Starting phenix.real_space_refine on Thu Sep 18 14:14:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ka4_9954/09_2025/6ka4_9954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ka4_9954/09_2025/6ka4_9954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ka4_9954/09_2025/6ka4_9954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ka4_9954/09_2025/6ka4_9954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ka4_9954/09_2025/6ka4_9954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ka4_9954/09_2025/6ka4_9954.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 11244 2.51 5 N 2960 2.21 5 O 3188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17500 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4375 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 511} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: D, B, C Time building chain proxies: 4.13, per 1000 atoms: 0.24 Number of scatterers: 17500 At special positions: 0 Unit cell: (129.347, 121.508, 105.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3188 8.00 N 2960 7.00 C 11244 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: 1.69 Conformation dependent library (CDL) restraints added in 793.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 8 sheets defined 66.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 24 Processing helix chain 'A' and resid 27 through 53 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 88 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 109 through 131 Proline residue: A 119 - end of helix removed outlier: 3.700A pdb=" N VAL A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 180 removed outlier: 4.049A pdb=" N GLU A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 200 removed outlier: 3.731A pdb=" N GLN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.635A pdb=" N ASP A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 276 Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.517A pdb=" N LEU A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.592A pdb=" N LYS A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 434 through 448 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.960A pdb=" N LEU A 457 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.738A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.297A pdb=" N LEU A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 517 removed outlier: 3.922A pdb=" N ARG A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 521 Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 removed outlier: 3.560A pdb=" N THR A 552 " --> pdb=" O TRP A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 552' Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'D' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 24 Processing helix chain 'D' and resid 27 through 53 Processing helix chain 'D' and resid 54 through 58 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 65 through 88 Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 109 through 131 Proline residue: D 119 - end of helix removed outlier: 3.701A pdb=" N VAL D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 150 Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU D 169 " --> pdb=" O ARG D 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 180 removed outlier: 4.049A pdb=" N GLU D 179 " --> pdb=" O CYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 200 removed outlier: 3.730A pdb=" N GLN D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 228 through 234 removed outlier: 3.635A pdb=" N ASP D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 276 Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.516A pdb=" N LEU D 281 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 removed outlier: 3.591A pdb=" N LYS D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 318 " --> pdb=" O MET D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 350 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 434 through 448 Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.961A pdb=" N LEU D 457 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 468 removed outlier: 3.738A pdb=" N ARG D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 490 removed outlier: 4.296A pdb=" N LEU D 485 " --> pdb=" O PHE D 481 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR D 486 " --> pdb=" O ILE D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 517 removed outlier: 3.921A pdb=" N ARG D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 509 " --> pdb=" O ARG D 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 521 Processing helix chain 'D' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN D 545 " --> pdb=" O THR D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 552 removed outlier: 3.561A pdb=" N THR D 552 " --> pdb=" O TRP D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 549 through 552' Processing helix chain 'D' and resid 556 through 558 No H-bonds generated for 'chain 'D' and resid 556 through 558' Processing helix chain 'D' and resid 559 through 574 Processing helix chain 'B' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 24 Processing helix chain 'B' and resid 27 through 53 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 109 through 131 Proline residue: B 119 - end of helix removed outlier: 3.700A pdb=" N VAL B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 150 Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU B 169 " --> pdb=" O ARG B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 171 through 180 removed outlier: 4.050A pdb=" N GLU B 179 " --> pdb=" O CYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 200 removed outlier: 3.730A pdb=" N GLN B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.635A pdb=" N ASP B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 276 Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.517A pdb=" N LEU B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.592A pdb=" N LYS B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 318 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 350 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 434 through 448 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.961A pdb=" N LEU B 457 