Starting phenix.real_space_refine on Fri Sep 27 22:54:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/09_2024/6ka4_9954.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/09_2024/6ka4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/09_2024/6ka4_9954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/09_2024/6ka4_9954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/09_2024/6ka4_9954.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ka4_9954/09_2024/6ka4_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.13, per 1000 atoms: 0.52 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: 4.17 Conformation dependent library (CDL) restraints added in 2.2 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: 1.78 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: 5.11 Time building geometry restraints manager: 4.84 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.600 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: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.890 Find NCS groups from input model: 0.510 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.730 ------------------------------------------------------------------------------- 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= 0.417 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.984 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: 0.3253 time to fit residues: 119.2153 Evaluate side-chains 207 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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= 0.214 Angle : 0.607 9.150 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 246 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7244 (mm-30) REVERT: A 210 ASP cc_start: 0.7119 (m-30) cc_final: 0.6709 (m-30) REVERT: A 238 GLN cc_start: 0.7042 (tm130) cc_final: 0.6698 (tm-30) REVERT: A 410 TYR cc_start: 0.7695 (m-80) cc_final: 0.7128 (m-80) REVERT: A 440 MET cc_start: 0.8473 (mmm) cc_final: 0.7983 (tpt) REVERT: D 210 ASP cc_start: 0.6945 (m-30) cc_final: 0.6563 (m-30) REVERT: D 238 GLN cc_start: 0.6984 (tm130) cc_final: 0.6681 (tm-30) REVERT: D 410 TYR cc_start: 0.7720 (m-80) cc_final: 0.7136 (m-80) REVERT: D 440 MET cc_start: 0.8497 (mmm) cc_final: 0.8211 (mmm) REVERT: B 138 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7238 (mm-30) REVERT: B 210 ASP cc_start: 0.7294 (m-30) cc_final: 0.6900 (m-30) REVERT: B 238 GLN cc_start: 0.7103 (tm130) cc_final: 0.6751 (tm-30) REVERT: B 410 TYR cc_start: 0.7677 (m-80) cc_final: 0.7097 (m-80) REVERT: C 210 ASP cc_start: 0.7288 (m-30) cc_final: 0.6896 (m-30) REVERT: C 238 GLN cc_start: 0.7103 (tm130) cc_final: 0.6748 (tm-30) REVERT: C 410 TYR cc_start: 0.7753 (m-80) cc_final: 0.7190 (m-80) REVERT: C 440 MET cc_start: 0.8509 (mmm) cc_final: 0.8023 (tpt) outliers start: 12 outliers final: 9 residues processed: 250 average time/residue: 0.3187 time to fit residues: 116.8968 Evaluate side-chains 223 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17900 Z= 0.204 Angle : 0.551 8.712 24112 Z= 0.284 Chirality : 0.041 0.134 2612 Planarity : 0.004 0.051 3032 Dihedral : 4.582 19.703 2300 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.12 % Allowed : 10.17 % Favored : 88.70 % 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: 0.61 (0.19), residues: 2088 helix: 0.99 (0.15), residues: 1284 sheet: -1.32 (0.40), residues: 136 loop : -0.15 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 254 HIS 0.004 0.001 HIS B 204 PHE 0.009 0.001 PHE C 4 TYR 0.021 0.001 TYR B 509 ARG 0.003 0.000 ARG B 54 *********************** 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 281 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 259 time to evaluate : 2.065 Fit side-chains REVERT: A 138 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7198 (mm-30) REVERT: A 210 ASP cc_start: 0.7260 (m-30) cc_final: 0.6898 (m-30) REVERT: A 238 GLN cc_start: 0.6909 (tm130) cc_final: 0.6462 (tm-30) REVERT: A 410 TYR cc_start: 0.7854 (m-80) cc_final: 0.7357 (m-80) REVERT: A 530 ILE cc_start: 0.6929 (mp) cc_final: 0.6719 (mp) REVERT: D 138 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D 195 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7602 (tm-30) REVERT: D 210 ASP cc_start: 0.7098 (m-30) cc_final: 0.6756 (m-30) REVERT: D 238 GLN cc_start: 0.6851 (tm-30) cc_final: 0.6403 (tm-30) REVERT: D 410 TYR cc_start: 0.7922 (m-80) cc_final: 0.7389 (m-80) REVERT: D 530 ILE cc_start: 0.7006 (mp) cc_final: 0.6805 (mp) REVERT: B 138 