=" O LEU H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 519 through 526 Processing helix chain 'H' and resid 531 through 543 1872 hydrogen bonds defined for protein. 5439 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5198 1.32 - 1.44: 7456 1.44 - 1.57: 18010 1.57 - 1.69: 8 1.69 - 1.81: 168 Bond restraints: 30840 Sorted by residual: bond pdb=" O5R NMN G 801 " pdb=" P NMN G 801 " ideal model delta sigma weight residual 1.730 1.626 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" O5R NMN F 801 " pdb=" P NMN F 801 " ideal model delta sigma weight residual 1.730 1.626 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" O5R NMN E 801 " pdb=" P NMN E 801 " ideal model delta sigma weight residual 1.730 1.626 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" O5R NMN B 801 " pdb=" P NMN B 801 " ideal model delta sigma weight residual 1.730 1.626 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O5R NMN D 801 " pdb=" P NMN D 801 " ideal model delta sigma weight residual 1.730 1.627 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 30835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 38710 1.49 - 2.97: 2403 2.97 - 4.46: 507 4.46 - 5.95: 67 5.95 - 7.43: 17 Bond angle restraints: 41704 Sorted by residual: angle pdb=" CA ASP G 483 " pdb=" CB ASP G 483 " pdb=" CG ASP G 483 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" N ASP C 326 " pdb=" CA ASP C 326 " pdb=" C ASP C 326 " ideal model delta sigma weight residual 113.28 108.43 4.85 1.22e+00 6.72e-01 1.58e+01 angle pdb=" N VAL A 211 " pdb=" CA VAL A 211 " pdb=" C VAL A 211 " ideal model delta sigma weight residual 110.72 106.71 4.01 1.01e+00 9.80e-01 1.57e+01 angle pdb=" N ASP H 326 " pdb=" CA ASP H 326 " pdb=" C ASP H 326 " ideal model delta sigma weight residual 113.28 108.53 4.75 1.22e+00 6.72e-01 1.51e+01 angle pdb=" CA PRO H 106 " pdb=" C PRO H 106 " pdb=" O PRO H 106 " ideal model delta sigma weight residual 121.23 117.07 4.16 1.07e+00 8.73e-01 1.51e+01 ... (remaining 41699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 17532 17.23 - 34.45: 1284 34.45 - 51.68: 191 51.68 - 68.90: 35 68.90 - 86.13: 14 Dihedral angle restraints: 19056 sinusoidal: 7888 harmonic: 11168 Sorted by residual: dihedral pdb=" C ASP G 483 " pdb=" N ASP G 483 " pdb=" CA ASP G 483 " pdb=" CB ASP G 483 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA LEU G 406 " pdb=" C LEU G 406 " pdb=" N PRO G 407 " pdb=" CA PRO G 407 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LEU A 406 " pdb=" C LEU A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 19053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3984 0.050 - 0.101: 588 0.101 - 0.151: 187 0.151 - 0.201: 46 0.201 - 0.252: 11 Chirality restraints: 4816 Sorted by residual: chirality pdb=" CG LEU A 105 " pdb=" CB LEU A 105 " pdb=" CD1 LEU A 105 " pdb=" CD2 LEU A 105 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL B 364 " pdb=" CA VAL B 364 " pdb=" CG1 VAL B 364 " pdb=" CG2 VAL B 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP G 483 " pdb=" N ASP G 483 " pdb=" C ASP G 483 " pdb=" CB ASP G 483 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4813 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 214 " 0.019 2.00e-02 2.50e+03 1.71e-02 7.29e+00 pdb=" CG TRP E 214 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP E 214 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 214 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 214 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 214 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 214 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 214 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 328 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" C GLN A 328 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN A 328 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 329 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 214 " 0.018 2.00e-02 2.50e+03 1.58e-02 6.26e+00 pdb=" CG TRP B 214 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 214 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 214 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 214 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 214 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 214 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 214 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 214 " -0.000 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2679 2.74 - 3.28: 31650 3.28 - 3.82: 47728 3.82 - 4.36: 59759 4.36 - 4.90: 101263 Nonbonded interactions: 243079 Sorted by model distance: nonbonded pdb=" OD1 ASP B 441 " pdb=" OH TYR B 503 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP H 441 " pdb=" OH TYR H 503 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP F 441 " pdb=" OH TYR F 503 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP D 441 " pdb=" OH TYR D 503 " model vdw 2.199 3.040 nonbonded pdb=" O ASP B 483 " pdb=" OD1 ASP B 483 " model vdw 2.216 3.040 ... (remaining 243074 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 : 0.005 0.104 30840 Z= 0.369 Angle : 0.794 7.434 41704 Z= 0.532 Chirality : 0.044 0.252 4816 Planarity : 0.004 0.045 5424 Dihedral : 12.114 86.127 11824 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 3872 helix: 1.37 (0.10), residues: 2792 sheet: None (None), residues: 0 loop : 0.23 (0.22), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 244 TYR 0.008 0.001 TYR C 348 PHE 0.011 0.001 PHE E 192 TRP 0.046 0.002 TRP E 214 HIS 0.008 