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 468 removed outlier: 3.739A pdb=" N ARG B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.296A pdb=" N LEU B 485 " --> pdb=" O PHE B 481 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 517 removed outlier: 3.922A pdb=" N ARG B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 509 " --> pdb=" O ARG B 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 521 Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN B 545 " --> pdb=" O THR B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 552 removed outlier: 3.561A pdb=" N THR B 552 " --> pdb=" O TRP B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 552' Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.437A pdb=" N PHE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 27 through 53 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 65 through 88 Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.636A pdb=" N VAL C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 109 through 131 Proline residue: C 119 - end of helix removed outlier: 3.701A pdb=" N VAL C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 150 Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 166 through 169 removed outlier: 3.659A pdb=" N LEU C 169 " --> pdb=" O ARG C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 171 through 180 removed outlier: 4.050A pdb=" N GLU C 179 " --> pdb=" O CYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 200 removed outlier: 3.731A pdb=" N GLN C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 228 through 234 removed outlier: 3.634A pdb=" N ASP C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 276 Proline residue: C 273 - end of helix Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.518A pdb=" N LEU C 281 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 320 removed outlier: 3.592A pdb=" N LYS C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 318 " --> pdb=" O MET C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 350 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 434 through 448 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.960A pdb=" N LEU C 457 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 468 removed outlier: 3.738A pdb=" N ARG C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.296A pdb=" N LEU C 485 " --> pdb=" O PHE C 481 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR C 486 " --> pdb=" O ILE C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 517 removed outlier: 3.922A pdb=" N ARG C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR C 509 " --> pdb=" O ARG C 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 521 Processing helix chain 'C' and resid 535 through 548 removed outlier: 3.742A pdb=" N GLN C 545 " --> pdb=" O THR C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 552 removed outlier: 3.560A pdb=" N THR C 552 " --> pdb=" O TRP C 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 549 through 552' Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR A 289 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU A 306 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS A 291 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 251 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AA3, first strand: chain 'D' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR D 289 " --> pdb=" O GLU D 306 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU D 306 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS D 291 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 251 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 362 through 366 Processing sheet with id=AA5, first strand: chain 'B' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR B 289 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU B 306 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N CYS B 291 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 251 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 362 through 366 Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 8.286A pdb=" N TYR C 289 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU C 306 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C 291 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 251 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 362 through 366 936 hydrogen bonds defined for protein. 2700 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: 3.19 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5532 1.34 - 1.46: 2939 1.46 - 1.57: 9257 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 17900 Sorted by residual: bond pdb=" CA VAL D 560 " pdb=" CB VAL D 560 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.74e+00 bond pdb=" CA SER D 222 " pdb=" C SER D 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.66e+00 bond pdb=" CA SER A 222 " pdb=" C SER A 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.62e+00 bond pdb=" CA SER B 222 " pdb=" C SER B 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.62e+00 bond pdb=" CA SER C 222 " pdb=" C SER C 222 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.60e+00 ... (remaining 17895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 22750 1.55 - 3.10: 1083 3.10 - 4.64: 204 4.64 - 6.19: 59 6.19 - 7.74: 16 Bond angle restraints: 24112 Sorted by residual: angle pdb=" N GLN D 3 " pdb=" CA GLN D 3 " pdb=" C GLN D 3 " ideal model delta sigma weight residual 113.43 106.18 7.25 1.26e+00 6.30e-01 3.31e+01 angle pdb=" N GLN A 3 " pdb=" CA GLN A 3 " pdb=" C GLN A 3 " ideal model delta sigma weight residual 113.43 106.19 7.24 1.26e+00 6.30e-01 3.30e+01 angle pdb=" N GLN C 3 " pdb=" CA GLN C 3 " pdb=" C GLN C 3 " ideal model delta sigma weight residual 113.43 106.21 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" N GLN B 3 " pdb=" CA GLN B 3 " pdb=" C GLN B 3 " ideal model delta sigma weight residual 113.43 106.21 7.22 1.26e+00 6.30e-01 3.28e+01 angle pdb=" N SER C 222 " pdb=" CA SER C 222 " pdb=" C SER C 222 " ideal model delta sigma weight residual 113.16 120.90 -7.74 1.42e+00 4.96e-01 2.97e+01 ... (remaining 24107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 9480 15.41 - 30.82: 1059 30.82 - 46.23: 237 46.23 - 61.64: 32 