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 195 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 210 ASP cc_start: 0.7259 (m-30) cc_final: 0.6899 (m-30) REVERT: B 238 GLN cc_start: 0.6924 (tm130) cc_final: 0.6464 (tm-30) REVERT: B 410 TYR cc_start: 0.7862 (m-80) cc_final: 0.7377 (m-80) REVERT: B 440 MET cc_start: 0.8585 (mmm) cc_final: 0.8243 (mmm) REVERT: C 195 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 210 ASP cc_start: 0.7252 (m-30) cc_final: 0.6891 (m-30) REVERT: C 238 GLN cc_start: 0.6883 (tm130) cc_final: 0.6460 (tm-30) REVERT: C 410 TYR cc_start: 0.7971 (m-80) cc_final: 0.7431 (m-80) REVERT: C 530 ILE cc_start: 0.6911 (mp) cc_final: 0.6691 (mp) outliers start: 22 outliers final: 20 residues processed: 266 average time/residue: 0.2969 time to fit residues: 120.1834 Evaluate side-chains 247 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 227 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 520 CYS 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 520 CYS 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 520 CYS 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 520 CYS 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 190 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 0.0870 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 B 238 GLN C 238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17900 Z= 0.260 Angle : 0.565 7.241 24112 Z= 0.288 Chirality : 0.041 0.140 2612 Planarity : 0.004 0.045 3032 Dihedral : 4.479 18.483 2300 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.89 % Allowed : 10.63 % Favored : 87.47 % 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: 0.76 (0.18), residues: 2088 helix: 1.17 (0.15), residues: 1236 sheet: -0.28 (0.43), residues: 112 loop : -0.38 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 254 HIS 0.003 0.001 HIS B 204 PHE 0.013 0.001 PHE C 4 TYR 0.012 0.001 TYR C 521 ARG 0.003 0.000 ARG B 77 *********************** 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 257 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 1.878 Fit side-chains REVERT: A 138 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7206 (mm-30) REVERT: A 195 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 238 GLN cc_start: 0.6921 (tm-30) cc_final: 0.6419 (tm-30) REVERT: A 440 MET cc_start: 0.8527 (mmm) cc_final: 0.8185 (mmm) REVERT: A 530 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6733 (mp) REVERT: D 138 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7178 (mm-30) REVERT: D 195 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7655 (tm-30) REVERT: D 238 GLN cc_start: 0.6998 (tm-30) cc_final: 0.6501 (tm-30) REVERT: D 440 MET cc_start: 0.8519 (mmm) cc_final: 0.8099 (mmm) REVERT: D 487 LYS cc_start: 0.8573 (mptt) cc_final: 0.8071 (mptt) REVERT: D 530 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6805 (mp) REVERT: B 138 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7170 (mm-30) REVERT: B 195 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 238 GLN cc_start: 0.6973 (tm-30) cc_final: 0.6472 (tm-30) REVERT: B 410 TYR cc_start: 0.7985 (m-80) cc_final: 0.7390 (m-80) REVERT: B 440 MET cc_start: 0.8526 (mmm) cc_final: 0.8286 (mmm) REVERT: B 509 TYR cc_start: 0.8900 (t80) cc_final: 0.8624 (t80) REVERT: C 138 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7138 (mm-30) REVERT: C 195 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7648 (tm-30) REVERT: C 238 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6514 (tm-30) REVERT: C 410 TYR cc_start: 0.8059 (m-80) cc_final: 0.7477 (m-80) REVERT: C 530 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6752 (mp) outliers start: 37 outliers final: 32 residues processed: 235 average time/residue: 0.2816 time to fit residues: 102.2747 Evaluate side-chains 243 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 385 LEU 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 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 385 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 520 CYS 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 385 LEU Chi-restraints excluded: chain C residue 520 CYS Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 chunk 152 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 0.0670 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 0.0070 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS D 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17900 Z= 0.135 Angle : 0.505 6.195 24112 Z= 0.259 