Starting phenix.real_space_refine on Sat Jul 4 09:17:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aa5_11690/07_2026/7aa5_11690_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aa5_11690/07_2026/7aa5_11690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aa5_11690/07_2026/7aa5_11690_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aa5_11690/07_2026/7aa5_11690_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aa5_11690/07_2026/7aa5_11690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aa5_11690/07_2026/7aa5_11690.map" } resolution = 4.18 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= 0.002 sd= 0.025 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 108 5.16 5 C 12804 2.51 5 N 3268 2.21 5 O 3516 1.98 5 H 8 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19705 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "B" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "C" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "D" Number of atoms: 4926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4926 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 22, 'TRANS': 589} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 4.06, per 1000 atoms: 0.21 Number of scatterers: 19705 At special positions: 0 Unit cell: (147.609, 147.609, 116.937, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 108 16.00 O 3516 8.00 N 3268 7.00 C 12804 6.00 H 8 1.00 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: 1.68 Conformation dependent library (CDL) restraints added in 814.2 milliseconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 61.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.999A pdb=" N ASP A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 336 through 357 removed outlier: 3.736A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 400' Processing helix chain 'A' and resid 432 through 439 removed outlier: 3.515A pdb=" N ILE A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.623A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 4.119A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 570 removed outlier: 3.546A pdb=" N SER A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 593 removed outlier: 3.897A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 3.625A pdb=" N LEU A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 4.006A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 635 Processing helix chain 'A' and resid 667 through 678 Processing helix chain 'A' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 729 through 748 removed outlier: 3.638A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.735A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP B 165 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 Processing helix chain 'B' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.692A pdb=" N THR B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 400' Processing helix chain 'B' and resid 432 through 439 removed outlier: 3.515A pdb=" N ILE B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.624A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 removed outlier: 3.544A pdb=" N SER B 557 " --> pdb=" O TYR B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 4.007A pdb=" N GLN B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 635 Processing helix chain 'B' and resid 667 through 678 Processing helix chain 'B' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP C 165 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.698A pdb=" N ASN C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 400' Processing helix chain 'C' and resid 432 through 439 removed outlier: 3.514A pdb=" N ILE C 436 " --> pdb=" O SER C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.624A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 460 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 530 removed outlier: 3.554A pdb=" N ILE C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 570 removed outlier: 3.545A pdb=" N SER C 557 " --> pdb=" O TYR C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU C 598 " --> pdb=" O GLY