Starting phenix.real_space_refine on Wed Mar 4 23:06:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqr_25391/03_2026/7sqr_25391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqr_25391/03_2026/7sqr_25391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sqr_25391/03_2026/7sqr_25391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqr_25391/03_2026/7sqr_25391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sqr_25391/03_2026/7sqr_25391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqr_25391/03_2026/7sqr_25391.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 56 5.16 5 C 10772 2.51 5 N 3128 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17272 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4072 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 1 Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 163 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Restraints were copied for chains: D, G, J, E, H, K, F, I, L Time building chain proxies: 3.29, per 1000 atoms: 0.19 Number of scatterers: 17272 At special positions: 0 Unit cell: (123.091, 123.091, 86.5695, 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 56 16.00 O 3316 8.00 N 3128 7.00 C 10772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 712.9 milliseconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 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: 88 helices and 20 sheets defined 41.6% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.879A pdb=" N SER A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.814A pdb=" N VAL A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP A 201 " --> pdb=" O VAL A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 202 through 226 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 360 through 367 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 379 through 386 removed outlier: 4.033A pdb=" N MET A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.811A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.668A pdb=" N ARG A 465 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 544 Processing helix chain 'A' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN B 600 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 601 " --> pdb=" O ILE B 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 597 through 601' Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 67 through 84 Processing helix chain 'D' and resid 157 through 162 removed outlier: 3.814A pdb=" N VAL D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 162' Processing helix chain 'D' and resid 163 through 179 Processing helix chain 'D' and resid 198 through 201 removed outlier: 3.716A pdb=" N ASP D 201 " --> pdb=" O VAL D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'D' and resid 202 through 226 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.991A pdb=" N LYS D 236 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 358 Processing helix chain 'D' and resid 360 through 367 Proline residue: D 365 - end of helix Processing helix chain 'D' and resid 379 through 386 removed outlier: 4.033A pdb=" N MET D 385 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY D 405 " --> pdb=" O ASP D 401 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU D 434 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 458 Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG D 465 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN D 472 " --> pdb=" O HIS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 500 through 508 Processing helix chain 'D' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN D 522 " --> pdb=" O PHE D 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 523 " --> pdb=" O TYR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 544 Processing helix chain 'D' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 565 " --> pdb=" O ALA D 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN E 600 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 601 " --> pdb=" O ILE E 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 597 through 601' Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 67 through 84 Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL G 161 " --> pdb=" O ASP G 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 162 " --> pdb=" O VAL G 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 162' Processing helix chain 'G' and resid 163 through 179 Processing helix chain 'G' and resid 198 through 201 removed outlier: 3.716A pdb=" N ASP G 201 " --> pdb=" O VAL G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 201' Processing helix chain 'G' and resid 202 through 226 Processing helix chain 'G' and resid 231 through 236 removed outlier: 3.991A pdb=" N LYS G 236 " --> pdb=" O ALA G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR G 346 " --> pdb=" O THR G 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP G 347 " --> pdb=" O PRO G 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE G 348 " --> pdb=" O GLU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 358 Processing helix chain 'G' and resid 360 through 367 Proline residue: G 365 - end of helix Processing helix chain 'G' and resid 379 through 386 removed outlier: 4.033A pdb=" N MET G 385 " --> pdb=" O LEU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY G 405 " --> pdb=" O ASP G 401 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN G 406 " --> pdb=" O ALA G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 440 removed outlier: 3.810A pdb=" N LEU G 434 " --> pdb=" O GLN G 430 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 458 Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG G 465 " --> pdb=" O GLY G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN G 