Starting phenix.real_space_refine on Sun Jun 15 13:23:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ka4_9954/06_2025/6ka4_9954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ka4_9954/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ka4_9954/06_2025/6ka4_9954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ka4_9954/06_2025/6ka4_9954.map" model { file = "/net/cci-nas-00/data/ceres_data/6ka4_9954/06_2025/6ka4_9954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ka4_9954/06_2025/6ka4_9954.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 9.94, per 1000 atoms: 0.57 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: 4.67 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.08 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: 5.93 Time building geometry restraints manager: 5.48 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.620 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: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 41.020 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (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 TRP 0.047 0.002 TRP C 254 HIS 0.005 0.001 HIS A 204 PHE 0.015 0.002 PHE B 438 TYR 0.012 0.002 TYR B 521 ARG 0.007 0.001 ARG C 186 Details of bonding type rmsd hydrogen bonds : bond 0.18461 ( 936) hydrogen bonds : angle 7.81641 ( 2700) covalent geometry : bond 0.00643 (17900) covalent geometry : angle 0.81633 (24112) *********************** 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 : 2.030 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: 0.3443 time to fit residues: 126.5451 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 : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.140462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112892 restraints weight = 24575.412| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.22 r_work: 0.3167 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1295 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= 0.139 Angle : 0.607 9.148 24112 Z= 0.317 Chirality : 0.042 0.145 2612 Planarity : 0.005 0.061 3032 Dihedral : 4.848 19.652 2300 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.61 % Allowed : 8.28 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2088 helix: 0.81 (0.15), residues: 1256 sheet: -1.23 (0.40), residues: 136 loop : -0.34 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 254 HIS 0.004 0.001 HIS D 204 PHE 0.010 0.002 PHE C 226 TYR 0.014 0.001 TYR B 521 ARG 0.003 0.001 ARG C 505 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 936) hydrogen bonds : angle 5.42019 ( 2700) covalent geometry : bond 0.00328 (17900) covalent geometry : angle 0.60655 (24112) *********************** 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 258 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 246 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7933 (mmm160) REVERT: A 138 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 210 ASP cc_start: 0.7541 (m-30) cc_final: 0.7163 (m-30) REVERT: A 238 GLN cc_start: 0.7307 (tm130) cc_final: 0.6966 (tm-30) REVERT: A 410 TYR cc_start: 0.7910 (m-80) cc_final: 0.7327 (m-80) REVERT: A 440 MET cc_start: 0.8796 (mmm) cc_final: 0.8341 (tpt) REVERT: D 50 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7913 (mtp-110) REVERT: D 210 ASP cc_start: 0.7347 (m-30) cc_final: 0.6984 (m-30) REVERT: D 238 GLN cc_start: 0.7229 (tm130) cc_final: 0.6928 (tm-30) REVERT: D 410 TYR cc_start: 0.7911 (m-80) cc_final: 0.7306 (m-80) REVERT: D 440 MET cc_start: 0.8777 (mmm) cc_final: 0.8538 (mmm) REVERT: B 50 ARG cc_start: 0.8183 (mmm160) cc_final: 0.7961 (mmm160) REVERT: B 138 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 210 ASP cc_start: 0.7692 (m-30) cc_final: 0.7329 (m-30) REVERT: B 238 GLN cc_start: 0.7357 (tm130) cc_final: 0.7001 (tm-30) REVERT: B 410 TYR cc_start: 0.7886 (m-80) cc_final: 0.7288 (m-80) REVERT: C 50 ARG cc_start: 0.8249 (mmm160) cc_final: 0.7829 (mtp-110) REVERT: C 210 ASP cc_start: 0.7657 (m-30) cc_final: 0.7296 (m-30) REVERT: C 238 GLN cc_start: 0.7343 (tm130) cc_final: 0.6992 (tm-30) REVERT: C 410 TYR cc_start: 0.7952 (m-80) cc_final: 0.7356 (m-80) REVERT: C 440 MET cc_start: 0.8803 (mmm) cc_final: 0.8346 (tpt) outliers start: 12 outliers final: 9 residues processed: 250 average time/residue: 0.3396 time to fit residues: 125.4777 Evaluate side-chains 223 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 329 SER 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 198 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 193 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 C 238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115022 restraints weight = 24651.160| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.17 r_work: 0.3188 