61.64 - 77.05: 24 Dihedral angle restraints: 10832 sinusoidal: 4568 harmonic: 6264 Sorted by residual: dihedral pdb=" CA THR B 253 " pdb=" C THR B 253 " pdb=" N TRP B 254 " pdb=" CA TRP B 254 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR A 253 " pdb=" C THR A 253 " pdb=" N TRP A 254 " pdb=" CA TRP A 254 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR D 253 " pdb=" C THR D 253 " pdb=" N TRP D 254 " pdb=" CA TRP D 254 " ideal model delta harmonic sigma weight residual -180.00 -155.16 -24.84 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2068 0.057 - 0.114: 502 0.114 - 0.171: 34 0.171 - 0.229: 4 0.229 - 0.286: 4 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA SER D 222 " pdb=" N SER D 222 " pdb=" C SER D 222 " pdb=" CB SER D 222 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA SER A 222 " pdb=" N SER A 222 " pdb=" C SER A 222 " pdb=" CB SER A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA SER C 222 " pdb=" N SER C 222 " pdb=" C SER C 222 " pdb=" CB SER C 222 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2609 not shown) Planarity restraints: 3032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 221 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C GLU B 221 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU B 221 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 222 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 221 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C GLU A 221 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU A 221 " 0.026 2.00e-02 2.50e+03 pdb=" N SER A 222 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 221 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C GLU C 221 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU C 221 " 0.026 2.00e-02 2.50e+03 pdb=" N SER C 222 " 0.023 2.00e-02 2.50e+03 ... (remaining 3029 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 236 2.64 - 3.21: 16805 3.21 - 3.77: 26724 3.77 - 4.34: 38005 4.34 - 4.90: 61814 Nonbonded interactions: 143584 Sorted by model distance: nonbonded pdb=" N GLU A 356 " pdb=" OE1 GLU A 356 " model vdw 2.076 3.120 nonbonded pdb=" N GLU B 356 " pdb=" OE1 GLU B 356 " model vdw 2.076 3.120 nonbonded pdb=" N GLU C 356 " pdb=" OE1 GLU C 356 " model vdw 2.076 3.120 nonbonded pdb=" N GLU D 356 " pdb=" OE1 GLU D 356 " model vdw 2.077 3.120 nonbonded pdb=" NZ LYS B 310 " pdb=" OE1 GLU B 318 " model vdw 2.206 3.120 ... (remaining 143579 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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: 0.610 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.460 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17900 Z= 0.289 Angle : 0.816 7.738 24112 Z= 0.499 Chirality : 0.048 0.286 2612 Planarity : 0.005 0.087 3032 Dihedral : 13.681 77.052 6752 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 aren not related in a simple way. whole: -0.10 (0.18), residues: 2088 helix: 0.41 (0.15), residues: 1212 sheet: 0.11 (0.50), residues: 104 loop : -0.70 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 186 TYR 0.012 0.002 TYR B 521 PHE 0.015 0.002 PHE B 438 TRP 0.047 0.002 TRP C 254 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00643 (17900) covalent geometry : angle 0.81633 (24112) hydrogen bonds : bond 0.18461 ( 936) hydrogen bonds : angle 7.81641 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.637 Fit side-chains REVERT: A 233 ASN cc_start: 0.7955 (m110) cc_final: 0.7691 (m-40) REVERT: A 410 TYR cc_start: 0.7909 (m-80) cc_final: 0.7194 (m-80) REVERT: A 440 MET cc_start: 0.8892 (mmm) cc_final: 0.8132 (tpt) REVERT: D 410 TYR cc_start: 0.7906 (m-80) cc_final: 0.7176 (m-80) REVERT: D 440 MET cc_start: 0.8865 (mmm) cc_final: 0.8135 (tpt) REVERT: D 530 ILE cc_start: 0.6225 (mp) cc_final: 0.5818 (tp) REVERT: B 233 ASN cc_start: 0.7798 (m110) cc_final: 0.7560 (m-40) REVERT: B 410 TYR cc_start: 0.7892 (m-80) cc_final: 0.7150 (m-80) REVERT: B 440 MET cc_start: 0.8883 (mmm) cc_final: 0.8129 (tpt) REVERT: C 410 TYR cc_start: 0.7740 (m-80) cc_final: 0.7028 (m-80) REVERT: C 440 MET cc_start: 0.8850 (mmm) cc_final: 0.8405 (tpt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1594 time to fit residues: 58.5901 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 ASN D 233 ASN B 233 ASN C 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113892 restraints weight = 24647.612| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.20 r_work: 0.3165 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17900 Z= 0.135 Angle : 0.600 8.727 24112 Z= 0.312 Chirality : 0.042 0.142 2612 Planarity : 0.005 0.060 3032 Dihedral : 4.826 19.522 2300 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.61 % Allowed : 7.92 % Favored : 91.46 % 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 aren not related in a simple way. whole: 0.28 (0.18), residues: 2088 helix: 0.74 (0.15), residues: 1260 sheet: -1.26 (0.39), residues: 136 loop : -0.34 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 505 TYR 0.014 0.001 TYR B 521 PHE 0.011 0.002 PHE C 226 TRP 0.022 0.001 TRP B 254 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00320 (17900) covalent geometry : angle 0.59954 (24112) hydrogen bonds : bond 0.04212 ( 936) hydrogen bonds : angle 5.36176 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 263 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7937 (mmm160) REVERT: A 138 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 210 ASP cc_start: 0.7543 (m-30) cc_final: 0.7150 (m-30) REVERT: A 238 GLN cc_start: 0.7086 (tm130) cc_final: 0.6772 (tm-30) REVERT: A 251 GLU cc_start: 0.7310 (mp0) cc_final: 0.7068 (mt-10) REVERT: A 410 TYR cc_start: 0.7947 (m-80) cc_final: 0.7368 (m-80) REVERT: D 138 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7536 (mm-30) REVERT: D 210 ASP cc_start: 0.7341 (m-30) cc_final: 0.6957 (m-30) REVERT: D 238 GLN cc_start: 0.7202 (tm130) cc_final: 0.6883 (tm-30) REVERT: D 251 GLU cc_start: 0.7273 (mp0) cc_final: 0.7028 (mt-10) REVERT: D 410 TYR cc_start: 0.7959 (m-80) cc_final: 0.7359 (m-80) REVERT: D 440 MET cc_start: 0.8766 (mmm) cc_final: 0.8506 (mmm) REVERT: B 50 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7967 (mmm160) REVERT: B 138 