472 " --> pdb=" O HIS G 469 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 499 No H-bonds generated for 'chain 'G' and resid 497 through 499' Processing helix chain 'G' and resid 500 through 508 Processing helix chain 'G' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE G 515 " --> pdb=" O ASN G 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN G 522 " --> pdb=" O PHE G 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 523 " --> pdb=" O TYR G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 544 Processing helix chain 'G' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE G 564 " --> pdb=" O ASN G 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU G 565 " --> pdb=" O ALA G 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN H 600 " --> pdb=" O VAL H 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN H 601 " --> pdb=" O ILE H 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 597 through 601' Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'J' and resid 67 through 84 Processing helix chain 'J' and resid 157 through 162 removed outlier: 3.813A pdb=" N VAL J 161 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE J 162 " --> pdb=" O VAL J 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 157 through 162' Processing helix chain 'J' and resid 163 through 179 Processing helix chain 'J' and resid 198 through 201 removed outlier: 3.715A pdb=" N ASP J 201 " --> pdb=" O VAL J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 201' Processing helix chain 'J' and resid 202 through 226 Processing helix chain 'J' and resid 231 through 236 removed outlier: 3.992A pdb=" N LYS J 236 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 removed outlier: 3.739A pdb=" N TYR J 346 " --> pdb=" O THR J 342 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP J 347 " --> pdb=" O PRO J 343 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE J 348 " --> pdb=" O GLU J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 358 Processing helix chain 'J' and resid 360 through 367 Proline residue: J 365 - end of helix Processing helix chain 'J' and resid 379 through 386 removed outlier: 4.034A pdb=" N MET J 385 " --> pdb=" O LEU J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 412 removed outlier: 3.611A pdb=" N GLY J 405 " --> pdb=" O ASP J 401 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLN J 406 " --> pdb=" O ALA J 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 428 through 440 removed outlier: 3.811A pdb=" N LEU J 434 " --> pdb=" O GLN J 430 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 458 Processing helix chain 'J' and resid 462 through 466 removed outlier: 3.667A pdb=" N ARG J 465 " --> pdb=" O GLY J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 472 removed outlier: 3.847A pdb=" N GLN J 472 " --> pdb=" O HIS J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 499 No H-bonds generated for 'chain 'J' and resid 497 through 499' Processing helix chain 'J' and resid 500 through 508 Processing helix chain 'J' and resid 511 through 524 removed outlier: 3.607A pdb=" N PHE J 515 " --> pdb=" O ASN J 511 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN J 522 " --> pdb=" O PHE J 518 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU J 523 " --> pdb=" O TYR J 519 " (cutoff:3.500A) Processing helix chain 'J' and resid 528 through 544 Processing helix chain 'J' and resid 560 through 574 removed outlier: 3.561A pdb=" N ILE J 564 " --> pdb=" O ASN J 560 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU J 565 " --> pdb=" O ALA J 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 597 through 601 removed outlier: 3.502A pdb=" N ASN K 600 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN K 601 " --> pdb=" O ILE K 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 597 through 601' Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE A 143 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU A 476 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR A 559 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A 478 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS A 557 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN A 480 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 555 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A 482 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS A 553 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 559 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP A 331 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL A 332 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN A 292 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 291 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 270 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 243 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 255 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AA7, first strand: chain 'D' and resid 92 through 96 Processing sheet with id=AA8, first strand: chain 'D' and resid 140 through 145 removed outlier: 3.511A pdb=" N ILE D 143 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU D 476 " --> pdb=" O TYR D 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR D 559 " --> pdb=" O GLU D 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR D 478 " --> pdb=" O CYS D 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS D 557 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN D 480 " --> pdb=" O GLU D 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU D 555 " --> pdb=" O GLN D 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 482 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS D 553 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU D 484 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR D 559 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE D 418 " --> pdb=" O TYR D 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 331 " --> pdb=" O ASP D 421 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA D 294 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL D 332 " --> pdb=" O GLN D 292 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN D 292 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN D 291 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 270 " --> pdb=" O ASN D 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU D 243 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 254 through 255 Processing sheet with id=AB2, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=AB3, first strand: chain 'G' and resid 92 through 96 Processing sheet with id=AB4, first strand: chain 'G' and resid 140 through 145 removed outlier: 3.510A pdb=" N ILE G 143 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 493 through 495 removed outlier: 6.000A pdb=" N GLU G 476 " --> pdb=" O TYR G 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR G 559 " --> pdb=" O GLU G 476 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR G 478 " --> pdb=" O CYS G 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS G 557 " --> pdb=" O THR G 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN G 480 " --> pdb=" O GLU G 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU G 555 " --> pdb=" O GLN G 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE G 482 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS G 553 " --> pdb=" O ILE G 482 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU G 484 " --> pdb=" O THR G 551 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR G 559 " --> pdb=" O PHE G 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE G 418 " --> pdb=" O TYR G 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP G 331 " --> pdb=" O ASP G 421 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA G 294 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL G 332 " --> pdb=" O GLN G 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN G 292 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN G 291 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR G 270 " --> pdb=" O ASN G 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU G 243 " --> pdb=" O THR G 579 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 255 Processing sheet with id=AB7, first strand: chain 'J' and resid 92 through 96 Processing sheet with id=AB8, first strand: chain 'J' and resid 92 through 96 Processing sheet with id=AB9, first strand: chain 'J' and resid 140 through 145 removed outlier: 3.510A pdb=" N ILE J 143 " --> pdb=" O ASP J 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 493 through 495 removed outlier: 5.999A pdb=" N GLU J 476 " --> pdb=" O TYR J 559 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TYR J 559 " --> pdb=" O GLU J 476 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR J 478 " --> pdb=" O CYS J 557 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS J 557 " --> pdb=" O THR J 478 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN J 480 " --> pdb=" O GLU J 555 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU J 555 " --> pdb=" O GLN J 480 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE J 482 " --> pdb=" O LYS J 553 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS J 553 " --> pdb=" O ILE J 482 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU J 484 " --> pdb=" O THR J 551 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR J 559 " --> pdb=" O PHE J 418 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE J 418 " --> pdb=" O TYR J 559 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP J 331 " --> pdb=" O ASP J 421 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA J 294 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL J 332 " --> pdb=" O GLN J 292 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLN J 292 " --> pdb=" O VAL J 332 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN J 291 " --> pdb=" O THR J 270 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR J 270 " --> pdb=" O ASN J 291 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU J 243 " --> pdb=" O THR J 579 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 254 through 255 764 hydrogen bonds defined for protein. 1968 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: 2.24 Time building geometry restraints manager: 1.84 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: 5998 1.34 - 1.46: 2144 1.46 - 1.57: 9342 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 17588 Sorted by residual: bond pdb=" CG LEU G 527 " pdb=" CD2 LEU G 527 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 bond pdb=" CG LEU D 527 " pdb=" CD2 LEU D 527 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 bond pdb=" CG LEU J 527 " pdb=" CD2 LEU J 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 bond pdb=" CG LEU A 527 " pdb=" CD2 LEU A 527 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 bond pdb=" CA ASN A 511 " pdb=" CB ASN A 511 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.27e-02 6.20e+03 1.94e+00 ... (remaining 17583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 23099 1.56 - 3.12: 565 3.12 - 4.69: 134 4.69 - 6.25: 38 6.25 - 7.81: 8 Bond angle restraints: 23844 Sorted by residual: angle pdb=" CA GLN A 278 " pdb=" C GLN A 278 " pdb=" N GLN A 279 " ideal model delta sigma weight residual 114.90 119.72 -4.82 1.37e+00 5.33e-01 1.24e+01 angle pdb=" CA GLN D 278 " pdb=" C GLN D 278 " pdb=" N GLN D 279 " ideal model delta sigma weight residual 114.90 119.71 -4.81 1.37e+00 5.33e-01 1.24e+01 angle pdb=" CA GLN J 278 " pdb=" C