Chirality : 0.039 0.122 2612 Planarity : 0.003 0.040 3032 Dihedral : 4.233 17.204 2300 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.38 % Allowed : 12.73 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.18), residues: 2088 helix: 1.22 (0.15), residues: 1264 sheet: -2.43 (0.40), residues: 80 loop : -0.28 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 254 HIS 0.004 0.001 HIS B 204 PHE 0.010 0.001 PHE C 407 TYR 0.011 0.001 TYR D 567 ARG 0.001 0.000 ARG B 77 *********************** 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 254 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 1.895 Fit side-chains REVERT: A 138 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7180 (mm-30) REVERT: A 195 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7652 (tm-30) REVERT: A 238 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6308 (tm-30) REVERT: A 410 TYR cc_start: 0.7833 (m-80) cc_final: 0.7282 (m-80) REVERT: A 440 MET cc_start: 0.8451 (mmm) cc_final: 0.8018 (mmm) REVERT: A 530 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6593 (mp) REVERT: D 138 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7221 (mm-30) REVERT: D 195 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7685 (tm-30) REVERT: D 238 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6308 (tm-30) REVERT: D 344 MET cc_start: 0.8897 (mmm) cc_final: 0.8690 (mmp) REVERT: D 410 TYR cc_start: 0.7871 (m-80) cc_final: 0.7285 (m-80) REVERT: D 440 MET cc_start: 0.8564 (mmm) cc_final: 0.8056 (mmm) REVERT: D 487 LYS cc_start: 0.8438 (mptt) cc_final: 0.7977 (mptt) REVERT: B 138 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7194 (mm-30) REVERT: B 195 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 238 GLN cc_start: 0.6844 (tm-30) cc_final: 0.6272 (tm-30) REVERT: B 410 TYR cc_start: 0.8010 (m-80) cc_final: 0.7486 (m-80) REVERT: C 138 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 195 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7658 (tm-30) REVERT: C 238 GLN cc_start: 0.6882 (tm-30) cc_final: 0.6303 (tm-30) REVERT: C 410 TYR cc_start: 0.8028 (m-80) cc_final: 0.7478 (m-80) REVERT: C 440 MET cc_start: 0.8504 (mmm) cc_final: 0.7999 (mmm) REVERT: C 538 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6962 (mm-30) outliers start: 27 outliers final: 19 residues processed: 239 average time/residue: 0.2910 time to fit residues: 106.8816 Evaluate side-chains 228 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 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 68 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17900 Z= 0.200 Angle : 0.526 5.594 24112 Z= 0.266 Chirality : 0.040 0.136 2612 Planarity : 0.003 0.039 3032 Dihedral : 4.181 17.132 2300 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.74 % Allowed : 13.80 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.18), residues: 2088 helix: 1.30 (0.15), residues: 1264 sheet: -2.14 (0.43), residues: 80 loop : -0.29 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 254 HIS 0.004 0.001 HIS B 204 PHE 0.011 0.001 PHE C 4 TYR 0.011 0.001 TYR A 42 ARG 0.002 0.000 ARG A 508 *********************** 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 252 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 218 time to evaluate : 2.041 Fit side-chains REVERT: A 195 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 238 GLN cc_start: 0.6844 (tm-30) cc_final: 0.6183 (tm-30) REVERT: A 440 MET cc_start: 0.8449 (mmm) cc_final: 0.7582 (mmm) REVERT: A 530 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6592 (mp) REVERT: D 138 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7194 (mm-30) REVERT: D 195 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 238 GLN cc_start: 0.6964 (tm-30) cc_final: 0.6337 (tm-30) REVERT: D 410 TYR cc_start: 0.7970 (m-80) cc_final: 0.7377 (m-80) REVERT: D 440 MET cc_start: 0.8603 (mmm) cc_final: 0.7607 (mmm) REVERT: D 487 LYS cc_start: 0.8474 (mptt) cc_final: 0.7950 (mptt) REVERT: B 138 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 195 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7673 (tm-30) REVERT: B 238 GLN cc_start: 0.6868 (tm-30) cc_final: 0.6189 (tm-30) REVERT: C 195 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 238 GLN cc_start: 0.6911 (tm-30) cc_final: 0.6227 (tm-30) REVERT: C 410 TYR cc_start: 0.8044 (m-80) cc_final: 0.7420 (m-80) REVERT: C 440 MET cc_start: 0.8519 (mmm) cc_final: 0.7922 (mmm) outliers start: 34 outliers final: 23 residues processed: 236 