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.37 (30840) covalent geometry : angle 0.79406 / 0.53 (41704) hydrogen bonds : bond 0.16317 / 11.09 ( 1872) hydrogen bonds : angle 5.67196 / 4.06 ( 5439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 1.277 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8121 (tt0) cc_final: 0.7775 (pp30) REVERT: B 239 GLN cc_start: 0.8032 (tt0) cc_final: 0.7746 (pp30) REVERT: C 239 GLN cc_start: 0.8058 (tt0) cc_final: 0.7691 (tm-30) REVERT: C 253 TRP cc_start: 0.6694 (m100) cc_final: 0.5766 (m100) REVERT: E 239 GLN cc_start: 0.8106 (tt0) cc_final: 0.7771 (pp30) REVERT: F 239 GLN cc_start: 0.8117 (tt0) cc_final: 0.7788 (pp30) REVERT: G 239 GLN cc_start: 0.8146 (tt0) cc_final: 0.7787 (pp30) REVERT: H 239 GLN cc_start: 0.7959 (tt0) cc_final: 0.7657 (pp30) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.6946 time to fit residues: 369.5514 Evaluate side-chains 301 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 190 HIS A 200 GLN A 239 GLN A 478 ASN A 521 GLN B 134 GLN B 337 ASN C 134 GLN C 190 HIS C 200 GLN C 239 GLN C 478 ASN C 521 GLN D 134 GLN D 337 ASN D 521 GLN E 190 HIS E 239 GLN E 478 ASN E 500 GLN E 521 GLN F 134 GLN F 337 ASN F 521 GLN G 134 GLN G 190 HIS G 239 GLN G 478 ASN G 500 GLN G 521 GLN H 134 GLN H 337 ASN H 521 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.207865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151936 restraints weight = 34159.031| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.78 r_work: 0.3455 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 30840 Z= 0.242 Angle : 0.672 7.334 41704 Z= 0.332 Chirality : 0.041 0.149 4816 Planarity : 0.004 0.042 5424 Dihedral : 6.157 48.194 4528 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.74 % Allowed : 8.38 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.14), residues: 3872 helix: 1.05 (0.10), residues: 2896 sheet: None (None), residues: 0 loop : 0.44 (0.23), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 310 TYR 0.009 0.002 TYR B 429 PHE 0.013 0.002 PHE H 192 TRP 0.026 0.002 TRP B 214 HIS 0.008 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.24 (30840) covalent geometry : angle 0.67193 / 0.33 (41704) hydrogen bonds : bond 0.05125 / 3.52 ( 1872) hydrogen bonds : angle 4.53827 / 3.27 ( 5439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 357 time to evaluate : 1.039 Fit side-chains REVERT: A 104 LEU cc_start: 0.8205 (mp) cc_final: 0.8005 (mp) REVERT: A 159 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6899 (mtp85) REVERT: A 244 ARG cc_start: 0.8111 (tmt-80) cc_final: 0.7609 (tmt-80) REVERT: A 282 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 156 ASN cc_start: 0.8174 (m110) cc_final: 0.7702 (m-40) REVERT: B 239 GLN cc_start: 0.8336 (tt0) cc_final: 0.7440 (pp30) REVERT: B 244 ARG cc_start: 0.8125 (tmt-80) cc_final: 0.7712 (tmt-80) REVERT: B 318 THR cc_start: 0.8481 (p) cc_final: 0.8005 (t) REVERT: C 126 LEU cc_start: 0.7865 (tp) cc_final: 0.7412 (tm) REVERT: C 159 ARG cc_start: 0.7333 (mtp85) cc_final: 0.7079 (mtp85) REVERT: C 239 GLN cc_start: 0.8097 (tt0) cc_final: 0.7157 (pp30) REVERT: C 253 TRP cc_start: 0.7411 (m100) cc_final: 0.6734 (m100) REVERT: D 126 LEU cc_start: 0.7498 (tp) cc_final: 0.7282 (tm) REVERT: D 156 ASN cc_start: 0.8303 (m110) cc_final: 0.7866 (m-40) REVERT: D 244 ARG cc_start: 0.8090 (tmt-80) cc_final: 0.7632 (tmt-80) REVERT: D 318 THR cc_start: 0.8598 (p) cc_final: 0.8106 (t) REVERT: E 159 ARG cc_start: 0.7231 (mtp85) cc_final: 0.6910 (mtp85) REVERT: E 239 GLN cc_start: 0.7984 (tt0) cc_final: 0.6936 (pp30) REVERT: E 310 ARG cc_start: 0.7454 (tpp80) cc_final: 0.6871 (tpp80) REVERT: F 126 LEU cc_start: 0.7503 (tp) cc_final: 0.7286 (tm) REVERT: F 132 LEU cc_start: 0.7742 (mp) cc_final: 0.7532 (mp) REVERT: F 156 ASN cc_start: 0.8242 (m110) cc_final: 0.7833 (m-40) REVERT: F 217 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6118 (mmp-170) REVERT: F 239 GLN cc_start: 0.8316 (tt0) cc_final: 0.7389 (pp30) REVERT: F 244 ARG cc_start: 0.8116 (tmt-80) cc_final: 0.7682 (tmt-80) REVERT: F 318 THR cc_start: 0.8483 (p) cc_final: 0.8001 (t) REVERT: G 146 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6289 (mtp85) REVERT: G 222 LEU cc_start: 0.8761 (tp) cc_final: 0.8525 (tp) REVERT: G 282 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7967 (mt-10) REVERT: G 310 ARG cc_start: 0.7466 (tpp80) cc_final: 0.6886 (tpp80) REVERT: G 325 ASP cc_start: 0.8359 (t0) cc_final: 0.8069 (t0) REVERT: H 126 LEU cc_start: 0.7442 (tp) cc_final: 0.7197 (tm) REVERT: H 156 ASN cc_start: 0.8221 (m110) cc_final: 0.7812 (m-40) REVERT: H 239 GLN cc_start: 0.8193 (tt0) cc_final: 0.7299 (pp30) REVERT: H 244 ARG cc_start: 0.8170 (tmt-80) cc_final: 0.7762 (tmt-80) REVERT: H 318 THR cc_start: 0.8410 (p) cc_final: 0.7918 (t) REVERT: H 484 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7559 (mpt90) outliers start: 87 outliers final: 52 residues processed: 403 average time/residue: 0.5847 time to fit residues: 280.7171 Evaluate side-chains 359 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 304 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 146 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 406 LEU Chi-restraints excluded: chain H residue 484 ARG Chi-restraints excluded: chain H residue 531 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 233 optimal weight: 0.7980 chunk 313 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 202 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 142 