GLN J 278 " pdb=" N GLN J 279 " ideal model delta sigma weight residual 114.90 119.70 -4.80 1.37e+00 5.33e-01 1.23e+01 angle pdb=" CA GLN G 278 " pdb=" C GLN G 278 " pdb=" N GLN G 279 " ideal model delta sigma weight residual 114.90 119.69 -4.79 1.37e+00 5.33e-01 1.22e+01 angle pdb=" CA GLN A 411 " pdb=" CB GLN A 411 " pdb=" CG GLN A 411 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.47e+00 ... (remaining 23839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9606 17.92 - 35.83: 834 35.83 - 53.75: 76 53.75 - 71.67: 24 71.67 - 89.59: 28 Dihedral angle restraints: 10568 sinusoidal: 4240 harmonic: 6328 Sorted by residual: dihedral pdb=" CA ARG J 76 " pdb=" CB ARG J 76 " pdb=" CG ARG J 76 " pdb=" CD ARG J 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.88 51.88 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA ARG G 76 " pdb=" CB ARG G 76 " pdb=" CG ARG G 76 " pdb=" CD ARG G 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.88 51.88 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " pdb=" CG ARG A 76 " pdb=" CD ARG A 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.86 51.86 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 10565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1673 0.033 - 0.065: 639 0.065 - 0.098: 149 0.098 - 0.131: 140 0.131 - 0.163: 23 Chirality restraints: 2624 Sorted by residual: chirality pdb=" CA MET B 602 " pdb=" N MET B 602 " pdb=" C MET B 602 " pdb=" CB MET B 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA MET E 602 " pdb=" N MET E 602 " pdb=" C MET E 602 " pdb=" CB MET E 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA MET K 602 " pdb=" N MET K 602 " pdb=" C MET K 602 " pdb=" CB MET K 602 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2621 not shown) Planarity restraints: 3212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO D 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 321 " 0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO G 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO G 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 322 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 321 " 0.064 5.00e-02 4.00e+02 9.57e-02 1.47e+01 pdb=" N PRO A 322 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.053 5.00e-02 4.00e+02 ... (remaining 3209 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 817 2.73 - 3.27: 16561 3.27 - 3.81: 26493 3.81 - 4.36: 29713 4.36 - 4.90: 53526 Nonbonded interactions: 127110 Sorted by model distance: nonbonded pdb=" OE2 GLU G 514 " pdb=" OH TYR G 543 " model vdw 2.185 3.040 nonbonded pdb=" OE2 GLU D 514 " pdb=" OH TYR D 543 " model vdw 2.185 3.040 nonbonded pdb=" OE2 GLU J 514 " pdb=" OH TYR J 543 " model vdw 2.185 3.040 nonbonded pdb=" OE2 GLU A 514 " pdb=" OH TYR A 543 " model vdw 2.185 3.040 nonbonded pdb=" OD2 ASP A 540 " pdb=" OH TYR A 550 " model vdw 2.253 3.040 ... (remaining 127105 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 0.150 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.060 Process input model: 14.490 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.003 0.057 17588 Z= 0.129 Angle : 0.632 7.812 23844 Z= 0.349 Chirality : 0.044 0.163 2624 Planarity : 0.005 0.096 3212 Dihedral : 13.785 89.586 6488 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 2184 helix: 2.13 (0.20), residues: 744 sheet: 0.46 (0.24), residues: 524 loop : -0.31 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 541 TYR 0.009 0.001 TYR D 539 PHE 0.016 0.001 PHE D 466 TRP 0.021 0.002 TRP D 516 HIS 0.001 0.000 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00267 (17588) covalent geometry : angle 0.63165 (23844) hydrogen bonds : bond 0.19850 ( 740) hydrogen bonds : angle 6.26158 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.635 Fit side-chains REVERT: A 218 ASP cc_start: 0.8155 (m-30) cc_final: 0.7638 (m-30) REVERT: A 376 MET cc_start: 0.9021 (tpp) cc_final: 0.8648 (tpp) REVERT: B 591 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7581 (pmt170) REVERT: B 600 ASN cc_start: 0.8866 (m110) cc_final: 0.8635 (m110) REVERT: D 218 ASP cc_start: 0.8157 (m-30) cc_final: 0.7641 (m-30) REVERT: D 376 MET cc_start: 0.9012 (tpp) cc_final: 0.8643 (tpp) REVERT: E 591 ARG cc_start: 0.7830 (ptm160) cc_final: 0.7582 (pmt170) REVERT: E 600 ASN cc_start: 0.8864 (m110) cc_final: 0.8633 (m110) REVERT: G 218 ASP cc_start: 0.8147 (m-30) cc_final: 0.7633 (m-30) REVERT: G 376 MET cc_start: 0.9015 (tpp) cc_final: 0.8646 (tpp) REVERT: H 591 ARG cc_start: 0.7825 (ptm160) cc_final: 0.7586 (pmt170) REVERT: H 600 ASN cc_start: 0.8869 (m110) cc_final: 0.8640 (m110) REVERT: J 218 ASP cc_start: 0.8153 (m-30) cc_final: 0.7635 (m-30) REVERT: J 376 MET cc_start: 0.9014 (tpp) cc_final: 0.8645 (tpp) REVERT: K 591 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7584 (pmt170) REVERT: K 600 ASN cc_start: 0.8858 (m110) cc_final: 0.8629 (m110) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1186 time to fit residues: 21.1460 Evaluate side-chains 88 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.102386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.080238 restraints weight = 45589.863| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 4.52 r_work: 0.3228 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17588 Z= 0.094 Angle : 0.500 5.857 23844 Z= 0.256 Chirality : 0.042 0.149 2624 Planarity : 0.004 0.047 3212 Dihedral : 3.274 11.307 2388 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.09 % Allowed : 2.84 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 2184 helix: 1.97 (0.20), residues: 780 sheet: 0.13 (0.23), residues: 528 loop : -0.40 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 301 TYR 0.004 0.001 TYR J 570 PHE 0.009 0.001 PHE D 404 TRP 0.010 0.001 TRP D 516 HIS 