C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 removed outlier: 4.007A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 635 Processing helix chain 'C' and resid 667 through 678 Processing helix chain 'C' and resid 693 through 709 removed outlier: 4.255A pdb=" N ILE C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 698 " --> pdb=" O VAL C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 722 Processing helix chain 'C' and resid 723 through 725 No H-bonds generated for 'chain 'C' and resid 723 through 725' Processing helix chain 'C' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.734A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 4.000A pdb=" N ASP D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.699A pdb=" N ASN D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.939A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 336 through 357 removed outlier: 3.735A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL D 342 " --> pdb=" O ASN D 338 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 392 removed outlier: 3.791A pdb=" N ARG D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.691A pdb=" N THR D 399 " --> pdb=" O ASP D 396 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 400' Processing helix chain 'D' and resid 432 through 439 removed outlier: 3.514A pdb=" N ILE D 436 " --> pdb=" O SER D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 450 removed outlier: 3.623A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 removed outlier: 4.120A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.904A pdb=" N PHE D 471 " --> pdb=" O GLY D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 530 removed outlier: 3.553A pdb=" N ILE D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 570 removed outlier: 3.544A pdb=" N SER D 557 " --> pdb=" O TYR D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 593 removed outlier: 3.898A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 599 removed outlier: 3.626A pdb=" N LEU D 598 " --> pdb=" O GLY D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 610 removed outlier: 4.006A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 635 Processing helix chain 'D' and resid 667 through 678 Processing helix chain 'D' and resid 693 through 709 removed outlier: 4.254A pdb=" N ILE D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 698 " --> pdb=" O VAL D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 722 Processing helix chain 'D' and resid 723 through 725 No H-bonds generated for 'chain 'D' and resid 723 through 725' Processing helix chain 'D' and resid 729 through 748 removed outlier: 3.639A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU A 418 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.652A pdb=" N LEU B 418 " --> pdb=" O PHE B 406 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU C 418 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 406 removed outlier: 3.651A pdb=" N LEU D 418 " --> pdb=" O PHE D 406 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 8 1.17 - 1.33: 4161 1.33 - 1.49: 7284 1.49 - 1.65: 8513 1.65 - 1.81: 178 Bond restraints: 20144 Sorted by residual: bond pdb=" N PRO D 772 " pdb=" CD PRO D 772 " ideal model delta sigma weight residual 1.473 1.714 -0.241 1.40e-02 5.10e+03 2.96e+02 bond pdb=" N PRO B 772 " pdb=" CD PRO B 772 " ideal model delta sigma weight residual 1.473 1.714 -0.241 1.40e-02 5.10e+03 2.96e+02 bond pdb=" N PRO D 772 " pdb=" CA PRO D 772 " ideal model delta sigma weight residual 1.469 1.292 0.177 1.28e-02 6.10e+03 1.91e+02 bond pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta sigma weight residual 1.469 1.292 0.177 1.28e-02 6.10e+03 1.90e+02 bond pdb=" N PRO C 772 " pdb=" CD PRO C 772 " ideal model delta sigma weight residual 1.473 1.629 -0.156 1.40e-02 5.10e+03 1.25e+02 ... (remaining 20139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.99: 27222 5.99 - 11.97: 62 11.97 - 17.96: 5 17.96 - 23.94: 6 23.94 - 29.93: 1 Bond angle restraints: 27296 Sorted by residual: angle pdb=" C THR C 771 " pdb=" N PRO C 772 " pdb=" CA PRO C 772 " ideal model delta sigma weight