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1771 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= 0.121 Angle : 0.543 9.045 24112 Z= 0.279 Chirality : 0.041 0.132 2612 Planarity : 0.004 0.051 3032 Dihedral : 4.517 19.537 2300 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.12 % Allowed : 10.12 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2088 helix: 1.03 (0.15), residues: 1264 sheet: -1.12 (0.41), residues: 128 loop : -0.14 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 254 HIS 0.004 0.001 HIS B 204 PHE 0.010 0.001 PHE C 407 TYR 0.022 0.001 TYR A 509 ARG 0.002 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 936) hydrogen bonds : angle 4.81997 ( 2700) covalent geometry : bond 0.00283 (17900) covalent geometry : angle 0.54299 (24112) *********************** 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 292 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 2.197 Fit side-chains REVERT: A 50 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7860 (mtp-110) REVERT: A 138 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 195 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 210 ASP cc_start: 0.7652 (m-30) cc_final: 0.7313 (m-30) REVERT: A 238 GLN cc_start: 0.7111 (tm130) cc_final: 0.6646 (tm-30) REVERT: A 410 TYR cc_start: 0.8056 (m-80) cc_final: 0.7442 (m-80) REVERT: A 530 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6600 (mp) REVERT: D 50 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7905 (mtp-110) REVERT: D 138 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7496 (mm-30) REVERT: D 159 MET cc_start: 0.9233 (tpp) cc_final: 0.8781 (tpp) REVERT: D 195 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8008 (tm-30) REVERT: D 210 ASP cc_start: 0.7259 (m-30) cc_final: 0.6919 (m-30) REVERT: D 238 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6610 (tm-30) REVERT: D 410 TYR cc_start: 0.8139 (m-80) cc_final: 0.7522 (m-80) REVERT: D 530 ILE cc_start: 0.6964 (OUTLIER) cc_final: 0.6717 (mp) REVERT: B 50 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7871 (mtp-110) REVERT: B 138 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7475 (mm-30) REVERT: B 195 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 210 ASP cc_start: 0.7633 (m-30) cc_final: 0.7295 (m-30) REVERT: B 238 GLN cc_start: 0.7072 (tm-30) cc_final: 0.6605 (tm-30) REVERT: B 410 TYR cc_start: 0.8082 (m-80) cc_final: 0.7484 (m-80) REVERT: B 440 MET cc_start: 0.8902 (mmm) cc_final: 0.8635 (mmm) REVERT: B 530 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6604 (mp) REVERT: C 50 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7812 (mtp-110) REVERT: C 195 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 210 ASP cc_start: 0.7411 (m-30) cc_final: 0.7061 (m-30) REVERT: C 238 GLN cc_start: 0.7233 (tm-30) cc_final: 0.6768 (tm-30) REVERT: C 410 TYR cc_start: 0.8163 (m-80) cc_final: 0.7569 (m-80) REVERT: C 530 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6592 (mp) outliers start: 22 outliers final: 16 residues processed: 275 average time/residue: 0.2896 time to fit residues: 121.8292 Evaluate side-chains 249 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 385 LEU 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 385 LEU 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 385 LEU 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 385 LEU 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 177 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN D 263 HIS C 263 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114258 restraints weight = 24636.198| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.25 r_work: 0.3210 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2068 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 : 0.529 6.916 24112 Z= 0.269 Chirality : 0.039 0.131 2612 Planarity : 0.004 0.045 3032 Dihedral : 4.308 17.682 2300 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.02 % Allowed : 11.71 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2088 helix: 1.19 (0.15), residues: 1264 sheet: -1.95 (0.52), residues: 48 loop : -0.42 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 254 HIS 0.003 0.001 HIS A 204 PHE 0.009 0.001 PHE C 407 TYR 0.011 0.001 TYR D 521 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 936) hydrogen bonds : angle 4.63732 ( 2700) covalent geometry : bond 0.00271 (17900) covalent geometry : angle 0.52932 (24112) *********************** 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 253 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 2.255 Fit side-chains REVERT: A 50 ARG cc_start: 0.8233 (mmm160) cc_final: 0.7875 (mtm110) REVERT: A 138 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7547 (mm-30) REVERT: A 184 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8188 (mt-10) REVERT: A 195 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 210 ASP cc_start: 0.7664 (m-30) cc_final: 0.7341 (m-30) REVERT: A 238 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6603 (tm-30) REVERT: A 410 TYR cc_start: 0.8155 (m-80) cc_final: 0.7528 (m-80) REVERT: A 440 MET cc_start: 0.8831 (mmm) cc_final: 0.8569 (mmm) REVERT: D 50 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7906 (mtm110) REVERT: D 138 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 184 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8175 (mt-10) REVERT: D 195 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8062 (tm-30) REVERT: D 210 ASP cc_start: 0.7272 (m-30) cc_final: 0.6958 (m-30) REVERT: D 238 GLN cc_start: 0.7155 (tm-30) cc_final: 0.6662 (tm-30) REVERT: D 410 TYR cc_start: 0.8210 (m-80) cc_final: 0.7568 (m-80) REVERT: D 440 MET cc_start: 0.8828 (mmm) cc_final: 0.8511 (mmm) REVERT: D 530 ILE cc_start: 0.6971 (mp) cc_final: 0.6501 (mp) REVERT: B 50 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7882 (mtm110) REVERT: B 138 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 195 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 210 ASP cc_start: 0.7488 (m-30) cc_final: 0.7158 (m-30) REVERT: B 238 GLN cc_start: 0.7149 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 410 TYR cc_start: 0.8217 (m-80) cc_final: 0.7594 (m-80) REVERT: B 530 ILE cc_start: 0.6926 (mp) cc_final: 0.6444 (mp) REVERT: C 50 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7871 (mtp-110) REVERT: C 138 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7504 (mm-30) REVERT: C 195 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8068 (tm-30) REVERT: C 210 ASP cc_start: 0.7425 (m-30) cc_final: 0.7101 (m-30) REVERT: C 238 GLN cc_start: 0.7144 (tm-30) cc_final: 0.6643 (tm-30) REVERT: C 410 TYR cc_start: 0.8211 (m-80) cc_final: 0.7601 (m-80) REVERT: C 440 MET cc_start: 0.8858 (mmm) cc_final: 0.8596 (mmm) REVERT: C 530 ILE cc_start: 0.6933 (mp) cc_final: 0.6458 (mp) outliers start: 20 outliers final: 19 residues processed: 243 average time/residue: 0.2958 time to fit residues: 109.4909 Evaluate side-chains 241 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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 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 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 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 520 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS B 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111549 restraints weight = 25078.751| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.29 r_work: 0.3156 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17900 Z= 0.146 Angle : 0.539 5.997 24112 Z= 0.275 Chirality : 0.040 0.139 2612 Planarity : 0.004 0.042 3032 Dihedral : 4.302 18.053 2300 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 12.07 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2088 helix: 1.20 (0.15), residues: 1264 sheet: -1.04 (0.40), residues: 136 loop : -0.18 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 254 HIS 0.004 0.001 HIS D 204 PHE 0.013 0.001 PHE C 4 TYR 0.011 0.001 TYR B 521 ARG 0.003 0.000 ARG C 508 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 936) hydrogen bonds : angle 4.59639 ( 2700) covalent geometry : bond 0.00359 (17900) covalent geometry : angle 0.53931 (24112) *********************** 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 275 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 2.194 Fit side-chains REVERT: A 50 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7893 (mtm110) REVERT: A 138 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 184 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8175 (mt-10) REVERT: A 195 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 238 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6611 (tm-30) REVERT: A 440 MET cc_start: 0.8856 (mmm) cc_final: 0.8397 (mmm) REVERT: A 530 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6585 (mp) REVERT: D 50 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7943 (mtp-110) REVERT: D 138 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7531 (mm-30) REVERT: D 184 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8189 (mt-10) REVERT: D 192 GLU cc_start: 0.8543 (tt0) cc_final: 0.8266 (tt0) REVERT: D 195 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 238 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6665 (tm-30) REVERT: D 440 MET cc_start: 0.8860 (mmm) cc_final: 0.8358 (mmm) REVERT: D 530 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6659 (mp) REVERT: B 50 ARG cc_start: 0.8304 (mmm160) cc_final: 0.7901 (mtm110) REVERT: B 138 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 195 