average time/residue: 0.2771 time to fit residues: 101.6399 Evaluate side-chains 229 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 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 555 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 0.1980 chunk 94 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 HIS C 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17900 Z= 0.163 Angle : 0.517 7.787 24112 Z= 0.259 Chirality : 0.039 0.127 2612 Planarity : 0.003 0.037 3032 Dihedral : 4.096 17.061 2300 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.79 % Allowed : 13.75 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.18), residues: 2088 helix: 1.38 (0.15), residues: 1264 sheet: -2.03 (0.44), residues: 80 loop : -0.32 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 254 HIS 0.004 0.001 HIS B 204 PHE 0.009 0.001 PHE C 407 TYR 0.011 0.001 TYR B 42 ARG 0.002 0.000 ARG D 186 *********************** 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 253 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 218 time to evaluate : 2.089 Fit side-chains REVERT: A 138 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 195 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 238 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6248 (tm-30) REVERT: A 257 GLU cc_start: 0.6175 (tp30) cc_final: 0.5974 (tp30) REVERT: A 344 MET cc_start: 0.8963 (mmm) cc_final: 0.8712 (mmp) REVERT: A 440 MET cc_start: 0.8740 (mmm) cc_final: 0.7619 (mmm) REVERT: A 530 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6530 (mp) REVERT: D 195 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 238 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6233 (tm-30) REVERT: D 410 TYR cc_start: 0.8036 (m-80) cc_final: 0.7457 (m-80) REVERT: D 440 MET cc_start: 0.8578 (mmm) cc_final: 0.7546 (mmm) REVERT: D 487 LYS cc_start: 0.8462 (mptt) cc_final: 0.7943 (mptt) REVERT: B 195 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 238 GLN cc_start: 0.6990 (tm-30) cc_final: 0.6260 (tm-30) REVERT: B 257 GLU cc_start: 0.6184 (tp30) cc_final: 0.5983 (tp30) REVERT: B 344 MET cc_start: 0.8956 (mmm) cc_final: 0.8715 (mmp) REVERT: B 410 TYR cc_start: 0.7908 (m-80) cc_final: 0.7311 (m-80) REVERT: C 159 MET cc_start: 0.8812 (tpp) cc_final: 0.8426 (mmm) REVERT: C 195 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7799 (tm-30) REVERT: C 238 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6249 (tm-30) REVERT: C 344 MET cc_start: 0.8958 (mmm) cc_final: 0.8720 (mmp) REVERT: C 440 MET cc_start: 0.8568 (mmm) cc_final: 0.7979 (mmm) outliers start: 35 outliers final: 26 residues processed: 239 average time/residue: 0.2681 time to fit residues: 99.8598 Evaluate side-chains 233 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 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 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 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.0370 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2621 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= 0.148 Angle : 0.518 7.963 24112 Z= 0.257 Chirality : 0.039 0.127 2612 Planarity : 0.003 0.036 3032 Dihedral : 4.013 16.713 2300 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.94 % Allowed : 14.62 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.02 (0.19), residues: 2088 helix: 1.47 (0.15), residues: 1264 sheet: -1.79 (0.45), residues: 80 loop : -0.30 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 204 PHE 0.009 0.001 PHE C 407 TYR 0.011 0.001 TYR B 42 ARG 0.003 0.000 ARG D 29 *********************** 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 245 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 2.048 Fit side-chains REVERT: A 42 TYR cc_start: 0.8073 (t80) cc_final: 0.7859 (t80) REVERT: A 138 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 195 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 238 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6202 (tm-30) REVERT: A 257 GLU cc_start: 0.6202 (tp30) cc_final: 0.5997 (tp30) REVERT: A 344 MET cc_start: 0.8965 (mmm) cc_final: 0.8701 (mmp) REVERT: A 410 TYR cc_start: 0.7914 (m-80) cc_final: 0.7331 (m-80) REVERT: A 440 MET cc_start: 0.8560 (mmm) cc_final: 0.8164 (mmm) REVERT: A 530 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6490 (mp) REVERT: D 195 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7921 (tm-30) REVERT: D 238 GLN cc_start: 0.6981 (tm-30) cc_final: 0.6260 (tm-30) REVERT: D 257 GLU cc_start: 0.6353 (tp30) cc_final: 0.6147 (tp30) REVERT: D 410 TYR cc_start: 0.8046 (m-80) cc_final: 0.7476 (m-80) REVERT: D 440 MET cc_start: 0.8555 (mmm) cc_final: 0.8098 (mmm) REVERT: D 487 LYS cc_start: 0.8447 (mptt) cc_final: 0.7901 (mptt) REVERT: B 42 TYR cc_start: 0.8067 (t80) cc_final: 0.7859 (t80) REVERT: B 195 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7906 (tm-30) REVERT: B 238 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6211 (tm-30) REVERT: B 257 GLU cc_start: 0.6208 (tp30) cc_final: 0.6001 (tp30) REVERT: B 344 MET cc_start: 0.8964 (mmm) cc_final: 0.8704 (mmp) REVERT: B 410 TYR cc_start: 0.7979 (m-80) cc_final: 0.7366 (m-80) REVERT: C 195 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 238 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6211 (tm-30) REVERT: C 257 GLU cc_start: 0.6211 (tp30) cc_final: 0.5996 (tp30) REVERT: C 344 MET cc_start: 0.8964 (mmm) cc_final: 0.8704 (mmp) REVERT: C 410 TYR cc_start: 0.8031 (m-80) cc_final: 0.7265 (m-80) REVERT: C 440 MET cc_start: 0.8577 (mmm) cc_final: 0.7536 (mmm) outliers start: 38 outliers final: 32 residues processed: 226 average time/residue: 0.2755 time to fit residues: 97.8008 Evaluate side-chains 227 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 2.003 ------------------------------------------------------------------------------- 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 328 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain D residue 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 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 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 377 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 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 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 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 195 optimal weight: 0.6980 chunk 178 optimal weight: 0.6980 chunk 190 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 82 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN D 263 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2656 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= 0.174 Angle : 0.532 7.892 24112 Z= 0.262 Chirality : 0.039 0.131 2612 Planarity : 0.003 0.036 3032 Dihedral : 4.012 16.718 2300 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.79 % Allowed : 15.34 % Favored : 82.87 % 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: 1.06 (0.19), residues: 2088 helix: 1.48 (0.15), residues: 1264 sheet: -1.58 (0.47), residues: 80 loop : -0.27 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.004 0.001 HIS B 204 PHE 0.010 0.001 PHE D 4 TYR 0.013 0.001 TYR C 42 ARG 0.002 0.000 ARG D 29 *********************** 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 236 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 1.862 Fit side-chains REVERT: A 42 TYR cc_start: 0.8090 (t80) cc_final: 0.7859 (t80) REVERT: A 138 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7058 (mm-30) REVERT: A 195 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 238 GLN cc_start: 0.6957 (tm-30) cc_final: 0.6199 (tm-30) REVERT: A 344 MET cc_start: 0.8987 (mmm) cc_final: 0.8758 (mmp) REVERT: A 410 TYR cc_start: 0.8026 (m-80) cc_final: 0.7468 (m-80) REVERT: A 530 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6508 (mp) REVERT: D 42 TYR cc_start: 0.8043 (t80) cc_final: 0.7828 (t80) REVERT: D 238 GLN cc_start: 0.6996 (tm-30) cc_final: 0.6258 (tm-30) REVERT: D 410 TYR cc_start: 0.8090 (m-80) cc_final: 0.7498 (m-80) REVERT: D 440 MET cc_start: 0.8491 (mmm) cc_final: 0.8291 (mmm) REVERT: D 487 LYS cc_start: 0.8459 (mptt) cc_final: 0.7916 (mptt) REVERT: B 42 TYR cc_start: 0.8088 (t80) cc_final: 0.7858 (t80) REVERT: B 195 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 238 GLN cc_start: 0.6966 (tm-30) cc_final: 0.6198 (tm-30) REVERT: B 344 MET cc_start: 0.8984 (mmm) cc_final: 0.8757 (mmp) REVERT: B 410 TYR cc_start: 0.7995 (m-80) cc_final: 0.7358 (m-80) REVERT: C 195 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 238 GLN cc_start: 0.6951 (tm-30) cc_final: 0.6212 (tm-30) REVERT: C 257 GLU cc_start: 0.6208 (tp30) cc_final: 0.5994 (tp30) REVERT: C 344 MET cc_start: 0.8986 (mmm) cc_final: 0.8756 (mmp) REVERT: C 410 TYR cc_start: 0.8005 (m-80) cc_final: 0.7417 (m-80) REVERT: C 440 MET cc_start: 0.8591 (mmm) cc_final: 0.7499 (mmm) outliers start: 35 outliers final: 32 residues processed: 219 average time/residue: 0.2584 time to fit residues: 88.2551 Evaluate side-chains 