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 190 HIS B 337 ASN C 190 HIS D 337 ASN E 134 GLN E 190 HIS F 337 ASN G 190 HIS H 190 HIS H 337 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.211898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156805 restraints weight = 34389.537| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.66 r_work: 0.3526 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30840 Z= 0.114 Angle : 0.547 7.885 41704 Z= 0.270 Chirality : 0.036 0.139 4816 Planarity : 0.004 0.043 5424 Dihedral : 5.122 38.624 4528 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.52 % Allowed : 10.80 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.14), residues: 3872 helix: 1.24 (0.10), residues: 2944 sheet: None (None), residues: 0 loop : 0.52 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 216 TYR 0.005 0.001 TYR F 213 PHE 0.010 0.001 PHE F 192 TRP 0.017 0.001 TRP C 214 HIS 0.005 0.001 HIS F 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (30840) covalent geometry : angle 0.54713 / 0.27 (41704) hydrogen bonds : bond 0.03685 / 2.49 ( 1872) hydrogen bonds : angle 4.12329 / 2.97 ( 5439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 341 time to evaluate : 1.190 Fit side-chains REVERT: A 159 ARG cc_start: 0.7167 (mtp85) cc_final: 0.6961 (mtp85) REVERT: A 244 ARG cc_start: 0.7989 (tmt-80) cc_final: 0.7718 (tmt-80) REVERT: A 282 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7928 (mt-10) REVERT: A 318 THR cc_start: 0.8358 (p) cc_final: 0.7929 (t) REVERT: B 156 ASN cc_start: 0.8156 (m110) cc_final: 0.7672 (m-40) REVERT: B 239 GLN cc_start: 0.8201 (tt0) cc_final: 0.7334 (pp30) REVERT: B 244 ARG cc_start: 0.8160 (tmt-80) cc_final: 0.7462 (tmt-80) REVERT: B 318 THR cc_start: 0.8436 (p) cc_final: 0.7920 (t) REVERT: B 397 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8002 (mp) REVERT: C 121 ARG cc_start: 0.6632 (ttm110) cc_final: 0.6424 (ttm110) REVERT: C 126 LEU cc_start: 0.7849 (tp) cc_final: 0.7427 (tm) REVERT: C 214 TRP cc_start: 0.7451 (m-10) cc_final: 0.7204 (m-90) REVERT: C 239 GLN cc_start: 0.8442 (tt0) cc_final: 0.7449 (pp30) REVERT: C 253 TRP cc_start: 0.7528 (m100) cc_final: 0.7218 (m100) REVERT: C 318 THR cc_start: 0.8247 (p) cc_final: 0.7779 (t) REVERT: D 156 ASN cc_start: 0.8200 (m110) cc_final: 0.7713 (m-40) REVERT: D 212 LEU cc_start: 0.7665 (mt) cc_final: 0.7417 (mp) REVERT: D 244 ARG cc_start: 0.8174 (tmt-80) cc_final: 0.7906 (tmt-80) REVERT: D 253 TRP cc_start: 0.7081 (m-90) cc_final: 0.6748 (m-90) REVERT: D 318 THR cc_start: 0.8580 (p) cc_final: 0.8064 (t) REVERT: E 310 ARG cc_start: 0.7139 (tpp80) cc_final: 0.6642 (tpp80) REVERT: E 318 THR cc_start: 0.8344 (p) cc_final: 0.7896 (t) REVERT: F 156 ASN cc_start: 0.8156 (m110) cc_final: 0.7652 (m-40) REVERT: F 239 GLN cc_start: 0.8178 (tt0) cc_final: 0.7296 (pp30) REVERT: F 244 ARG cc_start: 0.8182 (tmt-80) cc_final: 0.7872 (tmt-80) REVERT: F 245 MET cc_start: 0.7643 (mtp) cc_final: 0.7428 (mtp) REVERT: F 253 TRP cc_start: 0.6846 (m100) cc_final: 0.5139 (m100) REVERT: F 254 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7879 (mm) REVERT: F 318 THR cc_start: 0.8465 (p) cc_final: 0.7954 (t) REVERT: G 254 LEU cc_start: 0.8583 (mt) cc_final: 0.8287 (mp) REVERT: G 282 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7905 (mt-10) REVERT: G 310 ARG cc_start: 0.7151 (tpp80) cc_final: 0.6682 (tpp80) REVERT: G 318 THR cc_start: 0.8352 (p) cc_final: 0.7925 (t) REVERT: H 132 LEU cc_start: 0.7631 (mp) cc_final: 0.7419 (mp) REVERT: H 156 ASN cc_start: 0.8178 (m110) cc_final: 0.7736 (m-40) REVERT: H 244 ARG cc_start: 0.8208 (tmt-80) cc_final: 0.7801 (tmt-80) REVERT: H 253 TRP cc_start: 0.7462 (m100) cc_final: 0.7191 (m100) REVERT: H 318 THR cc_start: 0.8415 (p) cc_final: 0.7896 (t) REVERT: H 484 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7451 (mmm160) outliers start: 80 outliers final: 24 residues processed: 385 average time/residue: 0.5198 time to fit residues: 242.2556 Evaluate side-chains 332 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 305 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 484 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 182 optimal weight: 0.8980 chunk 338 optimal weight: 20.0000 chunk 322 optimal weight: 0.0030 chunk 237 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 GLN A 190 HIS B 190 HIS C 190 HIS D 190 HIS E 190 HIS F 190 HIS G 190 HIS G 232 ASN H 190 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.210006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152790 restraints weight = 34062.475| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.69 r_work: 0.3489 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30840 Z= 0.146 Angle : 0.571 15.174 41704 Z= 0.277 Chirality : 0.037 0.168 4816 Planarity : 0.003 0.037 5424 Dihedral : 4.912 31.978 4528 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.80 % Allowed : 12.34 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.14), residues: 3872 helix: 1.23 (0.10), residues: 2944 sheet: None (None), residues: 0 loop : 0.41 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 146 TYR 0.007 0.001 TYR B 429 PHE 0.014 0.001 PHE D 192 TRP 0.011 0.001 TRP F 253 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (30840) covalent geometry : angle 0.57077 / 0.28 (41704) hydrogen bonds : bond 0.03941 / 2.70 ( 1872) hydrogen bonds : angle 4.06513 / 2.93 ( 5439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.7905 (mp) cc_final: 0.7647 (mm) REVERT: A 244 ARG cc_start: 0.7983 (tmt-80) cc_final: 0.7762 (tmt-80) REVERT: A 282 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 318 THR cc_start: 0.8484 (p) cc_final: 0.7993 (t) REVERT: B 156 ASN cc_start: 0.8220 (m110) cc_final: 0.7709 (m-40) REVERT: B 239 GLN cc_start: 0.8140 (tt0) cc_final: 0.7265 (pp30) REVERT: B 244 ARG cc_start: 0.8075 (tmt-80) cc_final: 0.7536 (tmt-80) REVERT: B 318 THR cc_start: 0.8531 (p) cc_final: 0.7996 (t) REVERT: C 171 LEU cc_start: 0.8381 (tp) cc_final: 0.8175 (tt) REVERT: C 214 TRP cc_start: 0.7614 (m-10) cc_final: 0.7340 (m-90) REVERT: C 244 ARG cc_start: 0.8161 (tmt-80) cc_final: 0.7876 (tmt-80) REVERT: C 318 THR cc_start: 0.8424 (p) cc_final: 0.7921 (t) REVERT: D 156 ASN cc_start: 0.8234 (m110) cc_final: 0.7717 (m-40) REVERT: D 244 ARG cc_start: 0.8071 (tmt-80) cc_final: 0.7398 (tmt-80) REVERT: D 318 THR cc_start: 0.8618 (p) cc_final: 0.8134 (t) REVERT: E 310 ARG cc_start: 0.7179 (tpp80) cc_final: 0.6718 (tpp80) REVERT: E 318 THR cc_start: 0.8420 (p) cc_final: 0.7963 (t) REVERT: F 146 ARG cc_start: 0.7141 (mtp-110) cc_final: 0.6895 (ttt90) REVERT: F 239 GLN cc_start: 0.8189 (tt0) cc_final: 0.7316 (pp30) REVERT: F 244 ARG cc_start: 0.8165 (tmt-80) cc_final: 0.7889 (tmt-80) REVERT: F 245 MET cc_start: 0.7638 (mtp) cc_final: 0.7356 (mtp) REVERT: F 253 TRP cc_start: 0.6897 (m100) cc_final: 0.5195 (m100) REVERT: F 254 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7874 (mm) REVERT: F 318 THR cc_start: 0.8570 (p) cc_final: 0.8082 (t) REVERT: G 244 ARG cc_start: 0.8084 (tmt-80) cc_final: 0.7647 (tmt-80) REVERT: G 282 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7909 (mt-10) REVERT: G 310 ARG cc_start: 0.7140 (tpp80) cc_final: 0.6687 (tpp80) REVERT: G 318 THR cc_start: 0.8441 (p) cc_final: 0.8008 (t) REVERT: H 132 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7484 (mp) REVERT: H 156 ASN cc_start: 0.8230 (m110) cc_final: 0.7781 (m-40) REVERT: H 244 ARG cc_start: 0.8082 (tmt-80) cc_final: 0.7549 (tmt-80) REVERT: H 253 TRP cc_start: 0.7483 (m100) cc_final: 0.6964 (m100) REVERT: H 318 THR cc_start: 0.8502 (p) cc_final: 0.7986 (t) outliers start: 89 outliers final: 40 residues processed: 361 average time/residue: 0.5170 time to fit residues: 225.9028 Evaluate side-chains 336 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 459 SER Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 87 optimal weight: 2.9990 chunk 363 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 377 optimal weight: 1.9990 chunk 212 optimal weight: 0.1980 chunk 239 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 275 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 521 GLN C 190 HIS D 190 HIS E 190 HIS F 190 HIS G 134 GLN G 521 GLN H 190 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.212078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157282 restraints weight = 34186.312| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.65 r_work: 0.3528 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30840 Z= 0.112 Angle : 0.550 15.324 41704 Z= 0.262 Chirality : 0.036 0.206 4816 Planarity : 0.003 0.032 5424 Dihedral : 4.620 26.928 4528 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.05 % Allowed : 13.89 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.14), residues: 3872 helix: 1.33 (0.10), residues: 2944 sheet: None (None), residues: 0 loop : 0.46 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 121 TYR 0.005 0.001 TYR H 429 PHE 0.013 0.001 PHE D 192 TRP 0.011 0.001 TRP H 253 HIS 0.006 0.001 HIS G 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (30840) covalent geometry : angle 0.55006 / 0.26 (41704) hydrogen bonds : bond 0.03412 / 2.32 ( 1872) hydrogen bonds : angle 3.91755 / 2.82 ( 5439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 307 time to evaluate : 1.209 Fit side-chains REVERT: A 104 LEU cc_start: 0.7888 (mp) cc_final: 0.7634 (mm) REVERT: A 196 GLU cc_start: 0.7431 (pt0) cc_final: 0.7139 (tt0) REVERT: A 244 ARG cc_start: 0.8035 (tmt-80) cc_final: 0.7782 (tmt-80) REVERT: A 282 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 318 THR cc_start: 0.8539 (p) cc_final: 0.8029 (t) REVERT: B 244 ARG cc_start: 0.8038 (tmt-80) cc_final: 0.7427 (tmt-80) REVERT: B 318 THR cc_start: 0.8558 (p) cc_final: 0.8038 (t) REVERT: C 196 GLU cc_start: 0.7438 (pt0) cc_final: 0.7145 (tt0) REVERT: C 214 TRP cc_start: 0.7577 (m-10) cc_final: 0.7349 (m-90) REVERT: C 244 ARG cc_start: 0.8310 (tmt-80) cc_final: 0.8028 (tmt-80) REVERT: C 318 THR cc_start: 0.8498 (p) cc_final: 0.7935 (t) REVERT: D 156 ASN cc_start: 0.8270 (m110) cc_final: 0.7765 (m-40) REVERT: D 244 ARG cc_start: 0.8113 (tmt-80) cc_final: 0.7850 (tmt-80) REVERT: D 318 THR cc_start: 0.8639 (p) cc_final: 0.8154 (t) REVERT: E 196 GLU cc_start: 0.7442 (pt0) cc_final: 0.7164 (tt0) REVERT: E 244 ARG cc_start: 0.8054 (tmt-80) cc_final: 0.7791 (tmt-80) REVERT: E 310 ARG cc_start: 0.7141 (tpp80) cc_final: 0.6767 (tpp80) REVERT: E 318 THR cc_start: 0.8564 (p) cc_final: 0.8032 (t) REVERT: F 239 GLN cc_start: 0.8212 (tt0) cc_final: 0.7304 (pp30) REVERT: F 244 ARG cc_start: 0.8180 (tmt-80) cc_final: 0.7906 (tmt-80) REVERT: F 245 MET cc_start: 0.7883 (mtp) cc_final: 0.7596 (mtp) REVERT: F 253 TRP cc_start: 0.6911 (m100) cc_final: 0.6192 (m100) REVERT: F 254 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7968 (mm) REVERT: F 318 THR cc_start: 0.8519 (p) cc_final: 0.8005 (t) REVERT: G 146 ARG cc_start: 0.7286 (mtp85) cc_final: 0.7016 (ptm-80) REVERT: G 171 LEU cc_start: 0.8366 (tp) cc_final: 0.8161 (tt) REVERT: G 196 GLU