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 238 GLN cc_start: 0.7224 (tm-30) cc_final: 0.6613 (tm-30) REVERT: B 530 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6574 (mp) REVERT: C 50 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7851 (mtp-110) REVERT: C 138 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7478 (mm-30) REVERT: C 195 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8060 (tm-30) REVERT: C 238 GLN cc_start: 0.7239 (tm-30) cc_final: 0.6622 (tm-30) REVERT: C 410 TYR cc_start: 0.8266 (m-80) cc_final: 0.7542 (m-80) REVERT: C 440 MET cc_start: 0.8867 (mmm) cc_final: 0.8406 (mmm) REVERT: C 530 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6552 (mp) outliers start: 48 outliers final: 40 residues processed: 247 average time/residue: 0.2960 time to fit residues: 111.1201 Evaluate side-chains 260 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 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 516 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 239 VAL Chi-restraints excluded: chain D residue 276 THR 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 482 ILE Chi-restraints excluded: chain D residue 516 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 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 516 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 239 VAL 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 516 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 127 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.140906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112566 restraints weight = 24799.009| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.26 r_work: 0.3171 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17900 Z= 0.128 Angle : 0.520 5.545 24112 Z= 0.266 Chirality : 0.040 0.133 2612 Planarity : 0.003 0.038 3032 Dihedral : 4.222 17.594 2300 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.71 % Allowed : 12.47 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2088 helix: 1.24 (0.15), residues: 1264 sheet: -2.07 (0.44), residues: 80 loop : -0.28 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.004 0.001 HIS C 204 PHE 0.011 0.001 PHE C 4 TYR 0.011 0.001 TYR B 42 ARG 0.002 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 936) hydrogen bonds : angle 4.52998 ( 2700) covalent geometry : bond 0.00312 (17900) covalent geometry : angle 0.51995 (24112) *********************** 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 274 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 2.190 Fit side-chains REVERT: A 50 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7871 (mtm110) REVERT: A 138 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 184 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8171 (mt-10) REVERT: A 192 GLU cc_start: 0.8549 (tt0) cc_final: 0.8268 (tt0) REVERT: A 195 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 238 GLN cc_start: 0.7224 (tm-30) cc_final: 0.6510 (tm-30) REVERT: A 440 MET cc_start: 0.8832 (mmm) cc_final: 0.8066 (mmm) REVERT: A 530 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6510 (mp) REVERT: D 50 ARG cc_start: 0.8339 (mmm160) cc_final: 0.7947 (mtp-110) REVERT: D 138 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7530 (mm-30) REVERT: D 184 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8184 (mt-10) REVERT: D 192 GLU cc_start: 0.8542 (tt0) cc_final: 0.8267 (tt0) REVERT: D 195 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 238 GLN cc_start: 0.7266 (tm-30) cc_final: 0.6621 (tm-30) REVERT: D 440 MET cc_start: 0.8921 (mmm) cc_final: 0.8100 (mmm) REVERT: D 530 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6419 (mp) REVERT: B 50 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7876 (mtm110) REVERT: B 138 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 192 GLU cc_start: 0.8520 (tt0) cc_final: 0.8246 (tt0) REVERT: B 195 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 238 GLN cc_start: 0.7222 (tm-30) cc_final: 0.6497 (tm-30) REVERT: B 440 MET cc_start: 0.8859 (mmm) cc_final: 0.8419 (mmm) REVERT: B 530 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6503 (mp) REVERT: C 50 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7859 (mtp-110) REVERT: C 138 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7487 (mm-30) REVERT: C 195 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 238 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6588 (tm-30) REVERT: C 410 TYR cc_start: 0.8251 (m-80) cc_final: 0.7542 (m-80) REVERT: C 440 MET cc_start: 0.8940 (mmm) cc_final: 0.8180 (mmm) REVERT: C 530 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6353 (mp) outliers start: 53 outliers final: 40 residues processed: 254 average time/residue: 0.2877 time to fit residues: 112.5415 Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 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 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 291 CYS 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 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 291 CYS Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU 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 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 520 CYS 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 198 optimal weight: 0.1980 chunk 160 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 148 optimal weight: 0.6980 chunk 149 optimal weight: 0.2980 chunk 68 optimal weight: 0.0980 chunk 156 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.143193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115243 restraints weight = 24584.051| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.27 r_work: 0.3209 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17900 Z= 0.096 Angle : 0.510 7.817 24112 Z= 0.256 Chirality : 0.039 0.128 2612 Planarity : 0.003 0.036 3032 Dihedral : 4.091 16.836 2300 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.30 % Allowed : 13.75 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2088 helix: 1.37 (0.15), residues: 1264 sheet: -1.87 (0.44), residues: 80 loop : -0.28 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 254 HIS 0.003 0.001 HIS A 204 PHE 0.009 0.001 PHE C 407 TYR 0.011 0.001 TYR C 42 ARG 0.002 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 936) hydrogen bonds : angle 4.37174 ( 2700) covalent geometry : bond 0.00224 (17900) covalent geometry : angle 0.51024 (24112) *********************** 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 280 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 2.179 Fit side-chains REVERT: A 50 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7836 (mtm110) REVERT: A 138 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 192 GLU cc_start: 0.8511 (tt0) cc_final: 0.8236 (tt0) REVERT: A 195 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 230 LEU cc_start: 0.7316 (mp) cc_final: 0.7088 (mp) REVERT: A 238 GLN cc_start: 0.7209 (tm-30) cc_final: 0.6489 (tm-30) REVERT: A 257 GLU cc_start: 0.6593 (tp30) cc_final: 0.6351 (tp30) REVERT: A 410 TYR cc_start: 0.8136 (m-80) cc_final: 0.7444 (m-80) REVERT: A 440 MET cc_start: 0.9050 (mmm) cc_final: 0.8099 (mmm) REVERT: A 530 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6408 (mp) REVERT: D 50 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7855 (mtm110) REVERT: D 138 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7514 (mm-30) REVERT: D 192 GLU cc_start: 0.8532 (tt0) cc_final: 0.8257 (tt0) REVERT: D 195 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8179 (tm-30) REVERT: D 230 LEU cc_start: 0.7258 (mp) cc_final: 0.7055 (mp) REVERT: D 238 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6466 (tm-30) REVERT: D 410 TYR cc_start: 0.8124 (m-80) cc_final: 0.7419 (m-80) REVERT: D 440 MET cc_start: 0.8892 (mmm) cc_final: 0.8023 (mmm) REVERT: D 530 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6325 (mp) REVERT: B 50 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7832 (mtm110) REVERT: B 138 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 192 GLU cc_start: 0.8506 (tt0) cc_final: 0.8237 (tt0) REVERT: B 195 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 230 LEU cc_start: 0.7524 (mp) cc_final: 0.7323 (mp) REVERT: B 238 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6477 (tm-30) REVERT: B 257 GLU cc_start: 0.6478 (tp30) cc_final: 0.6245 (tp30) REVERT: B 410 TYR cc_start: 0.8126 (m-80) cc_final: 0.7437 (m-80) REVERT: B 440 MET cc_start: 0.8960 (mmm) cc_final: 0.8472 (mmm) REVERT: B 530 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6410 (mp) REVERT: C 50 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7806 (mtp-110) REVERT: C 138 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7376 (mm-30) REVERT: C 192 GLU cc_start: 0.8503 (tt0) cc_final: 0.8242 (tt0) REVERT: C 195 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8161 (tm-30) REVERT: C 238 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6416 (tm-30) REVERT: C 440 MET cc_start: 0.8922 (mmm) cc_final: 0.8115 (mmm) REVERT: C 530 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6447 (mp) outliers start: 45 outliers final: 33 residues processed: 262 average time/residue: 0.3098 time to fit residues: 127.2503 Evaluate side-chains 259 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 2.751 ------------------------------------------------------------------------------- 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 276 THR 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 520 CYS 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 