residual 119.84 99.71 20.13 1.25e+00 6.40e-01 2.59e+02 angle pdb=" CA THR B 771 " pdb=" C THR B 771 " pdb=" O THR B 771 " ideal model delta sigma weight residual 120.16 100.91 19.25 1.37e+00 5.33e-01 1.97e+02 angle pdb=" CA THR D 771 " pdb=" C THR D 771 " pdb=" O THR D 771 " ideal model delta sigma weight residual 120.16 100.93 19.23 1.37e+00 5.33e-01 1.97e+02 angle pdb=" C THR D 771 " pdb=" N PRO D 772 " pdb=" CA PRO D 772 " ideal model delta sigma weight residual 119.84 102.33 17.51 1.25e+00 6.40e-01 1.96e+02 angle pdb=" C THR B 771 " pdb=" N PRO B 772 " pdb=" CA PRO B 772 " ideal model delta sigma weight residual 119.84 102.34 17.50 1.25e+00 6.40e-01 1.96e+02 ... (remaining 27291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10620 17.58 - 35.16: 1116 35.16 - 52.73: 209 52.73 - 70.31: 46 70.31 - 87.89: 9 Dihedral angle restraints: 12000 sinusoidal: 4820 harmonic: 7180 Sorted by residual: dihedral pdb=" CA GLY C 770 " pdb=" C GLY C 770 " pdb=" N THR C 771 " pdb=" CA THR C 771 " ideal model delta harmonic sigma weight residual 180.00 106.78 73.22 0 5.00e+00 4.00e-02 2.14e+02 dihedral pdb=" CA GLY D 770 " pdb=" C GLY D 770 " pdb=" N THR D 771 " pdb=" CA THR D 771 " ideal model delta harmonic sigma weight residual 180.00 122.37 57.63 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA GLY B 770 " pdb=" C GLY B 770 " pdb=" N THR B 771 " pdb=" CA THR B 771 " ideal model delta harmonic sigma weight residual 180.00 122.41 57.59 0 5.00e+00 4.00e-02 1.33e+02 ... (remaining 11997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3052 0.095 - 0.190: 78 0.190 - 0.286: 2 0.286 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA PRO B 772 " pdb=" N PRO B 772 " pdb=" C PRO B 772 " pdb=" CB PRO B 772 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA PRO D 772 " pdb=" N PRO D 772 " pdb=" C PRO D 772 " pdb=" CB PRO D 772 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CB THR A 771 " pdb=" CA THR A 771 " pdb=" OG1 THR A 771 " pdb=" CG2 THR A 771 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.45 2.00e-01 2.50e+01 4.99e+00 ... (remaining 3133 not shown) Planarity restraints: 3408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 770 " 0.024 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C GLY A 770 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY A 770 " 0.037 2.00e-02 2.50e+03 pdb=" N THR A 771 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 771 " -0.021 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C THR B 771 " 0.075 2.00e-02 2.50e+03 pdb=" O THR B 771 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO B 772 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 771 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C THR D 771 " -0.075 2.00e-02 2.50e+03 pdb=" O THR D 771 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO D 772 " 0.028 2.00e-02 2.50e+03 ... (remaining 3405 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.62: 403 2.62 - 3.11: 17172 3.11 - 3.61: 25393 3.61 - 4.10: 32478 4.10 - 4.60: 47585 Nonbonded interactions: 123031 Sorted by model distance: nonbonded pdb=" O THR A 339 " pdb=" OG1 THR A 343 " model vdw 2.119 2.800 nonbonded pdb=" O THR B 339 " pdb=" OG1 THR B 343 " model vdw 2.120 2.800 nonbonded pdb=" O THR C 339 " pdb=" OG1 THR C 343 " model vdw 2.120 2.800 nonbonded pdb=" O THR D 339 " pdb=" OG1 THR D 343 " model vdw 2.120 2.800 nonbonded pdb=" O ALA D 217 " pdb=" OG1 THR D 220 " model vdw 2.199 2.800 ... (remaining 123026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 148 through 786) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 13.140 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: 0.200 Extract box with map and model: 0.510 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 20136 Z= 0.336 Angle : 0.921 29.930 27288 Z= 0.544 Chirality : 0.045 0.476 3136 Planarity : 0.005 0.072 3408 Dihedral : 14.673 87.890 7360 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 15.06 % Favored : 84.74 % Rotamer: Outliers : 2.04 % Allowed : 4.72 % Favored : 93.24 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.34 % 