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 210 ASP cc_start: 0.7675 (m-30) cc_final: 0.7291 (m-30) REVERT: B 238 GLN cc_start: 0.7365 (tm130) cc_final: 0.7017 (tm-30) REVERT: B 251 GLU cc_start: 0.7302 (mp0) cc_final: 0.7046 (mt-10) REVERT: B 410 TYR cc_start: 0.7981 (m-80) cc_final: 0.7403 (m-80) REVERT: C 50 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7985 (mmm160) REVERT: C 210 ASP cc_start: 0.7488 (m-30) cc_final: 0.7093 (m-30) REVERT: C 238 GLN cc_start: 0.7312 (tm130) cc_final: 0.6956 (tm-30) REVERT: C 251 GLU cc_start: 0.7340 (mp0) cc_final: 0.7081 (mt-10) REVERT: C 410 TYR cc_start: 0.7993 (m-80) cc_final: 0.7397 (m-80) outliers start: 12 outliers final: 6 residues processed: 267 average time/residue: 0.1534 time to fit residues: 59.9656 Evaluate side-chains 232 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 385 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 200 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN C 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111142 restraints weight = 24885.035| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.24 r_work: 0.3144 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17900 Z= 0.156 Angle : 0.573 9.031 24112 Z= 0.295 Chirality : 0.042 0.139 2612 Planarity : 0.004 0.051 3032 Dihedral : 4.625 19.912 2300 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.43 % Allowed : 10.84 % Favored : 87.73 % 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 aren not related in a simple way. whole: 0.59 (0.18), residues: 2088 helix: 1.01 (0.15), residues: 1240 sheet: -1.23 (0.40), residues: 136 loop : -0.18 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.019 0.002 TYR A 509 PHE 0.011 0.001 PHE C 4 TRP 0.018 0.001 TRP B 254 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00383 (17900) covalent geometry : angle 0.57311 (24112) hydrogen bonds : bond 0.03806 ( 936) hydrogen bonds : angle 4.95896 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.783 Fit side-chains REVERT: A 50 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7888 (mtp-110) REVERT: A 138 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 210 ASP cc_start: 0.7678 (m-30) cc_final: 0.7342 (m-30) REVERT: A 238 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6628 (tm-30) REVERT: A 410 TYR cc_start: 0.8095 (m-80) cc_final: 0.7497 (m-80) REVERT: A 440 MET cc_start: 0.8932 (mmm) cc_final: 0.8644 (mmm) REVERT: A 530 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6634 (mp) REVERT: D 50 ARG cc_start: 0.8322 (mmm160) cc_final: 0.7920 (mtp-110) REVERT: D 138 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7571 (mm-30) REVERT: D 195 GLU cc_start: 0.8599 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 210 ASP cc_start: 0.7675 (m-30) cc_final: 0.7327 (m-30) REVERT: D 238 GLN cc_start: 0.7199 (tm130) cc_final: 0.6738 (tm-30) REVERT: D 410 TYR cc_start: 0.8099 (m-80) cc_final: 0.7468 (m-80) REVERT: D 530 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6755 (mp) REVERT: B 50 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7897 (mtp-110) REVERT: B 138 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 210 ASP cc_start: 0.7670 (m-30) cc_final: 0.7339 (m-30) REVERT: B 238 GLN cc_start: 0.7167 (tm130) cc_final: 0.6676 (tm-30) REVERT: B 410 TYR cc_start: 0.8118 (m-80) cc_final: 0.7534 (m-80) REVERT: B 440 MET cc_start: 0.8936 (mmm) cc_final: 0.8642 (mmm) REVERT: B 530 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6639 (mp) REVERT: C 50 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7826 (mtp-110) REVERT: C 138 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7484 (mm-30) REVERT: C 210 ASP cc_start: 0.7636 (m-30) cc_final: 0.7302 (m-30) REVERT: C 238 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6707 (tm-30) REVERT: C 410 TYR cc_start: 0.8178 (m-80) cc_final: 0.7511 (m-80) REVERT: C 440 MET cc_start: 0.8931 (mmm) cc_final: 0.8635 (mmm) REVERT: C 530 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6629 (mp) outliers start: 28 outliers final: 24 residues processed: 250 average time/residue: 0.1379 time to fit residues: 52.2617 Evaluate side-chains 254 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 520 CYS Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 109 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 63 optimal weight: 0.9980 chunk 102 optimal weight: 0.0170 chunk 164 optimal weight: 0.1980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 GLN B 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115279 restraints weight = 24786.483| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.27 r_work: 0.3208 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17900 Z= 0.099 Angle : 0.523 6.974 24112 Z= 0.268 Chirality : 0.039 0.127 2612 Planarity : 0.004 0.043 3032 Dihedral : 4.323 17.460 2300 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.77 % Allowed : 11.86 % Favored : 87.37 % 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 aren not related in a simple way. whole: 0.64 (0.18), residues: 2088 helix: 1.13 (0.15), residues: 1264 sheet: -2.87 (0.37), residues: 80 loop : -0.28 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 166 TYR 0.011 0.001 TYR C 42 PHE 0.010 0.001 PHE C 407 TRP 0.012 0.001 TRP C 254 HIS 0.003 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00227 (17900) covalent geometry : angle 0.52313 (24112) hydrogen bonds : bond 0.03107 ( 936) hydrogen bonds : angle 4.60718 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 0.763 Fit side-chains REVERT: A 50 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7835 (mtm110) REVERT: A 138 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7512 (mm-30) REVERT: A 195 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 238 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6640 (tm-30) REVERT: A 250 LYS cc_start: 0.8303 (mttm) cc_final: 0.8006 (mmmt) REVERT: A 251 GLU cc_start: 0.7340 (mp0) cc_final: 0.6976 (mt-10) REVERT: A 410 TYR cc_start: 0.8225 (m-80) cc_final: 0.7607 (m-80) REVERT: D 50 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7923 (mtp-110) REVERT: D 138 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7470 (mm-30) REVERT: D 195 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8063 (tm-30) REVERT: D 210 ASP cc_start: 0.7298 (m-30) cc_final: 0.6991 (m-30) REVERT: D 238 GLN cc_start: 0.7111 (tm-30) cc_final: 0.6622 (tm-30) REVERT: D 250 LYS cc_start: 0.8274 (mttm) cc_final: 0.7949 (mmmt) REVERT: D 251 GLU cc_start: 0.7358 (mp0) cc_final: 0.6985 (mt-10) REVERT: D 410 TYR cc_start: 0.8233 (m-80) cc_final: 0.7564 (m-80) REVERT: D 530 ILE cc_start: 0.6911 (mp) cc_final: 0.6452 (mp) REVERT: B 50 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7843 (mtm110) REVERT: B 138 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 195 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 238 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6615 (tm-30) REVERT: B 250 LYS cc_start: 0.8280 (mttm) cc_final: 0.7970 (mmmt) REVERT: B 251 GLU cc_start: 0.7397 (mp0) cc_final: 0.7028 (mt-10) REVERT: B 410 TYR cc_start: 0.8240 (m-80) cc_final: 0.7618 (m-80) REVERT: B 487 LYS cc_start: 0.8723 (mptt) cc_final: 0.8236 (mptt) REVERT: C 50 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7789 (mtp-110) REVERT: C 138 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7483 (mm-30) REVERT: C 195 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 238 GLN cc_start: 0.7261 (tm-30) cc_final: 0.6743 (tm-30) REVERT: C 250 LYS cc_start: 0.8286 (mttm) cc_final: 0.7957 (mmmt) REVERT: C 251 GLU cc_start: 0.7374 (mp0) cc_final: 0.6994 (mt-10) REVERT: C 410 TYR cc_start: 0.8235 (m-80) cc_final: 0.7590 (m-80) outliers start: 15 outliers final: 15 residues processed: 252 average time/residue: 0.1396 time to fit residues: 53.6802 Evaluate side-chains 245 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 133 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 208 optimal weight: 0.0010 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS D 263 HIS B 263 HIS C 263 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114071 restraints weight = 24722.853| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.28 r_work: 0.3192 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17900 Z= 0.113 Angle : 0.520 6.130 24112 Z= 0.264 Chirality : 0.039 0.132 2612 Planarity : 0.004 0.041 3032 Dihedral : 4.207 17.251 2300 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.58 % Allowed : 12.83 % Favored : 85.58 % 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 aren not related in a simple way. whole: 0.85 (0.19), residues: 2088 helix: 1.25 (0.15), residues: 1264 sheet: -1.22 (0.39), residues: 136 loop : -0.19 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.010 0.001 TYR D 521 PHE 0.009 0.001 PHE C 407 TRP 0.011 0.001 TRP D 254 HIS 0.004 0.001 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00274 (17900) covalent geometry : angle 0.52046 (24112) hydrogen bonds : bond 0.03122 ( 936) hydrogen bonds : angle 4.50244 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.759 Fit side-chains REVERT: A 50 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7851 (mtm110) REVERT: A 138 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7471 (mm-30) REVERT: A 195 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 238 GLN cc_start: 0.7231 (tm-30) cc_final: 0.6636 (tm-30) REVERT: A 530 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6542 (mp) REVERT: D 50 ARG cc_start: 0.8377 (mmm160) cc_final: 0.7950 (mtp-110) REVERT: D 138 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7482 (mm-30) REVERT: D 159 MET cc_start: 0.9179 (tpp) cc_final: 0.8752 (mmm) REVERT: D 195 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8080 (tm-30) REVERT: D 210 ASP cc_start: 0.7450 (m-30) cc_final: 0.7127 (m-30) REVERT: D 238 GLN cc_start: 0.7257 (tm-30) cc_final: 0.6667 (tm-30) REVERT: D 410 TYR cc_start: 0.8240 (m-80) cc_final: 0.7562 (m-80) REVERT: D 440 MET cc_start: 0.8817 (mmm) cc_final: 0.8330 (mmm) REVERT: D 530 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6634 (mp) REVERT: B 50 ARG cc_start: 0.8241 (mmm160) cc_final: 0.7849 (mtm110) REVERT: B 138 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 195 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8023 (tm-30) REVERT: B 238 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6611 (tm-30) REVERT: B 487 LYS cc_start: 0.8668 (mptt) cc_final: 0.8192 (mptt) REVERT: B 530 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6536 (mp) REVERT: C 50 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7795 (mtp-110) REVERT: C 138 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7437 (mm-30) REVERT: C 195 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 238 GLN cc_start: 0.7310 (tm-30) cc_final: 0.6704 (tm-30) REVERT: C 530 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6528 (mp) outliers start: 31 outliers final: 23 residues processed: 246 average time/residue: 0.1383 time to fit residues: 52.1117 Evaluate side-chains 246 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 104 optimal weight: 0.0050 chunk 155 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113779 restraints weight = 24699.719| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.26 r_work: 0.3187 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17900 Z= 0.120 Angle : 0.519 5.543 24112 Z= 0.264 Chirality : 0.039 0.132 2612 Planarity : 0.003 0.038 3032 Dihedral : 4.151 17.135 2300 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.10 % Allowed : 13.85 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2088 helix: 1.29 (0.15), residues: 1264 sheet: -2.22 (0.42), residues: 80 loop : -0.31 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.010 0.001 TYR B 42 PHE 0.010 0.001 PHE C 4 TRP 0.010 0.001 TRP D 254 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00292 (17900) covalent geometry : angle 0.51950 (24112) hydrogen bonds : bond 0.03058 ( 936) hydrogen bonds : angle 4.46742 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.765 Fit side-chains REVERT: A 50 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7846 (mtm110) REVERT: A 138 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 195 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 238 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6555 (tm-30) REVERT: A 251 GLU cc_start: 0.7255 (mp0) cc_final: 0.6771 (mt-10) REVERT: A 440 MET cc_start: 0.8849 (mmm) cc_final: 0.8371 (mmm) REVERT: A 530 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6479 (mp) REVERT: D 50 ARG cc_start: 0.8420 (mmm160) cc_final: 0.7979 (mtp-110) REVERT: D 138 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7482 (mm-30) REVERT: D 195 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8159 (tm-30) REVERT: D 238 GLN cc_start: 0.7311 (tm-30) cc_final: 0.6592 (tm-30) REVERT: D 251 GLU cc_start: 0.7484 (mp0) cc_final: 0.6999 (mt-10) REVERT: D 344 MET cc_start: 0.9284 (mmm) cc_final: 0.9081 (mmp) REVERT: D 410 TYR cc_start: 0.8239 (m-80) cc_final: 0.7589 (m-80) REVERT: D 440 MET cc_start: 0.8819 (mmm) cc_final: 0.8366 (mmm) REVERT: D 530 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6568 (mp) REVERT: B 50 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7839 (mtm110) REVERT: B 138 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 195 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B 238 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6542 (tm-30) REVERT: B 251 GLU cc_start: 0.7330 (mp0) cc_final: 0.6808 (mt-10) REVERT: B 440 MET cc_start: 0.8851 (mmm) cc_final: 0.8369 (mmm) REVERT: B 487 LYS cc_start: 0.8618 (mptt) cc_final: 0.8071 (mptt) REVERT: B 530 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6480 (mp) REVERT: C 50 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7834 (mtp-110) REVERT: C 138 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7472 (mm-30) REVERT: C 195 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 238 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6708 (tm-30) REVERT: C 440 MET cc_start: 0.8858 (mmm) cc_final: 0.8384 (mmm) REVERT: C 530 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6535 (mp) outliers start: 41 outliers final: 28 residues processed: 243 average time/residue: 0.1438 time to fit residues: 53.3201 Evaluate side-chains 247 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 149 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112855 restraints weight = 24681.685| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.25 r_work: 0.3173 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17900 Z= 0.131 Angle : 0.534 7.613 24112 Z= 0.268 Chirality : 0.040 0.136 2612 Planarity : 0.003 0.036 3032 Dihedral : 4.147 17.186 2300 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.20 % Allowed : 13.60 % Favored : 84.20 % 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 aren not related in a simple way. whole: 0.87 (0.18), residues: 2088 helix: 1.32 (0.15), residues: 1264 sheet: -1.92 (0.46), residues: 80 loop : -0.31 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.012 0.001 TYR B 42 PHE 0.010 0.001 PHE C 4 TRP 0.011 0.001 TRP C 254 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00323 (17900) covalent geometry : angle 0.53381 (24112) hydrogen bonds : bond 0.03118 ( 936) hydrogen bonds : angle 4.44246 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.596 Fit side-chains REVERT: A 50 ARG cc_start: 0.8244 (mmm160) cc_final: 0.7869 (mtm110) REVERT: A 138 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7477 (mm-30) REVERT: A 192 GLU cc_start: 0.8568 (tt0) cc_final: 0.8288 (tt0) REVERT: A 195 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 230 LEU cc_start: 0.7202 (mp) cc_final: 0.6982 (mp) REVERT: A 238 GLN cc_start: 0.7398 (tm-30) cc_final: 0.6661 (tm-30) REVERT: A 251 GLU cc_start: 0.7068 (mp0) cc_final: 0.6731 (mt-10) REVERT: A 440 MET cc_start: 0.8875 (mmm) cc_final: 0.8396 (mmm) REVERT: A 530 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6336 (mp) REVERT: D 50 ARG cc_start: 0.8458 (mmm160) cc_final: 0.8012 (mtp-110) REVERT: D 138 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7493 (mm-30) REVERT: D 192 GLU cc_start: 0.8527 (tt0) cc_final: 0.8263 (tt0) REVERT: D 195 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8153 (tm-30) REVERT: D 238 GLN cc_start: 0.7426 (tm-30) cc_final: 0.6691 (tm-30) REVERT: D 251 GLU cc_start: 0.7282 (mp0) cc_final: 0.6826 (mt-10) REVERT: D 440 MET cc_start: 0.8920 (mmm) cc_final: 0.8054 (mmm) REVERT: D 530 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6419 (mp) REVERT: B 50 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7866 (mtm110) REVERT: B 192 GLU cc_start: 0.8547 (tt0) cc_final: 0.8284 (tt0) REVERT: B 195 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 230 LEU cc_start: 0.7215 (mp) cc_final: 0.6998 (mp) REVERT: B 238 GLN cc_start: 0.7379 (tm-30) cc_final: 0.6628 (tm-30) REVERT: B 251 GLU cc_start: 0.7369 (mp0) cc_final: 0.6909 (mt-10) REVERT: B 440 MET cc_start: 0.8879 (mmm) cc_final: 0.8397 (mmm) REVERT: B 487 LYS cc_start: 0.8631 (mptt) cc_final: 0.8113 (mptt) REVERT: B 530 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6321 (mp) REVERT: C 50 ARG cc_start: 0.8267 (mmm160) cc_final: 0.7862 (mtp-110) REVERT: C 138 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 159 MET cc_start: 0.9211 (tpp) cc_final: 0.8831 (mmm) REVERT: C 192 GLU cc_start: 0.8559 (tt0) cc_final: 0.8278 (tt0) REVERT: C 195 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 238 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6726 (tm-30) REVERT: C 440 MET cc_start: 0.8974 (mmm) cc_final: 0.8503 (mmm) REVERT: C 530 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6376 (mp) outliers start: 43 outliers final: 32 residues processed: 243 average time/residue: 0.1397 time to fit residues: 51.9811 Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 188 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.142679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114584 restraints weight = 24649.810| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.28 r_work: 0.3198 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17900 Z= 0.106 Angle : 0.522 8.139 24112 Z= 0.261 Chirality : 0.039 0.130 2612 Planarity : 0.003 0.034 3032 Dihedral : 4.069 16.749 2300 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.94 % Allowed : 14.37 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.18), residues: 2088 helix: 1.41 (0.15), residues: 1264 sheet: -1.83 (0.46), residues: 80 loop : -0.32 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 166 TYR 0.012 0.001 TYR A 42 PHE 0.009 0.001 PHE C 407 TRP 0.009 0.001 TRP C 254 