0.002 0.000 HIS G 101 Details of bonding type rmsd covalent geometry : bond 0.00202 (17588) covalent geometry : angle 0.50023 (23844) hydrogen bonds : bond 0.03335 ( 740) hydrogen bonds : angle 4.18584 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.706 Fit side-chains REVERT: A 376 MET cc_start: 0.9119 (tpp) cc_final: 0.8715 (tpp) REVERT: B 591 ARG cc_start: 0.7931 (ptm160) cc_final: 0.7477 (pmt170) REVERT: D 376 MET cc_start: 0.9135 (tpp) cc_final: 0.8739 (tpp) REVERT: E 591 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7487 (pmt170) REVERT: G 376 MET cc_start: 0.9128 (tpp) cc_final: 0.8731 (tpp) REVERT: H 591 ARG cc_start: 0.7928 (ptm160) cc_final: 0.7488 (pmt170) REVERT: J 376 MET cc_start: 0.9118 (tpp) cc_final: 0.8714 (tpp) REVERT: K 591 ARG cc_start: 0.7933 (ptm160) cc_final: 0.7481 (pmt170) outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 0.1336 time to fit residues: 21.6536 Evaluate side-chains 100 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 43 optimal weight: 10.0000 chunk 219 optimal weight: 0.0870 chunk 183 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.098625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.076441 restraints weight = 46645.294| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.54 r_work: 0.3148 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17588 Z= 0.135 Angle : 0.518 7.678 23844 Z= 0.260 Chirality : 0.042 0.140 2624 Planarity : 0.003 0.043 3212 Dihedral : 3.418 16.061 2388 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.75 % Allowed : 4.20 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2184 helix: 2.05 (0.20), residues: 780 sheet: -0.19 (0.23), residues: 508 loop : -0.36 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 532 TYR 0.007 0.001 TYR A 284 PHE 0.011 0.001 PHE G 515 TRP 0.009 0.001 TRP G 105 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00313 (17588) covalent geometry : angle 0.51791 (23844) hydrogen bonds : bond 0.03396 ( 740) hydrogen bonds : angle 4.02777 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7902 (mmt) cc_final: 0.7668 (mmt) REVERT: A 580 MET cc_start: 0.8562 (pmm) cc_final: 0.8028 (pmm) REVERT: B 591 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7624 (pmt170) REVERT: D 408 MET cc_start: 0.7890 (mmt) cc_final: 0.7659 (mmt) REVERT: D 580 MET cc_start: 0.8552 (pmm) cc_final: 0.8013 (pmm) REVERT: E 591 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7628 (pmt170) REVERT: G 408 MET cc_start: 0.7919 (mmt) cc_final: 0.7686 (mmt) REVERT: G 580 MET cc_start: 0.8553 (pmm) cc_final: 0.8011 (pmm) REVERT: H 591 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7632 (pmt170) REVERT: J 408 MET cc_start: 0.7923 (mmt) cc_final: 0.7689 (mmt) REVERT: J 580 MET cc_start: 0.8560 (pmm) cc_final: 0.8025 (pmm) REVERT: K 591 ARG cc_start: 0.8184 (ptm160) cc_final: 0.7624 (pmt170) outliers start: 32 outliers final: 24 residues processed: 120 average time/residue: 0.1363 time to fit residues: 25.0264 Evaluate side-chains 112 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 21 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 80 optimal weight: 0.0000 chunk 44 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.097126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.074865 restraints weight = 46493.207| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.52 r_work: 0.3147 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17588 Z= 0.147 Angle : 0.520 7.417 23844 Z= 0.260 Chirality : 0.042 0.139 2624 Planarity : 0.003 0.041 3212 Dihedral : 3.502 14.414 2388 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.58 % Allowed : 5.68 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 2184 helix: 2.19 (0.20), residues: 748 sheet: -0.24 (0.23), residues: 508 loop : -0.38 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 541 TYR 0.007 0.001 TYR G 519 PHE 0.009 0.001 PHE D 515 TRP 0.008 0.001 TRP A 384 HIS 0.002 0.001 HIS G 255 Details of bonding type rmsd covalent geometry : bond 0.00334 (17588) covalent geometry : angle 0.51961 (23844) hydrogen bonds : bond 0.03302 ( 740) hydrogen bonds : angle 4.01015 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.597 Fit side-chains REVERT: A 389 ARG cc_start: 0.7932 (tpm170) cc_final: 0.7663 (mmm160) REVERT: A 408 MET cc_start: 0.7926 (mmt) cc_final: 0.7676 (mmt) REVERT: A 580 MET cc_start: 0.8603 (pmm) cc_final: 0.7942 (pmm) REVERT: B 591 ARG cc_start: 0.8257 (ptm160) cc_final: 0.7554 (pmt170) REVERT: B 593 MET cc_start: 0.7992 (mtm) cc_final: 0.7654 (mmm) REVERT: D 389 ARG cc_start: 0.7921 (tpm170) cc_final: 0.7651 (mmm160) REVERT: D 408 MET cc_start: 0.7917 (mmt) cc_final: 0.7667 (mmt) REVERT: D 580 MET cc_start: 0.8584 (pmm) cc_final: 0.7925 (pmm) REVERT: E 591 ARG cc_start: 0.8253 (ptm160) cc_final: 0.7564 (pmt170) REVERT: E 593 MET cc_start: 0.7978 (mtm) cc_final: 0.7653 (mmm) REVERT: G 389 ARG cc_start: 0.7923 (tpm170) cc_final: 0.7651 (mmm160) REVERT: G 408 MET cc_start: 0.7938 (mmt) cc_final: 0.7686 (mmt) REVERT: G 580 MET cc_start: 0.8597 (pmm) cc_final: 0.7936 (pmm) REVERT: H 591 ARG cc_start: 0.8252 (ptm160) cc_final: 0.7560 (pmt170) REVERT: H 593 MET cc_start: 0.7964 (mtm) cc_final: 0.7751 (mmm) REVERT: J 389 ARG cc_start: 0.7931 (tpm170) cc_final: 0.7660 (mmm160) REVERT: J 408 MET cc_start: 0.7940 (mmt) cc_final: 0.7689 (mmt) REVERT: J 580 MET cc_start: 0.8600 (pmm) cc_final: 0.7941 (pmm) REVERT: K 591 ARG cc_start: 0.8254 (ptm160) cc_final: 0.7550 (pmt170) REVERT: K 593 MET cc_start: 0.7974 (mtm) cc_final: 0.7642 (mmm) outliers start: 29 outliers final: 20 residues processed: 104 average time/residue: 0.1413 time to fit residues: 22.1988 Evaluate side-chains 108 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 75 optimal weight: 5.9990 