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: -4.78 (0.13), residues: 2424 helix: -2.43 (0.11), residues: 1336 sheet: -1.80 (0.54), residues: 76 loop : -4.33 (0.15), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 757 TYR 0.012 0.001 TYR C 500 PHE 0.012 0.001 PHE B 756 TRP 0.022 0.002 TRP C 733 HIS 0.004 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.34 (20136) covalent geometry : angle 0.92061 / 0.54 (27288) hydrogen bonds : bond 0.15361 / 9.81 ( 944) hydrogen bonds : angle 7.01976 / 4.96 ( 2784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.7127 (mmm) cc_final: 0.6823 (mmm) REVERT: A 482 MET cc_start: 0.8206 (mmm) cc_final: 0.7707 (mmt) REVERT: A 578 MET cc_start: 0.6533 (mtp) cc_final: 0.6286 (tpp) REVERT: A 757 ARG cc_start: 0.8177 (ppt170) cc_final: 0.7956 (ppt170) REVERT: B 176 HIS cc_start: 0.8619 (t-170) cc_final: 0.8132 (m90) REVERT: B 482 MET cc_start: 0.7450 (mmm) cc_final: 0.6929 (mmt) REVERT: B 556 TYR cc_start: 0.9269 (t80) cc_final: 0.8726 (t80) REVERT: B 761 MET cc_start: 0.8316 (mmp) cc_final: 0.8035 (mmp) REVERT: C 223 MET cc_start: 0.7257 (mmm) cc_final: 0.6986 (mmm) REVERT: C 225 GLU cc_start: 0.7495 (tt0) cc_final: 0.7281 (tt0) REVERT: C 482 MET cc_start: 0.8305 (mmm) cc_final: 0.7802 (mmt) REVERT: D 223 MET cc_start: 0.7133 (mmm) cc_final: 0.6838 (mmm) REVERT: D 225 GLU cc_start: 0.7508 (tt0) cc_final: 0.7265 (tt0) REVERT: D 482 MET cc_start: 0.8211 (mmm) cc_final: 0.7717 (mmt) REVERT: D 713 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9099 (mmt) REVERT: D 757 ARG cc_start: 0.8230 (ppt170) cc_final: 0.7976 (ppt170) outliers start: 44 outliers final: 19 residues processed: 280 average time/residue: 0.1316 time to fit residues: 58.3652 Evaluate side-chains 205 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 overall best weight: 2.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.084990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064114 restraints weight = 106220.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.066417 restraints weight = 69034.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.067417 restraints weight = 43024.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.067725 restraints weight = 35486.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.067826 restraints weight = 32821.067| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20136 Z= 0.178 Angle : 0.618 8.515 27288 Z= 0.328 Chirality : 0.037 0.147 3136 Planarity : 0.004 0.043 3408 Dihedral : 5.814 40.892 2692 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 47.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.70 % Favored : 86.14 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.96 (0.15), residues: 2424 helix: -0.66 (0.13), residues: 1368 sheet: -1.51 (0.54), residues: 76 loop : -4.03 (0.16), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.013 0.001 TYR D 628 PHE 0.041 0.002 PHE B 615 TRP 0.014 0.001 TRP B 586 HIS 0.006 0.001 HIS C 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (20136) covalent geometry : angle 0.61829 / 0.33 (27288) hydrogen bonds : bond 0.03917 / 2.61 ( 944) hydrogen bonds : angle 5.56836 / 3.95 ( 2784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9301 (t-90) cc_final: 0.8579 (t-90) REVERT: A 178 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8437 (mmmt) REVERT: A 397 GLU cc_start: 0.9248 (pm20) cc_final: 0.8633 (tm-30) REVERT: A 482 MET cc_start: 0.8209 (mmm) cc_final: 0.7786 (mmt) REVERT: A 578 MET cc_start: 0.6288 (mtp) cc_final: 0.6004 (mtt) REVERT: A 587 MET cc_start: 0.9124 (mtm) cc_final: 0.8853 (mtp) REVERT: A 624 PHE cc_start: 0.9298 (m-80) cc_final: 0.9017 (m-80) REVERT: B 482 MET cc_start: 0.7467 (mmm) cc_final: 0.7239 (mmt) REVERT: B 578 MET cc_start: 0.4556 (mtt) cc_final: 0.4312 (tpp) REVERT: B 587 MET cc_start: 0.8907 (mtm) cc_final: 0.8546 (mtp) REVERT: B 624 PHE cc_start: 0.9250 (m-80) cc_final: 0.8954 (m-80) REVERT: B 761 MET cc_start: 0.8769 (mmp) cc_final: 0.8545 (mmp) REVERT: C 176 HIS cc_start: 0.9320 (t-90) cc_final: 0.8593 (t-90) REVERT: C 178 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8371 (mmmt) REVERT: C 397 GLU cc_start: 0.9219 (pm20) cc_final: 0.8568 (tm-30) REVERT: C 587 MET cc_start: 0.9149 (mtm) cc_final: 0.8877 (mtp) REVERT: C 624 PHE cc_start: 0.9213 (m-80) cc_final: 0.8990 (m-80) REVERT: D 176 HIS cc_start: 0.9325 (t-90) cc_final: 0.8623 (t-90) REVERT: D 178 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8429 (mmmt) REVERT: D 397 GLU cc_start: 0.9254 (pm20) cc_final: 0.8665 (tm-30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1314 time to fit residues: 46.5263 Evaluate side-chains 184 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 GLN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.084940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064346 restraints weight = 105959.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066541 restraints weight = 68388.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067593 restraints weight = 43093.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.067930 restraints weight = 37108.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068009 restraints weight = 31905.259| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20136 Z= 0.181 Angle : 0.606 8.816 27288 Z= 0.320 Chirality : 0.037 0.138 3136 Planarity : 0.004 0.037 3408 Dihedral : 5.561 36.342 2692 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 57.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.40 % Favored : 85.44 % Rotamer: Outliers : 0.19 % Allowed : 4.54 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.49 (0.16), residues: 2424 helix: -0.16 (0.13), residues: 1396 sheet: -1.34 (0.56), residues: 76 loop : -4.12 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.016 0.002 TYR C 303 PHE 0.022 0.001 PHE B 615 TRP 0.010 0.001 TRP A 586 HIS 0.006 0.001 HIS C 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (20136) covalent geometry : angle 0.60596 / 0.32 (27288) hydrogen bonds : bond 0.03506 / 2.31 ( 944) hydrogen bonds : angle 5.26299 / 3.73 ( 2784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 229 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9334 (t-90) cc_final: 0.9087 (t-90) REVERT: A 178 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8497 (mtpp) REVERT: A 587 MET cc_start: 0.9110 (mtm) cc_final: 0.8872 (mtp) REVERT: A 624 PHE cc_start: 0.9256 (m-80) cc_final: 0.8999 (m-80) REVERT: A 761 MET cc_start: 0.8692 (mmp) cc_final: 0.8384 (mmp) REVERT: B 219 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7794 (mmt90) REVERT: B 482 MET cc_start: 0.7600 (mmm) cc_final: 0.7316 (mmt) REVERT: B 578 MET cc_start: 0.4401 (mtt) cc_final: 0.4179 (tpp) REVERT: B 587 MET cc_start: 0.8919 (mtm) cc_final: 0.8607 (mpp) REVERT: B 624 PHE cc_start: 0.9220 (m-80) cc_final: 0.8968 (m-80) REVERT: B 761 MET cc_start: 0.8777 (mmp) cc_final: 0.8543 (mmp) REVERT: C 176 HIS cc_start: 0.9314 (t-90) cc_final: 0.9099 (t-90) REVERT: C 178 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8504 (mtpp) REVERT: C 587 MET cc_start: 0.9118 (mtm) cc_final: 0.8908 (mtp) REVERT: C 624 PHE cc_start: 0.9212 (m-80) cc_final: 0.9001 (m-80) REVERT: C 761 MET cc_start: 0.8773 (mmp) cc_final: 0.8513 (mmp) REVERT: D 176 HIS cc_start: 0.9309 (t-90) cc_final: 0.9091 (t-90) REVERT: D 397 GLU cc_start: 0.9250 (pm20) cc_final: 0.8656 (tm-30) REVERT: D 402 LEU cc_start: 0.9197 (pt) cc_final: 0.8981 (pt) REVERT: D 587 MET cc_start: 0.9037 (mtm) cc_final: 0.8744 (mtp) REVERT: D 761 MET cc_start: 0.8741 (mmp) cc_final: 0.8499 (mmp) REVERT: D 778 PHE cc_start: 0.7393 (t80) cc_final: 0.7183 (t80) outliers start: 4 outliers final: 0 residues processed: 233 average time/residue: 0.1278 time to fit residues: 47.6754 Evaluate side-chains 185 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 231 optimal weight: 0.0020 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.092603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069193 restraints weight = 88619.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071097 restraints weight = 53953.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.072370 restraints weight = 38850.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073305 restraints weight = 31036.