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00253 (17900) covalent geometry : angle 0.52227 (24112) hydrogen bonds : bond 0.02885 ( 936) hydrogen bonds : angle 4.35368 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.796 Fit side-chains REVERT: A 50 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7876 (mtp-110) REVERT: A 138 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 192 GLU cc_start: 0.8547 (tt0) cc_final: 0.8271 (tt0) REVERT: A 195 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 238 GLN cc_start: 0.7354 (tm-30) cc_final: 0.6596 (tm-30) REVERT: A 251 GLU cc_start: 0.7307 (mp0) cc_final: 0.6984 (mt-10) REVERT: A 257 GLU cc_start: 0.6515 (tp30) cc_final: 0.6292 (tp30) REVERT: A 408 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8798 (mp) REVERT: A 410 TYR cc_start: 0.8140 (m-80) cc_final: 0.7414 (m-80) REVERT: A 440 MET cc_start: 0.8957 (mmm) cc_final: 0.8439 (mmm) REVERT: A 530 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6329 (mp) REVERT: D 50 ARG cc_start: 0.8427 (mmm160) cc_final: 0.7934 (mtm110) REVERT: D 138 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 192 GLU cc_start: 0.8542 (tt0) cc_final: 0.8275 (tt0) REVERT: D 195 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8250 (tm-30) REVERT: D 238 GLN cc_start: 0.7409 (tm-30) cc_final: 0.6645 (tm-30) REVERT: D 408 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8799 (mp) REVERT: D 410 TYR cc_start: 0.8145 (m-80) cc_final: 0.7390 (m-80) REVERT: D 440 MET cc_start: 0.8925 (mmm) cc_final: 0.8047 (mmm) REVERT: D 530 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6392 (mp) REVERT: B 50 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7883 (mtp-110) REVERT: B 192 GLU cc_start: 0.8519 (tt0) cc_final: 0.8257 (tt0) REVERT: B 195 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8134 (tm-30) REVERT: B 238 GLN cc_start: 0.7342 (tm-30) cc_final: 0.6573 (tm-30) REVERT: B 251 GLU cc_start: 0.7092 (mp0) cc_final: 0.6757 (mt-10) REVERT: B 408 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8814 (mp) REVERT: B 410 TYR cc_start: 0.8164 (m-80) cc_final: 0.7438 (m-80) REVERT: B 440 MET cc_start: 0.8958 (mmm) cc_final: 0.8426 (mmm) REVERT: B 487 LYS cc_start: 0.8590 (mptt) cc_final: 0.8191 (mptt) REVERT: B 530 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6305 (mp) REVERT: C 42 TYR cc_start: 0.8515 (t80) cc_final: 0.8314 (t80) REVERT: C 50 ARG cc_start: 0.8259 (mmm160) cc_final: 0.7845 (mtp-110) REVERT: C 138 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7397 (mm-30) REVERT: C 192 GLU cc_start: 0.8542 (tt0) cc_final: 0.8265 (tt0) REVERT: C 195 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8144 (tm-30) REVERT: C 238 GLN cc_start: 0.7338 (tm-30) cc_final: 0.6637 (tm-30) REVERT: C 410 TYR cc_start: 0.8177 (m-80) cc_final: 0.7301 (m-80) REVERT: C 440 MET cc_start: 0.8934 (mmm) cc_final: 0.8471 (mmm) REVERT: C 530 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6337 (mp) outliers start: 38 outliers final: 27 residues processed: 246 average time/residue: 0.1512 time to fit residues: 56.5217 Evaluate side-chains 246 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 203 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 157 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114524 restraints weight = 24597.980| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.25 r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17900 Z= 0.111 Angle : 0.539 7.874 24112 Z= 0.266 Chirality : 0.039 0.133 2612 Planarity : 0.003 0.034 3032 Dihedral : 4.051 16.768 2300 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.20 % Allowed : 14.83 % Favored : 82.98 % 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 aren not related in a simple way. whole: 1.00 (0.18), residues: 2088 helix: 1.42 (0.15), residues: 1264 sheet: -1.66 (0.46), residues: 80 loop : -0.28 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 166 TYR 0.013 0.001 TYR B 42 PHE 0.010 0.001 PHE B 211 TRP 0.010 0.001 TRP C 254 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00269 (17900) covalent geometry : angle 0.53906 (24112) hydrogen bonds : bond 0.02949 ( 936) hydrogen bonds : angle 4.33620 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.764 Fit side-chains REVERT: A 50 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7901 (mtp-110) REVERT: A 192 GLU cc_start: 0.8530 (tt0) cc_final: 0.8257 (tt0) REVERT: A 195 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 238 GLN cc_start: 0.7363 (tm-30) cc_final: 0.6593 (tm-30) REVERT: A 251 GLU cc_start: 0.7287 (mp0) cc_final: 0.6952 (mt-10) REVERT: A 408 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 410 TYR cc_start: 0.8137 (m-80) cc_final: 0.7385 (m-80) REVERT: A 440 MET cc_start: 0.8936 (mmm) cc_final: 0.8440 (mmm) REVERT: A 530 ILE cc_start: 0.6659 (OUTLIER) cc_final: 0.6278 (mp) REVERT: D 50 ARG cc_start: 0.8430 (mmm160) cc_final: 0.7944 (mtm110) REVERT: D 138 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7392 (mm-30) REVERT: D 192 GLU cc_start: 0.8533 (tt0) cc_final: 0.8261 (tt0) REVERT: D 195 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8174 (tm-30) REVERT: D 238 GLN cc_start: 0.7399 (tm-30) cc_final: 0.6630 (tm-30) REVERT: D 251 GLU cc_start: 0.7411 (mp0) cc_final: 0.6938 (mt-10) REVERT: D 410 TYR cc_start: 0.8197 (m-80) cc_final: 0.7454 (m-80) REVERT: D 440 MET cc_start: 0.8950 (mmm) cc_final: 0.8062 (mmm) REVERT: D 530 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6378 (mp) REVERT: B 50 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7895 (mtp-110) REVERT: B 192 GLU cc_start: 0.8507 (tt0) cc_final: 0.8242 (tt0) REVERT: B 195 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 238 GLN cc_start: 0.7343 (tm-30) cc_final: 0.6569 (tm-30) REVERT: B 408 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8796 (mp) REVERT: B 410 TYR cc_start: 0.8211 (m-80) cc_final: 0.7473 (m-80) REVERT: B 440 MET cc_start: 0.8948 (mmm) cc_final: 0.8447 (mmm) REVERT: B 487 LYS cc_start: 0.8600 (mptt) cc_final: 0.8203 (mptt) REVERT: B 530 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6272 (mp) REVERT: C 42 TYR cc_start: 0.8529 (t80) cc_final: 0.8309 (t80) REVERT: C 50 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7844 (mtp-110) REVERT: C 138 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7371 (mm-30) REVERT: C 192 GLU cc_start: 0.8521 (tt0) cc_final: 0.8258 (tt0) REVERT: C 195 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 238 GLN cc_start: 0.7400 (tm-30) cc_final: 0.6661 (tm-30) REVERT: C 410 TYR cc_start: 0.8162 (m-80) cc_final: 0.7459 (m-80) REVERT: C 440 MET cc_start: 0.8937 (mmm) cc_final: 0.8446 (mmm) REVERT: C 530 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6296 (mp) outliers start: 43 outliers final: 32 residues processed: 244 average time/residue: 0.1510 time to fit residues: 56.5815 Evaluate side-chains 250 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 520 CYS Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 520 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 520 CYS Chi-restraints excluded: chain C residue 530 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 104 optimal weight: 0.2980 chunk 123 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 0.0470 chunk 189 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115932 restraints weight = 24462.567| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.25 r_work: 0.3219 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17900 Z= 0.100 Angle : 0.539 8.429 24112 Z= 0.264 Chirality : 0.039 0.131 2612 Planarity : 0.003 0.034 3032 Dihedral : 4.002 16.190 2300 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.89 % Allowed : 15.49 % Favored : 82.62 % 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 aren not related in a simple way. whole: 1.06 (0.18), residues: 2088 helix: 1.47 (0.15), residues: 1264 sheet: -1.61 (0.46), residues: 80 loop : -0.26 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.014 0.001 TYR A 42 PHE 0.010 0.001 PHE D 4 TRP 0.009 0.001 TRP C 254 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00236 (17900) covalent geometry : angle 0.53874 (24112) hydrogen bonds : bond 0.02774 ( 936) hydrogen bonds : angle 4.27399 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4176 Ramachandran restraints generated. 2088 Oldfield, 0 Emsley, 2088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.771 Fit side-chains REVERT: A 42 TYR cc_start: 0.8544 (t80) cc_final: 0.8342 (t80) REVERT: A 50 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7881 (mtp-110) REVERT: A 166 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.8364 (mpp-170) REVERT: A 192 GLU cc_start: 0.8518 (tt0) cc_final: 0.8241 (tt0) REVERT: A 195 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8092 (tm-30) REVERT: A 238 GLN cc_start: 0.7309 (tm-30) cc_final: 0.6525 (tm-30) REVERT: A 410 TYR cc_start: 0.8212 (m-80) cc_final: 0.7422 (m-80) REVERT: A 440 MET cc_start: 0.8926 (mmm) cc_final: 0.8412 (mmm) REVERT: A 530 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6264 (mp) REVERT: D 50 ARG cc_start: 0.8400 (mmm160) cc_final: 0.7973 (mtp-110) REVERT: D 138 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7345 (mm-30) REVERT: D 192 GLU cc_start: 0.8517 (tt0) cc_final: 0.8246 (tt0) REVERT: D 195 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8237 (tm-30) REVERT: D 238 GLN cc_start: 0.7325 (tm-30) cc_final: 0.6545 (tm-30) REVERT: D 251 GLU cc_start: 0.7404 (mp0) cc_final: 0.6925 (mt-10) REVERT: D 410 TYR cc_start: 0.8257 (m-80) cc_final: 0.7569 (m-80) REVERT: D 440 MET cc_start: 0.8937 (mmm) cc_final: 0.8027 (mmm) REVERT: D 530 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6300 (mp) REVERT: B 42 TYR cc_start: 0.8531 (t80) cc_final: 0.8326 (t80) REVERT: B 50 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7877 (mtp-110) REVERT: B 166 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8385 (mpp-170) REVERT: B 192 GLU cc_start: 0.8515 (tt0) cc_final: 0.8243 (tt0) REVERT: B 195 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 238 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6520 (tm-30) REVERT: B 251 GLU cc_start: 0.7460 (mp0) cc_final: 0.7024 (mt-10) REVERT: B 257 GLU cc_start: 0.6642 (tp30) cc_final: 0.6419 (tp30) REVERT: B 410 TYR cc_start: 0.8218 (m-80) cc_final: 0.7444 (m-80) REVERT: B 440 MET cc_start: 0.8938 (mmm) cc_final: 0.8418 (mmm) REVERT: B 487 LYS cc_start: 0.8591 (mptt) cc_final: 0.8188 (mptt) REVERT: B 530 ILE cc_start: 0.6609 (OUTLIER) cc_final: 0.6237 (mp) REVERT: C 42 TYR cc_start: 0.8519 (t80) cc_final: 0.8294 (t80) REVERT: C 50 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7840 (mtp-110) REVERT: C 192 GLU cc_start: 0.8509 (tt0) cc_final: 0.8234 (tt0) REVERT: C 195 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 238 GLN cc_start: 0.7407 (tm-30) cc_final: 0.6675 (tm-30) REVERT: C 410 TYR cc_start: 0.8187 (m-80) cc_final: 0.7410 (m-80) REVERT: C 440 MET cc_start: 0.8930 (mmm) cc_final: 0.8420 (mmm) REVERT: C 530 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6273 (mp) outliers start: 37 outliers final: 29 residues processed: 260 average time/residue: 0.1422 time to fit residues: 56.6984 Evaluate side-chains 248 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 530 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 164 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 191 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115646 restraints weight = 24547.577| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.24 r_work: 0.3212 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17900 Z= 0.104 Angle : 0.543 8.000 24112 Z= 0.266 Chirality : 0.039 0.128 2612 Planarity : 0.003 0.033 3032 Dihedral : 3.983 16.175 2300 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.10 % Allowed : 15.80 % Favored : 82.11 % 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 aren not related in a simple way. whole: 1.07 (0.19), residues: 2088 helix: 1.47 (0.15), residues: 1272 sheet: -1.43 (0.46), residues: 80 loop : -0.28 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.015 0.001 TYR A 42 PHE 0.010 0.001 PHE D 4 TRP 0.009 0.001 TRP C 254 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00248 (17900) covalent geometry : angle 0.54271 (24112) hydrogen bonds : bond 0.02788 ( 936) hydrogen bonds : angle 4.23133 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.19 seconds wall clock time: 70 minutes 35.29 seconds (4235.29 seconds total)