328 LEU 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 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU 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 328 LEU Chi-restraints excluded: chain C residue 377 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 128 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 140 optimal weight: 0.0170 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 263 HIS B 27 ASN C 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.143358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115400 restraints weight = 24593.703| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.25 r_work: 0.3208 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17900 Z= 0.103 Angle : 0.518 7.972 24112 Z= 0.258 Chirality : 0.039 0.128 2612 Planarity : 0.003 0.036 3032 Dihedral : 4.034 16.661 2300 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.25 % Allowed : 14.37 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2088 helix: 1.47 (0.15), residues: 1264 sheet: -1.64 (0.46), residues: 80 loop : -0.31 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 254 HIS 0.003 0.001 HIS D 204 PHE 0.009 0.001 PHE C 4 TYR 0.013 0.001 TYR A 42 ARG 0.002 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 936) hydrogen bonds : angle 4.29827 ( 2700) covalent geometry : bond 0.00242 (17900) covalent geometry : angle 0.51828 (24112) *********************** 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 266 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 2.496 Fit side-chains REVERT: A 50 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7843 (mtm110) REVERT: A 192 GLU cc_start: 0.8482 (tt0) cc_final: 0.8215 (tt0) REVERT: A 195 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 238 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6457 (tm-30) REVERT: A 257 GLU cc_start: 0.6547 (tp30) cc_final: 0.6310 (tp30) REVERT: A 410 TYR cc_start: 0.8154 (m-80) cc_final: 0.7508 (m-80) REVERT: A 440 MET cc_start: 0.8901 (mmm) cc_final: 0.8561 (mmm) REVERT: A 530 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6363 (mp) REVERT: D 42 TYR cc_start: 0.8515 (t80) cc_final: 0.8302 (t80) REVERT: D 50 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7860 (mtm110) REVERT: D 192 GLU cc_start: 0.8525 (tt0) cc_final: 0.8248 (tt0) REVERT: D 195 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8235 (tm-30) REVERT: D 238 GLN cc_start: 0.7184 (tm-30) cc_final: 0.6506 (tm-30) REVERT: D 257 GLU cc_start: 0.6608 (tp30) cc_final: 0.6368 (tp30) REVERT: D 410 TYR cc_start: 0.8263 (m-80) cc_final: 0.7626 (m-80) REVERT: D 440 MET cc_start: 0.8906 (mmm) cc_final: 0.8517 (mmm) REVERT: D 530 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6308 (mp) REVERT: B 50 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7841 (mtm110) REVERT: B 192 GLU cc_start: 0.8513 (tt0) cc_final: 0.8244 (tt0) REVERT: B 195 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 238 GLN cc_start: 0.7216 (tm-30) cc_final: 0.6472 (tm-30) REVERT: B 257 GLU cc_start: 0.6614 (tp30) cc_final: 0.6407 (tp30) REVERT: B 410 TYR cc_start: 0.8141 (m-80) cc_final: 0.7417 (m-80) REVERT: B 440 MET cc_start: 0.8969 (mmm) cc_final: 0.8419 (mmm) REVERT: B 530 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6354 (mp) REVERT: C 42 TYR cc_start: 0.8501 (t80) cc_final: 0.8282 (t80) REVERT: C 50 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7846 (mtp-110) REVERT: C 192 GLU cc_start: 0.8521 (tt0) cc_final: 0.8254 (tt0) REVERT: C 195 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8241 (tm-30) REVERT: C 238 GLN cc_start: 0.7206 (tm-30) cc_final: 0.6465 (tm-30) REVERT: C 257 GLU cc_start: 0.6629 (tp30) cc_final: 0.6393 (tp30) REVERT: C 410 TYR cc_start: 0.8155 (m-80) cc_final: 0.7482 (m-80) REVERT: C 440 MET cc_start: 0.8908 (mmm) cc_final: 0.8575 (mmm) REVERT: C 530 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6234 (mp) outliers start: 44 outliers final: 33 residues processed: 250 average time/residue: 0.3606 time to fit residues: 140.5717 Evaluate side-chains 250 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 276 THR 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 520 CYS 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 328 LEU 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 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 385 LEU 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 328 LEU Chi-restraints excluded: chain C residue 377 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 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 137 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 101 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN C 263 HIS C 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116138 restraints weight = 