chunk 93 optimal weight: 0.0170 chunk 77 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 overall best weight: 2.0622 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.091774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.067849 restraints weight = 47007.613| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 5.10 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17588 Z= 0.105 Angle : 0.482 6.594 23844 Z= 0.242 Chirality : 0.041 0.138 2624 Planarity : 0.003 0.039 3212 Dihedral : 3.318 13.579 2388 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.53 % Allowed : 6.99 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2184 helix: 2.34 (0.20), residues: 740 sheet: -0.21 (0.23), residues: 508 loop : -0.39 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 541 TYR 0.008 0.001 TYR G 519 PHE 0.007 0.001 PHE G 296 TRP 0.012 0.001 TRP J 384 HIS 0.002 0.001 HIS G 255 Details of bonding type rmsd covalent geometry : bond 0.00237 (17588) covalent geometry : angle 0.48228 (23844) hydrogen bonds : bond 0.02823 ( 740) hydrogen bonds : angle 3.87220 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7450 (mmt) cc_final: 0.7231 (mmt) REVERT: A 580 MET cc_start: 0.8115 (pmm) cc_final: 0.7418 (pmm) REVERT: B 591 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7352 (pmt170) REVERT: B 593 MET cc_start: 0.7897 (mtm) cc_final: 0.7607 (mmm) REVERT: D 408 MET cc_start: 0.7463 (mmt) cc_final: 0.7244 (mmt) REVERT: D 580 MET cc_start: 0.8108 (pmm) cc_final: 0.7479 (pmm) REVERT: E 591 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7373 (pmt170) REVERT: E 593 MET cc_start: 0.7901 (mtm) cc_final: 0.7613 (mmm) REVERT: G 408 MET cc_start: 0.7482 (mmt) cc_final: 0.7263 (mmt) REVERT: G 580 MET cc_start: 0.8118 (pmm) cc_final: 0.7488 (pmm) REVERT: H 591 ARG cc_start: 0.8219 (ptm160) cc_final: 0.7369 (pmt170) REVERT: H 593 MET cc_start: 0.7895 (mtm) cc_final: 0.7608 (mmm) REVERT: J 408 MET cc_start: 0.7468 (mmt) cc_final: 0.7246 (mmt) REVERT: J 580 MET cc_start: 0.8108 (pmm) cc_final: 0.7479 (pmm) REVERT: K 591 ARG cc_start: 0.8222 (ptm160) cc_final: 0.7364 (pmt170) REVERT: K 593 MET cc_start: 0.7893 (mtm) cc_final: 0.7607 (mmm) outliers start: 28 outliers final: 24 residues processed: 104 average time/residue: 0.1360 time to fit residues: 21.3706 Evaluate side-chains 112 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain G residue 557 CYS Chi-restraints excluded: chain H residue 596 SER Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Chi-restraints excluded: chain K residue 596 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 202 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 195 optimal weight: 0.2980 chunk 191 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 142 optimal weight: 0.1980 chunk 193 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.092535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069347 restraints weight = 47722.664| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 4.98 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17588 Z= 0.079 Angle : 0.465 7.127 23844 Z= 0.227 Chirality : 0.041 0.137 2624 Planarity : 0.003 0.038 3212 Dihedral : 3.030 12.614 2388 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.66 % Allowed : 8.95 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 2184 helix: 2.22 (0.20), residues: 768 sheet: -0.09 (0.24), residues: 508 loop : -0.47 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 541 TYR 0.005 0.001 TYR D 570 PHE 0.007 0.001 PHE G 296 TRP 0.010 0.001 TRP D 384 HIS 0.001 0.000 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00175 (17588) covalent geometry : angle 0.46488 (23844) hydrogen bonds : bond 0.02195 ( 740) hydrogen bonds : angle 3.66719 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.612 Fit side-chains REVERT: A 389 ARG cc_start: 0.8080 (tpm170) cc_final: 0.7827 (mmm160) REVERT: A 408 MET cc_start: 0.7517 (mmt) cc_final: 0.7245 (mmt) REVERT: A 580 MET cc_start: 0.8404 (pmm) cc_final: 0.7842 (pmm) REVERT: B 591 ARG cc_start: 0.8260 (ptm160) cc_final: 0.7323 (pmt170) REVERT: B 593 MET cc_start: 0.8048 (mtm) cc_final: 0.7743 (mmm) REVERT: D 389 ARG cc_start: 0.8076 (tpm170) cc_final: 0.7821 (mmm160) REVERT: D 408 MET cc_start: 0.7542 (mmt) cc_final: 0.7271 (mmt) REVERT: D 580 MET cc_start: 0.8391 (pmm) cc_final: 0.7826 (pmm) REVERT: E 591 ARG cc_start: 0.8258 (ptm160) cc_final: 0.7328 (pmt170) REVERT: E 593 MET cc_start: 0.8052 (mtm) cc_final: 0.7751 (mmm) REVERT: G 389 ARG cc_start: 0.7954 (tpm170) cc_final: 0.7679 (mmm160) REVERT: G 408 MET cc_start: 0.7576 (mmt) cc_final: 0.7302 (mmt) REVERT: G 580 MET cc_start: 0.8393 (pmm) cc_final: 0.7831 (pmm) REVERT: H 591 ARG cc_start: 0.8265 (ptm160) cc_final: 0.7338 (pmt170) REVERT: H 593 MET cc_start: 0.8054 (mtm) cc_final: 0.7752 (mmm) REVERT: J 389 ARG cc_start: 0.7956 (tpm170) cc_final: 0.7682 (mmm160) REVERT: J 408 MET cc_start: 0.7557 (mmt) cc_final: 0.7284 (mmt) REVERT: J 580 MET cc_start: 0.8386 (pmm) cc_final: 0.7824 (pmm) REVERT: K 591 ARG cc_start: 0.8271 (ptm160) cc_final: 0.7334 (pmt170) REVERT: K 593 MET cc_start: 0.8045 (mtm) cc_final: 0.7742 (mmm) outliers start: 12 outliers final: 12 residues processed: 116 average time/residue: 0.1680 time to fit residues: 28.0580 Evaluate side-chains 104 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 407 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 149 optimal weight: 3.9990 chunk 196 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 172 optimal weight: 0.1980 chunk 192 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.092435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069172 restraints weight = 47597.158| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.96 