cc_start: 0.7364 (pt0) cc_final: 0.7057 (tt0) REVERT: G 244 ARG cc_start: 0.8155 (tmt-80) cc_final: 0.7688 (tmt-80) REVERT: G 282 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7933 (mt-10) REVERT: G 310 ARG cc_start: 0.7143 (tpp80) cc_final: 0.6773 (tpp80) REVERT: G 318 THR cc_start: 0.8528 (p) cc_final: 0.8029 (t) REVERT: H 126 LEU cc_start: 0.7413 (tp) cc_final: 0.6901 (tm) REVERT: H 156 ASN cc_start: 0.8247 (m110) cc_final: 0.7686 (m110) REVERT: H 244 ARG cc_start: 0.8056 (tmt-80) cc_final: 0.7553 (tmt-80) REVERT: H 253 TRP cc_start: 0.7180 (m100) cc_final: 0.6325 (m100) REVERT: H 318 THR cc_start: 0.8554 (p) cc_final: 0.8044 (t) outliers start: 65 outliers final: 41 residues processed: 344 average time/residue: 0.4946 time to fit residues: 207.0622 Evaluate side-chains 337 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 295 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 459 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 243 optimal weight: 10.0000 chunk 171 optimal weight: 0.1980 chunk 227 optimal weight: 0.9990 chunk 325 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 331 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 232 ASN B 190 HIS C 232 ASN D 190 HIS E 232 ASN F 190 HIS G 232 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.212005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155156 restraints weight = 34207.434| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.82 r_work: 0.3509 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30840 Z= 0.109 Angle : 0.539 14.209 41704 Z= 0.257 Chirality : 0.035 0.198 4816 Planarity : 0.003 0.029 5424 Dihedral : 4.491 23.958 4528 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.68 % Allowed : 14.07 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.14), residues: 3872 helix: 1.37 (0.10), residues: 2944 sheet: None (None), residues: 0 loop : 0.46 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 121 TYR 0.005 0.001 TYR E 429 PHE 0.010 0.001 PHE B 192 TRP 0.011 0.001 TRP G 253 HIS 0.007 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (30840) covalent geometry : angle 0.53864 / 0.26 (41704) hydrogen bonds : bond 0.03323 / 2.26 ( 1872) hydrogen bonds : angle 3.84186 / 2.77 ( 5439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 313 time to evaluate : 1.245 Fit side-chains REVERT: A 244 ARG cc_start: 0.8169 (tmt-80) cc_final: 0.7710 (tmt-80) REVERT: A 282 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 318 THR cc_start: 0.8626 (p) cc_final: 0.8087 (t) REVERT: B 156 ASN cc_start: 0.8252 (m110) cc_final: 0.7877 (m-40) REVERT: B 244 ARG cc_start: 0.8033 (tmt-80) cc_final: 0.7560 (tmt-80) REVERT: B 318 THR cc_start: 0.8595 (p) cc_final: 0.8072 (t) REVERT: C 146 ARG cc_start: 0.7303 (mtp85) cc_final: 0.7012 (ptm-80) REVERT: C 171 LEU cc_start: 0.8428 (tp) cc_final: 0.8207 (tt) REVERT: C 244 ARG cc_start: 0.8311 (tmt-80) cc_final: 0.7993 (tmt-80) REVERT: C 318 THR cc_start: 0.8502 (p) cc_final: 0.7936 (t) REVERT: C 526 ASP cc_start: 0.8659 (m-30) cc_final: 0.8391 (m-30) REVERT: D 156 ASN cc_start: 0.8344 (m110) cc_final: 0.7845 (m-40) REVERT: D 244 ARG cc_start: 0.8118 (tmt-80) cc_final: 0.7874 (tmt-80) REVERT: D 318 THR cc_start: 0.8693 (p) cc_final: 0.8232 (t) REVERT: E 244 ARG cc_start: 0.8096 (tmt-80) cc_final: 0.7768 (tmt-80) REVERT: E 310 ARG cc_start: 0.7224 (tpp80) cc_final: 0.6852 (tpp80) REVERT: E 318 THR cc_start: 0.8580 (p) cc_final: 0.8039 (t) REVERT: E 526 ASP cc_start: 0.8656 (m-30) cc_final: 0.8396 (m-30) REVERT: F 146 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7177 (mtp-110) REVERT: F 239 GLN cc_start: 0.8229 (tt0) cc_final: 0.7330 (pp30) REVERT: F 245 MET cc_start: 0.7878 (mtp) cc_final: 0.7495 (mtp) REVERT: F 253 TRP cc_start: 0.6919 (m100) cc_final: 0.5250 (m100) REVERT: F 254 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7930 (mm) REVERT: F 318 THR cc_start: 0.8637 (p) cc_final: 0.8106 (t) REVERT: G 244 ARG cc_start: 0.8220 (tmt-80) cc_final: 0.7579 (tmt-80) REVERT: G 282 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7972 (mt-10) REVERT: G 310 ARG cc_start: 0.7196 (tpp80) cc_final: 0.6824 (tpp80) REVERT: G 318 THR cc_start: 0.8586 (p) cc_final: 0.8067 (t) REVERT: H 244 ARG cc_start: 0.8050 (tmt-80) cc_final: 0.7577 (tmt-80) REVERT: H 318 THR cc_start: 0.8617 (p) cc_final: 0.8078 (t) outliers start: 85 outliers final: 55 residues processed: 369 average time/residue: 0.5177 time to fit residues: 233.6125 Evaluate side-chains 350 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 294 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 459 SER Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 122 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 247 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 326 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN B 190 HIS C 232 ASN D 190 HIS E 232 ASN F 190 HIS G 232 ASN G 478 ASN ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.208217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151867 restraints weight = 34188.889| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.88 r_work: 0.3439 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30840 Z= 0.194 Angle : 0.611 13.606 41704 Z= 0.294 Chirality : 0.039 0.145 4816 Planarity : 0.004 0.055 5424 Dihedral : 4.951 25.512 4528 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.83 % Allowed : 14.86 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3872 helix: 1.16 (0.10), residues: 2944 sheet: None (None), residues: 0 loop : 