24687.353| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.27 r_work: 0.3218 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17900 Z= 0.096 Angle : 0.516 7.981 24112 Z= 0.254 Chirality : 0.039 0.127 2612 Planarity : 0.003 0.035 3032 Dihedral : 3.977 16.517 2300 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.84 % Allowed : 15.49 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 2088 helix: 1.53 (0.15), residues: 1264 sheet: -1.55 (0.46), residues: 80 loop : -0.31 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 254 HIS 0.003 0.001 HIS C 204 PHE 0.010 0.001 PHE A 407 TYR 0.012 0.001 TYR B 42 ARG 0.002 0.000 ARG C 166 Details of bonding type rmsd hydrogen bonds : bond 0.02747 ( 936) hydrogen bonds : angle 4.22980 ( 2700) covalent geometry : bond 0.00224 (17900) covalent geometry : angle 0.51645 (24112) *********************** 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 258 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 2.082 Fit side-chains REVERT: A 50 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7888 (mtp-110) REVERT: A 166 ARG cc_start: 0.8539 (mtm-85) cc_final: 0.8332 (mpp-170) REVERT: A 192 GLU cc_start: 0.8494 (tt0) cc_final: 0.8226 (tt0) REVERT: A 195 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 238 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6445 (tm-30) REVERT: A 257 GLU cc_start: 0.6669 (tp30) cc_final: 0.6460 (tp30) REVERT: A 410 TYR cc_start: 0.8264 (m-80) cc_final: 0.7635 (m-80) REVERT: A 440 MET cc_start: 0.8880 (mmm) cc_final: 0.8518 (mmm) REVERT: A 530 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6354 (mp) REVERT: D 42 TYR cc_start: 0.8516 (t80) cc_final: 0.8296 (t80) REVERT: D 50 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7855 (mtm110) REVERT: D 192 GLU cc_start: 0.8519 (tt0) cc_final: 0.8248 (tt0) REVERT: D 195 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8231 (tm-30) REVERT: D 238 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6501 (tm-30) REVERT: D 257 GLU cc_start: 0.6566 (tp30) cc_final: 0.6331 (tp30) REVERT: D 410 TYR cc_start: 0.8247 (m-80) cc_final: 0.7648 (m-80) REVERT: D 440 MET cc_start: 0.8894 (mmm) cc_final: 0.8522 (mmm) REVERT: D 530 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6266 (mp) REVERT: B 50 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7839 (mtm110) REVERT: B 192 GLU cc_start: 0.8486 (tt0) cc_final: 0.8221 (tt0) REVERT: B 195 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 238 GLN cc_start: 0.7213 (tm-30) cc_final: 0.6461 (tm-30) REVERT: B 257 GLU cc_start: 0.6624 (tp30) cc_final: 0.6421 (tp30) REVERT: B 410 TYR cc_start: 0.8248 (m-80) cc_final: 0.7582 (m-80) REVERT: B 440 MET cc_start: 0.8929 (mmm) cc_final: 0.8395 (mmm) REVERT: B 530 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6344 (mp) REVERT: C 42 TYR cc_start: 0.8508 (t80) cc_final: 0.8282 (t80) REVERT: C 50 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7844 (mtp-110) REVERT: C 192 GLU cc_start: 0.8492 (tt0) cc_final: 0.8225 (tt0) REVERT: C 195 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8231 (tm-30) REVERT: C 238 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6455 (tm-30) REVERT: C 257 GLU cc_start: 0.6586 (tp30) cc_final: 0.6360 (tp30) REVERT: C 410 TYR cc_start: 0.8226 (m-80) cc_final: 0.7492 (m-80) REVERT: C 440 MET cc_start: 0.8892 (mmm) cc_final: 0.8541 (mmm) REVERT: C 530 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.6214 (mp) outliers start: 36 outliers final: 30 residues processed: 243 average time/residue: 0.2811 time to fit residues: 105.5776 Evaluate side-chains 243 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.925 ------------------------------------------------------------------------------- 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 328 LEU 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 239 VAL Chi-restraints excluded: chain D residue 255 LEU 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 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 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 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 49 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 188 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN B 263 HIS B 274 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114104 restraints weight = 24599.379| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.27 r_work: 0.3188 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2644 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= 0.120 Angle : 0.540 7.894 24112 Z= 0.266 Chirality : 0.039 0.147 2612 Planarity : 0.003 0.035 3032 Dihedral : 4.003 16.436 2300 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.89 % Allowed : 15.70 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2088 