229 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 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 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 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 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 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 201 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 194 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN B 274 GLN C 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2721 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= 0.165 Angle : 0.532 7.903 24112 Z= 0.262 Chirality : 0.039 0.129 2612 Planarity : 0.003 0.035 3032 Dihedral : 3.991 16.383 2300 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.79 % Allowed : 15.95 % Favored : 82.26 % 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: 1.06 (0.19), residues: 2088 helix: 1.46 (0.15), residues: 1272 sheet: -1.44 (0.47), residues: 80 loop : -0.27 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 254 HIS 0.004 0.001 HIS A 204 PHE 0.011 0.001 PHE A 438 TYR 0.015 0.001 TYR C 42 ARG 0.003 0.000 ARG A 29 ********************** 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 238 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 2.358 Fit side-chains REVERT: A 42 TYR cc_start: 0.8087 (t80) cc_final: 0.7856 (t80) REVERT: A 195 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 238 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6179 (tm-30) REVERT: A 344 MET cc_start: 0.8985 (mmm) cc_final: 0.8749 (mmp) REVERT: A 410 TYR cc_start: 0.8020 (m-80) cc_final: 0.7423 (m-80) REVERT: A 440 MET cc_start: 0.8514 (mmm) cc_final: 0.8051 (mmm) REVERT: A 530 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6500 (mp) REVERT: D 238 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6240 (tm-30) REVERT: D 410 TYR cc_start: 0.8081 (m-80) cc_final: 0.7458 (m-80) REVERT: D 487 LYS cc_start: 0.8403 (mptt) cc_final: 0.7881 (mptt) REVERT: B 42 TYR cc_start: 0.8085 (t80) cc_final: 0.7864 (t80) REVERT: B 195 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7913 (tm-30) REVERT: B 238 GLN cc_start: 0.6949 (tm-30) cc_final: 0.6177 (tm-30) REVERT: B 344 MET cc_start: 0.8985 (mmm) cc_final: 0.8747 (mmp) REVERT: B 410 TYR cc_start: 0.8095 (m-80) cc_final: 0.7511 (m-80) REVERT: C 9 GLU cc_start: 0.8084 (pt0) cc_final: 0.7650 (pt0) REVERT: C 195 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 238 GLN cc_start: 0.6950 (tm-30) cc_final: 0.6202 (tm-30) REVERT: C 257 GLU cc_start: 0.6184 (tp30) cc_final: 0.5966 (tp30) REVERT: C 344 MET cc_start: 0.8987 (mmm) cc_final: 0.8748 (mmp) REVERT: C 410 TYR cc_start: 0.8037 (m-80) cc_final: 0.7369 (m-80) REVERT: C 440 MET cc_start: 0.8583 (mmm) cc_final: 0.7473 (mmm) outliers start: 35 outliers final: 32 residues processed: 221 average time/residue: 0.2638 time to fit residues: 91.4810 Evaluate side-chains 229 residues out of total 1960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 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 328 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 482 ILE Chi-restraints excluded: chain D residue 555 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 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 328 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 482 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 179 optimal weight: 0.9990 chunk 51 optimal weight: 0.0570 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 147 optimal weight: 0.0020 overall best weight: 0.5106 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.143603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115761 restraints weight = 24628.926| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.26 r_work: 0.3212 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17900 Z= 0.150 Angle : 0.529 8.548 24112 Z= 0.260 Chirality : 0.039 0.127 2612 Planarity : 0.003 0.035 3032 Dihedral : 3.939 16.199 2300 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.74 % Allowed : 16.21 % Favored : 82.06 % 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: 1.11 (0.19), residues: 2088 helix: 1.50 (0.15), residues: 1272 sheet: -1.36 (0.47), residues: 80 loop : -0.27 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 254 HIS 0.004 0.001 HIS B 204 PHE 0.012 0.001 PHE D 4 TYR 0.015 0.001 TYR C 42 ARG 0.002 0.000 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.88 seconds wall clock time: 60 minutes 19.41 seconds (3619.41 seconds total)