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17588 Z= 0.083 Angle : 0.482 8.610 23844 Z= 0.232 Chirality : 0.040 0.137 2624 Planarity : 0.002 0.036 3212 Dihedral : 2.994 11.981 2388 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.04 % Allowed : 8.57 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 2184 helix: 2.30 (0.20), residues: 764 sheet: -0.05 (0.24), residues: 508 loop : -0.44 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 541 TYR 0.005 0.001 TYR J 519 PHE 0.007 0.001 PHE G 296 TRP 0.008 0.001 TRP D 384 HIS 0.001 0.000 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00194 (17588) covalent geometry : angle 0.48190 (23844) hydrogen bonds : bond 0.02254 ( 740) hydrogen bonds : angle 3.60658 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.650 Fit side-chains REVERT: A 376 MET cc_start: 0.9273 (tpp) cc_final: 0.8844 (tpp) REVERT: A 389 ARG cc_start: 0.8097 (tpm170) cc_final: 0.7834 (mmm160) REVERT: A 408 MET cc_start: 0.7379 (mmt) cc_final: 0.7106 (mmt) REVERT: A 580 MET cc_start: 0.8379 (pmm) cc_final: 0.7811 (pmm) REVERT: B 591 ARG cc_start: 0.8268 (ptm160) cc_final: 0.7403 (pmt170) REVERT: B 593 MET cc_start: 0.7974 (mtm) cc_final: 0.7730 (mmm) REVERT: D 389 ARG cc_start: 0.8096 (tpm170) cc_final: 0.7833 (mmm160) REVERT: D 408 MET cc_start: 0.7383 (mmt) cc_final: 0.7111 (mmt) REVERT: D 580 MET cc_start: 0.8370 (pmm) cc_final: 0.7800 (pmm) REVERT: E 591 ARG cc_start: 0.8267 (ptm160) cc_final: 0.7408 (pmt170) REVERT: E 593 MET cc_start: 0.7977 (mtm) cc_final: 0.7736 (mmm) REVERT: G 389 ARG cc_start: 0.8100 (tpm170) cc_final: 0.7835 (mmm160) REVERT: G 408 MET cc_start: 0.7422 (mmt) cc_final: 0.7149 (mmt) REVERT: G 580 MET cc_start: 0.8374 (pmm) cc_final: 0.7806 (pmm) REVERT: H 591 ARG cc_start: 0.8270 (ptm160) cc_final: 0.7411 (pmt170) REVERT: H 593 MET cc_start: 0.7972 (mtm) cc_final: 0.7733 (mmm) REVERT: J 376 MET cc_start: 0.9271 (tpp) cc_final: 0.8845 (tpp) REVERT: J 389 ARG cc_start: 0.8097 (tpm170) cc_final: 0.7832 (mmm160) REVERT: J 408 MET cc_start: 0.7412 (mmt) cc_final: 0.7139 (mmt) REVERT: J 580 MET cc_start: 0.8375 (pmm) cc_final: 0.7807 (pmm) REVERT: K 591 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7410 (pmt170) REVERT: K 593 MET cc_start: 0.7963 (mtm) cc_final: 0.7723 (mmm) outliers start: 19 outliers final: 19 residues processed: 96 average time/residue: 0.1520 time to fit residues: 21.9148 Evaluate side-chains 107 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 557 CYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 407 LEU Chi-restraints excluded: chain J residue 523 LEU Chi-restraints excluded: chain J residue 557 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 163 optimal weight: 0.0970 chunk 117 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 0.0010 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.093342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070193 restraints weight = 47860.798| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.98 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17588 Z= 0.078 Angle : 0.471 7.183 23844 Z= 0.227 Chirality : 0.040 0.137 2624 Planarity : 0.002 0.035 3212 Dihedral : 2.874 11.597 2388 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 8.46 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 2184 helix: 2.62 (0.21), residues: 732 sheet: -0.02 (0.24), residues: 508 loop : -0.35 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 541 TYR 0.004 0.001 TYR J 570 PHE 0.007 0.001 PHE D 296 TRP 0.010 0.001 TRP D 384 HIS 0.001 0.000 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00182 (17588) covalent geometry : angle 0.47078 (23844) hydrogen bonds : bond 0.02000 ( 740) hydrogen bonds : angle 3.49221 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.8959 (m-40) cc_final: 0.8621 (m110) REVERT: A 376 MET cc_start: 0.9270 (tpp) cc_final: 0.8837 (tpp) REVERT: A 580 MET cc_start: 0.8422 (pmm) cc_final: 0.7898 (pmm) REVERT: B 591 ARG cc_start: 0.8294 (ptm160) cc_final: 0.7294 (pmt170) REVERT: B 593 MET cc_start: 0.7956 (mtm) cc_final: 0.7725 (mmm) REVERT: D 176 ASN cc_start: 0.8954 (m-40) cc_final: 0.8618 (m110) REVERT: D 376 MET cc_start: 0.9284 (tpp) cc_final: 0.8863 (tpp) REVERT: D 580 MET cc_start: 0.8405 (pmm) cc_final: 0.7881 (pmm) REVERT: E 591 ARG cc_start: 0.8291 (ptm160) cc_final: 0.7298 (pmt170) REVERT: E 593 MET cc_start: 0.7950 (mtm) cc_final: 0.7726 (mmm) REVERT: G 376 MET cc_start: 0.9275 (tpp) cc_final: 0.8852 (tpp) REVERT: G 580 MET cc_start: 0.8416 (pmm) cc_final: 0.7898 (pmm) REVERT: H 591 ARG cc_start: 0.8298 (ptm160) cc_final: 0.7308 (pmt170) REVERT: H 593 MET cc_start: 0.7945 (mtm) cc_final: 0.7721 (mmm) REVERT: J 176 ASN cc_start: 0.8959 (m-40) cc_final: 0.8625 (m110) REVERT: J 376 MET cc_start: 0.9270 (tpp) cc_final: 0.8839 (tpp) REVERT: J 580 MET cc_start: 0.8414 (pmm) cc_final: 0.7894 (pmm) REVERT: K 591 ARG cc_start: 0.8301 (ptm160) cc_final: 0.7295 (pmt170) REVERT: K 593 MET cc_start: 0.7940 (mtm) cc_final: 0.7713 (mmm) outliers start: 17 outliers final: 8 residues processed: 108 average time/residue: 0.1400 time to fit residues: 23.2869 Evaluate side-chains 99 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 148 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.089929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066583 restraints weight = 48430.906| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.96 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17588 Z= 0.156 Angle : 0.542 9.189 23844 Z= 0.263 Chirality : 0.041 0.149 2624 Planarity : 0.003 0.034 3212 Dihedral : 3.238 14.043 2388 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.04 % Allowed : 8.35 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 2184 helix: 2.20 (0.20), residues: 772 sheet: -0.21 (0.24), residues: 508 loop : -0.48 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 56 TYR 0.006 0.001 TYR A 570 PHE 0.009 0.001 PHE D 167 TRP 0.008 0.001 TRP J 105 HIS 0.003 0.001 HIS D 528 Details of bonding type rmsd covalent geometry : bond 0.00360 (17588) covalent geometry : angle 0.54200 (23844) hydrogen bonds : bond 0.03083 ( 740) hydrogen bonds : angle 3.80347 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9318 (tpp) cc_final: 0.8900 (tpp) REVERT: A 408 MET cc_start: 0.7678 (mmt) cc_final: 0.7383 (mmt) REVERT: A 580 MET cc_start: 0.8177 (pmm) cc_final: 0.7476 (pmm) REVERT: B 591 ARG cc_start: 0.8279 (ptm160) cc_final: 0.7283 (pmt170) REVERT: B 593 MET cc_start: 0.7836 (mtm) cc_final: 0.7598 (mmm) REVERT: D 376 MET cc_start: 0.9309 (tpp) cc_final: 0.8894 (tpp) REVERT: D 408 MET cc_start: 0.7682 (mmt) cc_final: 0.7388 (mmt) REVERT: D 580 MET cc_start: 0.8171 (pmm) cc_final: 0.7469 (pmm) REVERT: E 591 ARG cc_start: 0.8280 (ptm160) cc_final: 0.7291 (pmt170) REVERT: E 593 MET cc_start: 0.7840 (mtm) cc_final: 0.7605 (mmm) REVERT: G 376 MET cc_start: 0.9287 (tpp) cc_final: 0.8880 (tpp) REVERT: G 408 MET cc_start: 0.7712 (mmt) cc_final: 0.7418 (mmt) REVERT: G 580 MET cc_start: 0.8186 (pmm) cc_final: 0.7492 (pmm) REVERT: H 591 ARG cc_start: 0.8277 (ptm160) cc_final: 0.7289 (pmt170) REVERT: H 593 MET cc_start: 0.7835 (mtm) cc_final: 0.7604 (mmm) REVERT: J 376 MET cc_start: 0.9315 (tpp) cc_final: 0.8896 (tpp) REVERT: J 408 MET cc_start: 0.7681 (mmt) cc_final: 0.7405 (mmt) REVERT: J 580 MET cc_start: 0.8179 (pmm) cc_final: 0.7482 (pmm) REVERT: K 591 ARG cc_start: 0.8285 (ptm160) cc_final: 0.7291 (pmt170) REVERT: K 593 MET cc_start: 0.7835 (mtm) cc_final: 0.7600 (mmm) outliers start: 19 outliers final: 19 residues processed: 103 average time/residue: 0.1537 time to fit residues: 23.8642 Evaluate side-chains 111 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 512 GLU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain G residue 407 LEU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 523 LEU Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Chi-restraints excluded: chain J residue 512 GLU Chi-restraints excluded: chain J residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 174 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 207 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 164 optimal weight: 0.0070 chunk 38 optimal weight: 7.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.091915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068690 restraints weight = 47717.946| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.94 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17588 Z= 0.083 Angle : 0.502 9.446 23844 Z= 0.238 Chirality : 0.040 0.144 2624 Planarity : 0.002 0.034 3212 Dihedral : 3.011 14.096 2388 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.60 % Allowed : 8.79 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 2184 helix: 2.30 (0.20), residues: 764 sheet: -0.11 (0.24), residues: 508 loop : -0.43 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 274 TYR 0.005 0.001 TYR J 570 PHE 0.007 0.001 PHE G 296 TRP 0.009 0.001 TRP J 384 HIS 0.001 0.000 HIS D 255 Details of bonding type rmsd covalent geometry : bond 0.00193 (17588) covalent geometry : angle 0.50187 (23844) hydrogen bonds : bond 0.02275 ( 740) hydrogen bonds : angle 3.58140 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9294 (tpp) cc_final: 0.8870 (tpp) REVERT: A 580 MET cc_start: 0.8199 (pmm) cc_final: 0.7620 (pmm) REVERT: B 591 ARG cc_start: 0.8305 (ptm160) cc_final: 0.7337 (pmt170) REVERT: D 376 MET cc_start: 0.9265 (tpp) cc_final: 0.8849 (tpp) REVERT: D 580 MET cc_start: 0.8191 (pmm) cc_final: 0.7611 (pmm) REVERT: E 591 ARG cc_start: 0.8305 (ptm160) cc_final: 0.7340 (pmt170) REVERT: G 376 MET cc_start: 0.9263 (tpp) cc_final: 0.8846 (tpp) REVERT: G 580 MET cc_start: 0.8204 (pmm) cc_final: 0.7630 (pmm) REVERT: H 591 ARG cc_start: 0.8306 (ptm160) cc_final: 0.7343 (pmt170) REVERT: J 376 MET cc_start: 0.9290 (tpp) cc_final: 0.8863 (tpp) REVERT: J 580 MET cc_start: 0.8201 (pmm) cc_final: 0.7627 (pmm) REVERT: K 591 ARG cc_start: 0.8310 (ptm160) cc_final: 0.7340 (pmt170) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.1531 time to fit residues: 22.9158 Evaluate side-chains 100 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 295 MET Chi-restraints excluded: chain J residue 152 ILE Chi-restraints excluded: chain J residue 295 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 47 optimal weight: 8.9990 chunk 184 optimal weight: 0.0070 chunk 72 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 165 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.0804 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.091102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067717 restraints weight = 48168.501| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.95 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17588 Z= 0.103 Angle : 0.529 11.005 23844 Z= 0.246 Chirality : 0.040 0.145 2624 Planarity : 0.002 0.034 3212 Dihedral : 3.046 13.949 2388 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.66 % Allowed : 8.73 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2184 helix: 2.26 (0.20), residues: 772 sheet: -0.18 (0.24), residues: 508 loop : -0.44 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 391 TYR 0.005 0.001 TYR A 570 PHE 0.006 0.001 PHE J 296 TRP 0.005 0.001 TRP J 384 HIS 0.002 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00240 (17588) covalent geometry : angle 0.52871 (23844) hydrogen bonds : bond 0.02529 ( 740) hydrogen bonds : angle 3.61788 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.85 seconds wall clock time: 45 minutes 55.57 seconds (2755.57 seconds total)