helix: 1.49 (0.15), residues: 1272 sheet: -1.50 (0.47), residues: 80 loop : -0.29 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 254 HIS 0.003 0.001 HIS D 204 PHE 0.011 0.001 PHE C 4 TYR 0.010 0.001 TYR C 42 ARG 0.002 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 936) hydrogen bonds : angle 4.26326 ( 2700) covalent geometry : bond 0.00293 (17900) covalent geometry : angle 0.53989 (24112) ********************** 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 245 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 2.066 Fit side-chains REVERT: A 42 TYR cc_start: 0.8593 (t80) cc_final: 0.8346 (t80) REVERT: A 50 ARG cc_start: 0.8226 (mmm160) cc_final: 0.7859 (mtm110) REVERT: A 166 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8391 (mpp-170) REVERT: A 192 GLU cc_start: 0.8516 (tt0) cc_final: 0.8241 (tt0) REVERT: A 195 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 238 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6472 (tm-30) REVERT: A 257 GLU cc_start: 0.6556 (tp30) cc_final: 0.6316 (tp30) REVERT: A 410 TYR cc_start: 0.8250 (m-80) cc_final: 0.7587 (m-80) REVERT: A 530 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6257 (mp) REVERT: D 42 TYR cc_start: 0.8542 (t80) cc_final: 0.8329 (t80) REVERT: D 50 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7879 (mtm110) REVERT: D 192 GLU cc_start: 0.8547 (tt0) cc_final: 0.8268 (tt0) REVERT: D 195 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8248 (tm-30) REVERT: D 238 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6514 (tm-30) REVERT: D 257 GLU cc_start: 0.6590 (tp30) cc_final: 0.6347 (tp30) REVERT: D 410 TYR cc_start: 0.8240 (m-80) cc_final: 0.7609 (m-80) REVERT: D 530 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6306 (mp) REVERT: B 42 TYR cc_start: 0.8575 (t80) cc_final: 0.8330 (t80) REVERT: B 50 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7849 (mtm110) REVERT: B 192 GLU cc_start: 0.8504 (tt0) cc_final: 0.8238 (tt0) REVERT: B 195 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 238 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6498 (tm-30) REVERT: B 410 TYR cc_start: 0.8269 (m-80) cc_final: 0.7608 (m-80) REVERT: B 440 MET cc_start: 0.8960 (mmm) cc_final: 0.8411 (mmm) REVERT: B 530 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6257 (mp) REVERT: C 42 TYR cc_start: 0.8521 (t80) cc_final: 0.8315 (t80) REVERT: C 50 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7851 (mtp-110) REVERT: C 192 GLU cc_start: 0.8510 (tt0) cc_final: 0.8240 (tt0) REVERT: C 195 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8248 (tm-30) REVERT: C 238 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6489 (tm-30) REVERT: C 257 GLU cc_start: 0.6535 (tp30) cc_final: 0.6312 (tp30) REVERT: C 410 TYR cc_start: 0.8213 (m-80) cc_final: 0.7484 (m-80) REVERT: C 530 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6253 (mp) outliers start: 37 outliers final: 32 residues processed: 231 average time/residue: 0.2910 time to fit residues: 103.6027 Evaluate side-chains 241 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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 328 LEU 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 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 380 ILE 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 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 385 LEU 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 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 166 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 157 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.0020 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.3566 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.144913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117127 restraints weight = 24571.142| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.27 r_work: 0.3232 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17900 Z= 0.092 Angle : 0.522 7.767 24112 Z= 0.256 Chirality : 0.038 0.122 2612 Planarity : 0.003 0.034 3032 Dihedral : 3.914 16.115 2300 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.58 % Allowed : 16.05 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2088 helix: 1.55 (0.15), residues: 1272 sheet: -1.35 (0.47), residues: 80 loop : -0.34 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 154 HIS 0.002 0.000 HIS C 204 PHE 0.011 0.001 PHE A 438 TYR 0.011 0.001 TYR D 509 ARG 0.002 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.02646 ( 936) hydrogen bonds : angle 4.15593 ( 2700) covalent geometry : bond 0.00206 (17900) covalent geometry : angle 0.52186 (24112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8915.20 seconds wall clock time: 156 minutes 39.90 seconds (9399.90 seconds total)