0.47 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 146 TYR 0.008 0.001 TYR B 429 PHE 0.018 0.001 PHE D 192 TRP 0.014 0.001 TRP G 253 HIS 0.011 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (30840) covalent geometry : angle 0.61133 / 0.29 (41704) hydrogen bonds : bond 0.04279 / 2.94 ( 1872) hydrogen bonds : angle 4.01821 / 2.91 ( 5439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 305 time to evaluate : 1.179 Fit side-chains REVERT: A 104 LEU cc_start: 0.8105 (mp) cc_final: 0.7839 (mm) REVERT: A 244 ARG cc_start: 0.8113 (tmt-80) cc_final: 0.7904 (tmt-80) REVERT: A 282 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 318 THR cc_start: 0.8558 (p) cc_final: 0.8069 (t) REVERT: B 146 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.7074 (ttt90) REVERT: B 156 ASN cc_start: 0.8293 (m110) cc_final: 0.7892 (m-40) REVERT: B 244 ARG cc_start: 0.8026 (tmt-80) cc_final: 0.7437 (tmt-80) REVERT: B 282 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 318 THR cc_start: 0.8644 (p) cc_final: 0.8169 (t) REVERT: C 244 ARG cc_start: 0.8286 (tmt-80) cc_final: 0.7919 (tmt-80) REVERT: C 318 THR cc_start: 0.8616 (p) cc_final: 0.8078 (t) REVERT: C 526 ASP cc_start: 0.8721 (m-30) cc_final: 0.8444 (m-30) REVERT: D 126 LEU cc_start: 0.7543 (tp) cc_final: 0.7278 (tm) REVERT: D 146 ARG cc_start: 0.7397 (mtp-110) cc_final: 0.7196 (ttt90) REVERT: D 156 ASN cc_start: 0.8359 (m110) cc_final: 0.7782 (m110) REVERT: D 244 ARG cc_start: 0.8096 (tmt-80) cc_final: 0.7813 (tmt-80) REVERT: D 318 THR cc_start: 0.8706 (p) cc_final: 0.8260 (t) REVERT: E 318 THR cc_start: 0.8591 (p) cc_final: 0.8094 (t) REVERT: E 361 LYS cc_start: 0.7557 (tttt) cc_final: 0.7320 (tttt) REVERT: F 156 ASN cc_start: 0.8265 (m110) cc_final: 0.7782 (m-40) REVERT: F 239 GLN cc_start: 0.8274 (tt0) cc_final: 0.7279 (pp30) REVERT: F 244 ARG cc_start: 0.8272 (tmt-80) cc_final: 0.8027 (tmt-80) REVERT: F 253 TRP cc_start: 0.7070 (m100) cc_final: 0.6392 (m100) REVERT: F 254 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8004 (mm) REVERT: F 318 THR cc_start: 0.8617 (p) cc_final: 0.8128 (t) REVERT: G 171 LEU cc_start: 0.8317 (tp) cc_final: 0.8100 (tt) REVERT: G 244 ARG cc_start: 0.8156 (tmt-80) cc_final: 0.7529 (tmt-80) REVERT: G 282 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8008 (mt-10) REVERT: G 310 ARG cc_start: 0.7357 (tpp80) cc_final: 0.6955 (tpp80) REVERT: G 318 THR cc_start: 0.8602 (p) cc_final: 0.8144 (t) REVERT: H 151 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7243 (pp) REVERT: H 156 ASN cc_start: 0.8362 (m110) cc_final: 0.8023 (m-40) REVERT: H 244 ARG cc_start: 0.8110 (tmt-80) cc_final: 0.7673 (tmt-80) REVERT: H 318 THR cc_start: 0.8601 (p) cc_final: 0.8109 (t) outliers start: 90 outliers final: 63 residues processed: 356 average time/residue: 0.5127 time to fit residues: 223.0895 Evaluate side-chains 349 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 459 SER Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 312 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 186 optimal weight: 0.4980 chunk 149 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 291 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 379 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 190 HIS C 190 HIS C 521 GLN D 190 HIS E 190 HIS F 190 HIS ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.208875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154780 restraints weight = 34112.885| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.83 r_work: 0.3461 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30840 Z= 0.173 Angle : 0.618 18.101 41704 Z= 0.290 Chirality : 0.038 0.146 4816 Planarity : 0.004 0.043 5424 Dihedral : 4.856 24.784 4528 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.93 % Allowed : 14.86 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.14), residues: 3872 helix: 1.13 (0.10), residues: 2944 sheet: None (None), residues: 0 loop : 0.50 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 146 TYR 0.007 0.001 TYR D 429 PHE 0.015 0.001 PHE D 192 TRP 0.017 0.001 TRP G 253 HIS 0.006 0.001 HIS F 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (30840) covalent geometry : angle 0.61844 / 0.29 (41704) hydrogen bonds : bond 0.04009 / 2.74 ( 1872) hydrogen bonds : angle 3.98555 / 2.89 ( 5439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 292 time to evaluate : 1.178 Fit side-chains REVERT: A 69 LEU cc_start: 0.7363 (mt) cc_final: 0.7068 (mt) REVERT: A 244 ARG cc_start: 0.8106 (tmt-80) cc_final: 0.7609 (tmt-80) REVERT: A 282 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7930 (mt-10) REVERT: A 318 THR cc_start: 0.8525 (p) cc_final: 0.8042 (t) REVERT: B 146 ARG cc_start: 0.7355 (mtp-110) cc_final: 0.7027 (ttt90) REVERT: B 156 ASN cc_start: 0.8258 (m110) cc_final: 0.7846 (m-40) REVERT: B 244 ARG cc_start: 0.7938 (tmt-80) cc_final: 0.7447 (tmt-80) REVERT: B 282 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8071 (mt-10) REVERT: B 318 THR cc_start: 0.8674 (p) cc_final: 0.8227 (t) REVERT: C 171 LEU cc_start: 0.8366 (tp) cc_final: 0.8135 (tt) REVERT: C 244 ARG cc_start: 0.8213 (tmt-80) cc_final: 0.7493 (tmt-80) REVERT: C 318 THR cc_start: 0.8574 (p) cc_final: 0.8022 (t) REVERT: C 526 ASP cc_start: 0.8703 (m-30) cc_final: 0.8436 (m-30) REVERT: D 126 LEU cc_start: 0.7514 (tp) cc_final: 0.7259 (tm) REVERT: D 146 ARG cc_start: 0.7369 (mtp-110) cc_final: 0.7146 (ttt90) REVERT: D 156 ASN cc_start: 0.8324 (m110) cc_final: 0.7734 (m110) REVERT: D 244 ARG cc_start: 0.8069 (tmt-80) cc_final: 0.7781 (tmt-80) REVERT: D 318 THR cc_start: 0.8745 (p) cc_final: 0.8306 (t) REVERT: E 310 ARG cc_start: 0.7382 (tpp80) cc_final: 0.6945 (tpp80) REVERT: E 318 THR cc_start: 0.8572 (p) cc_final: 0.8068 (t) REVERT: F 146 ARG cc_start: 0.7479 (ttt90) cc_final: 0.7193 (mtp-110) REVERT: F 156 ASN cc_start: 0.8217 (m110) cc_final: 0.7701 (m-40) REVERT: F 239 GLN cc_start: 0.8379 (tt0) cc_final: 0.7383 (pp30) REVERT: F 253 TRP cc_start: 0.7036 (m100) cc_final: 0.6352 (m100) REVERT: F 254 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8005 (mm) REVERT: F 318 THR cc_start: 0.8648 (p) cc_final: 0.8181 (t) REVERT: G 159 ARG cc_start: 0.7636 (mtp85) cc_final: 0.7430 (mtp85) REVERT: G 244 ARG cc_start: 0.8153 (tmt-80) cc_final: 0.7514 (tmt-80) REVERT: G 282 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8012 (mt-10) REVERT: G 310 ARG cc_start: 0.7392 (tpp80) cc_final: 0.6961 (tpp80) REVERT: G 318 THR cc_start: 0.8562 (p) cc_final: 0.8094 (t) REVERT: H 156 ASN cc_start: 0.8291 (m110) cc_final: 0.7881 (m-40) REVERT: H 159 ARG cc_start: 0.7687 (ptp-110) cc_final: 0.6850 (ptp-110) REVERT: H 217 ARG cc_start: 0.6886 (mmp-170) cc_final: 0.6666 (mmp-170) REVERT: H 244 ARG cc_start: 0.8064 (tmt-80) cc_final: 0.7627 (tmt-80) REVERT: H 318 THR cc_start: 0.8675 (p) cc_final: 0.8207 (t) outliers start: 93 outliers final: 60 residues processed: 352 average time/residue: 0.4855 time to fit residues: 209.6353 Evaluate side-chains 344 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 459 SER Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 484 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 18 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 200 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 358 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 232 ASN B 190 HIS C 190 HIS C 232 ASN D 190 HIS E 190 HIS E 232 ASN F 190 HIS ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.210784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156957 restraints weight = 34164.617| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.82 r_work: 0.3492 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30840 Z= 0.127 Angle : 0.590 17.161 41704 Z= 0.275 Chirality : 0.036 0.153 4816 Planarity : 0.003 0.039 5424 Dihedral : 4.606 24.329 4528 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.74 % Allowed : 15.27 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 3872 helix: 1.24 (0.10), residues: 2968 sheet: None (None), residues: 0 loop : 0.46 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 146 TYR 0.007 0.001 TYR B 429 PHE 0.012 0.001 PHE D 192 TRP 0.019 0.001 TRP G 253 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (30840) covalent geometry : angle 0.59040 / 0.27 (41704) hydrogen bonds : bond 0.03545 / 2.42 ( 1872) hydrogen bonds : angle 3.87853 / 2.81 ( 5439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 298 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.7955 (tpp) cc_final: 0.7604 (mmp) REVERT: A 244 ARG cc_start: 0.8144 (tmt-80) cc_final: 0.7693 (tmt-80) REVERT: A 282 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 318 THR cc_start: 0.8518 (p) cc_final: 0.8002 (t) REVERT: B 146 ARG cc_start: 0.7353 (mtp-110) cc_final: 0.7065 (ttt90) REVERT: B 156 ASN cc_start: 0.8266 (m110) cc_final: 0.7844 (m-40) REVERT: B 244 ARG cc_start: 0.7997 (tmt-80) cc_final: 0.7556 (tmt-80) REVERT: B 318 THR cc_start: 0.8665 (p) cc_final: 0.8219 (t) REVERT: C 171 LEU cc_start: 0.8390 (tp) cc_final: 0.8182 (tt) REVERT: C 239 GLN cc_start: 0.8480 (tt0) cc_final: 0.7478 (pp30) REVERT: C 244 ARG cc_start: 0.8246 (tmt-80) cc_final: 0.7462 (tmt-80) REVERT: C 318 THR cc_start: 0.8520 (p) cc_final: 0.7980 (t) REVERT: C 526 ASP cc_start: 0.8689 (m-30) cc_final: 0.8388 (m-30) REVERT: D 126 LEU cc_start: 0.7515 (tp) cc_final: 0.7273 (tm) REVERT: D 156 ASN cc_start: 0.8323 (m110) cc_final: 0.7738 (m110) REVERT: D 244 ARG cc_start: 0.8133 (tmt-80) cc_final: 0.7849 (tmt-80) REVERT: D 318 THR cc_start: 0.8748 (p) cc_final: 0.8308 (t) REVERT: E 310 ARG cc_start: 0.7299 (tpp80) cc_final: 0.6872 (tpp80) REVERT: E 318 THR cc_start: 0.8588 (p) cc_final: 0.8039 (t) REVERT: F 156 ASN cc_start: 0.8242 (m110) cc_final: 0.7712 (m-40) REVERT: F 239 GLN cc_start: 0.8388 (tt0) cc_final: 0.7325 (pp30) REVERT: F 244 ARG cc_start: 0.8176 (tmt-80) cc_final: 0.7924 (tmt-80) REVERT: F 253 TRP cc_start: 0.7063 (m100) cc_final: 0.6661 (m100) REVERT: F 254 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7977 (mm) REVERT: F 318 THR cc_start: 0.8726 (p) cc_final: 0.8256 (t) REVERT: G 244 ARG cc_start: 0.8159 (tmt-80) cc_final: 0.7485 (tmt-80) REVERT: G 282 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7926 (mt-10) REVERT: G 310 ARG cc_start: 0.7335 (tpp80) cc_final: 0.6925 (tpp80) REVERT: G 318 THR cc_start: 0.8562 (p) cc_final: 0.8074 (t) REVERT: H 156 ASN cc_start: 0.8300 (m110) cc_final: 0.7911 (m-40) REVERT: H 159 ARG cc_start: 0.7536 (ptp-110) cc_final: 0.7292 (ptp-110) REVERT: H 217 ARG cc_start: 0.6700 (mmp-170) cc_final: 0.6406 (mmp-170) REVERT: H 244 ARG cc_start: 0.8040 (tmt-80) cc_final: 0.7550 (tmt-80) REVERT: H 318 THR cc_start: 0.8722 (p) cc_final: 0.8220 (t) outliers start: 87 outliers final: 55 residues processed: 350 average time/residue: 0.5250 time to fit residues: 225.2462 Evaluate side-chains 345 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 459 SER Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 165 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 130 optimal weight: 0.0870 chunk 187 optimal weight: 1.9990 chunk 367 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 142 optimal weight: 0.9990 chunk 275 optimal weight: 0.3980 chunk 363 optimal weight: 0.0670 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 232 ASN B 190 HIS C 190 HIS C 232 ASN D 190 HIS E 190 HIS E 232 ASN F 190 HIS G 232 ASN H 190 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.213292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155611 restraints weight = 34073.079| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.67 r_work: 0.3540 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30840 Z= 0.102 Angle : 0.571 16.875 41704 Z= 0.263 Chirality : 0.036 0.159 4816 Planarity : 0.003 0.036 5424 Dihedral : 4.320 23.549 4528 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.39 % Allowed : 15.87 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.14), residues: 3872 helix: 1.37 (0.10), residues: 2968 sheet: None (None), residues: 0 loop : 0.57 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 146 TYR 0.005 0.001 TYR E 429 PHE 0.010 0.001 PHE D 192 TRP 0.017 0.001 TRP G 253 HIS 0.004 0.001 HIS E 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (30840) covalent geometry : angle 0.57125 / 0.26 (41704) hydrogen bonds : bond 0.03094 / 2.10 ( 1872) hydrogen bonds : angle 3.77573 / 2.74 ( 5439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 304 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8112 (tmt-80) cc_final: 0.7682 (tmt-80) REVERT: A 282 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7906 (mt-10) REVERT: A 318 THR cc_start: 0.8454 (p) cc_final: 0.7930 (t) REVERT: B 146 ARG cc_start: 0.7289 (mtp-110) cc_final: 0.7021 (ttt90) REVERT: B 244 ARG cc_start: 0.7932 (tmt-80) cc_final: 0.7433 (tmt-80) REVERT: B 282 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 318 THR cc_start: 0.8686 (p) cc_final: 0.8212 (t) REVERT: C 244 ARG cc_start: 0.8238 (tmt-80) cc_final: 0.7949 (tmt-80) REVERT: C 318 THR cc_start: 0.8534 (p) cc_final: 0.7990 (t) REVERT: C 526 ASP cc_start: 0.8639 (m-30) cc_final: 0.8348 (m-30) REVERT: D 126 LEU cc_start: 0.7564 (tp) cc_final: 0.7332 (tm) REVERT: D 156 ASN cc_start: 0.8301 (m110) cc_final: 0.7726 (m-40) REVERT: D 190 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6680 (m170) REVERT: D 244 ARG cc_start: 0.7994 (tmt-80) cc_final: 0.7769 (tmt-80) REVERT: D 318 THR cc_start: 0.8731 (p) cc_final: 0.8298 (t) REVERT: E 310 ARG cc_start: 0.7206 (tpp80) cc_final: 0.6787 (tpp80) REVERT: E 318 THR cc_start: 0.8497 (p) cc_final: 0.7961 (t) REVERT: F 126 LEU cc_start: 0.7509 (tp) cc_final: 0.6902 (tm) REVERT: F 156 ASN cc_start: 0.8204 (m110) cc_final: 0.7675 (m-40) REVERT: F 244 ARG cc_start: 0.8047 (tmt-80) cc_final: 0.7801 (tmt-80) REVERT: F 253 TRP cc_start: 0.7200 (m100) cc_final: 0.6785 (m100) REVERT: F 254 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7916 (mm) REVERT: F 318 THR cc_start: 0.8687 (p) cc_final: 0.8216 (t) REVERT: G 104 LEU cc_start: 0.7722 (mp) cc_final: 0.7498 (mm) REVERT: G 217 ARG cc_start: 0.6553 (mpt180) cc_final: 0.5839 (mmp-170) REVERT: G 282 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7955 (mt-10) REVERT: G 310 ARG cc_start: 0.7210 (tpp80) cc_final: 0.6797 (tpp80) REVERT: G 318 THR cc_start: 0.8532 (p) cc_final: 0.8001 (t) REVERT: H 156 ASN cc_start: 0.8266 (m110) cc_final: 0.7894 (m-40) REVERT: H 217 ARG cc_start: 0.6564 (mmp-170) cc_final: 0.6254 (mmp-170) REVERT: H 244 ARG cc_start: 0.7913 (tmt-80) cc_final: 0.7472 (tmt-80) REVERT: H 318 THR cc_start: 0.8703 (p) cc_final: 0.8188 (t) outliers start: 76 outliers final: 48 residues processed: 347 average time/residue: 0.4700 time to fit residues: 201.5369 Evaluate side-chains 333 residues out of total 3176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 283 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 459 SER Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 459 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 196 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 339 optimal weight: 8.9990 chunk 324 optimal weight: 0.6980 chunk 88 optimal weight: 0.0970 chunk 383 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 286 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 232 ASN B 190 HIS C 190 HIS C 232 ASN D 190 HIS E 190 HIS E 232 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 ASN ** H 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.212065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157052 restraints weight = 34346.570| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.73 r_work: 0.3507 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30840 Z= 0.120 Angle : 0.596 15.980 41704 Z= 0.274 Chirality : 0.037 0.284 4816 Planarity : 0.003 0.037 5424 Dihedral : 4.400 23.872 4528 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.49 % Allowed : 16.22 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.14), residues: 3872 helix: 1.32 (0.10), residues: 2968 sheet: None (None), residues: 0 loop : 0.46 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 146 TYR 0.010 0.001 TYR E 429 PHE 0.010 0.001 PHE D 192 TRP 0.019 0.001 TRP G 253 HIS 0.005 0.000 HIS E 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (30840) covalent geometry : angle 0.59570 / 0.27 (41704) hydrogen bonds : bond 0.03386 / 2.30 ( 1872) hydrogen bonds : angle 3.82737 / 2.77 ( 5439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9989.55 seconds wall clock time: 170 minutes 44.04 seconds (10244.04 seconds total)