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.073960 restraints weight = 26558.123| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20136 Z= 0.103 Angle : 0.501 9.159 27288 Z= 0.267 Chirality : 0.035 0.132 3136 Planarity : 0.004 0.050 3408 Dihedral : 5.156 33.053 2692 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 52.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.29 % Favored : 87.54 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.75 (0.17), residues: 2424 helix: 0.44 (0.14), residues: 1400 sheet: -0.92 (0.57), residues: 76 loop : -3.82 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 320 TYR 0.013 0.001 TYR D 621 PHE 0.024 0.001 PHE D 624 TRP 0.011 0.001 TRP A 586 HIS 0.006 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (20136) covalent geometry : angle 0.50115 / 0.27 (27288) hydrogen bonds : bond 0.02969 / 1.96 ( 944) hydrogen bonds : angle 4.72345 / 3.33 ( 2784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9188 (t-90) cc_final: 0.8975 (t-90) REVERT: A 397 GLU cc_start: 0.9116 (pm20) cc_final: 0.8600 (tm-30) REVERT: A 587 MET cc_start: 0.8971 (mtm) cc_final: 0.8770 (mtp) REVERT: A 624 PHE cc_start: 0.9123 (m-80) cc_final: 0.8891 (m-80) REVERT: A 713 MET cc_start: 0.9077 (tpp) cc_final: 0.8726 (tpp) REVERT: A 761 MET cc_start: 0.8640 (mmp) cc_final: 0.8396 (mmp) REVERT: A 778 PHE cc_start: 0.7361 (t80) cc_final: 0.7153 (t80) REVERT: B 219 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7795 (mmt90) REVERT: B 482 MET cc_start: 0.7572 (mmm) cc_final: 0.7318 (mmt) REVERT: B 587 MET cc_start: 0.8756 (mtm) cc_final: 0.8478 (mtp) REVERT: B 624 PHE cc_start: 0.9130 (m-80) cc_final: 0.8868 (m-80) REVERT: B 710 LEU cc_start: 0.9837 (mm) cc_final: 0.9631 (mp) REVERT: B 761 MET cc_start: 0.8663 (mmp) cc_final: 0.8444 (mmp) REVERT: C 397 GLU cc_start: 0.9099 (pm20) cc_final: 0.8606 (tm-30) REVERT: C 761 MET cc_start: 0.8689 (mmp) cc_final: 0.8486 (mmp) REVERT: D 397 GLU cc_start: 0.9099 (pm20) cc_final: 0.8592 (tm-30) REVERT: D 482 MET cc_start: 0.8250 (mmm) cc_final: 0.7607 (mmt) REVERT: D 587 MET cc_start: 0.8883 (mtm) cc_final: 0.8596 (mtp) REVERT: D 778 PHE cc_start: 0.7335 (t80) cc_final: 0.7076 (t80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1263 time to fit residues: 46.2108 Evaluate side-chains 195 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 77 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 207 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.086457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.065132 restraints weight = 104856.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067010 restraints weight = 64828.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.068259 restraints weight = 46608.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069099 restraints weight = 36936.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069650 restraints weight = 31395.004| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20136 Z= 0.124 Angle : 0.516 5.695 27288 Z= 0.273 Chirality : 0.035 0.149 3136 Planarity : 0.003 0.038 3408 Dihedral : 4.990 31.167 2692 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 56.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.37 % Favored : 86.47 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.44 (0.17), residues: 2424 helix: 0.72 (0.14), residues: 1400 sheet: -0.94 (0.57), residues: 76 loop : -3.75 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.012 0.001 TYR A 628 PHE 0.023 0.001 PHE C 624 TRP 0.012 0.001 TRP A 586 HIS 0.004 0.001 HIS B 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (20136) covalent geometry : angle 0.51615 / 0.27 (27288) hydrogen bonds : bond 0.02882 / 1.90 ( 944) hydrogen bonds : angle 4.60012 / 3.25 ( 2784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9180 (t-90) cc_final: 0.8909 (t-90) REVERT: A 397 GLU cc_start: 0.9157 (pm20) cc_final: 0.8637 (tm-30) REVERT: A 482 MET cc_start: 0.8214 (mmm) cc_final: 0.7517 (mmt) REVERT: A 587 MET cc_start: 0.9109 (mtm) cc_final: 0.8899 (mtp) REVERT: A 621 TYR cc_start: 0.9385 (t80) cc_final: 0.9182 (t80) REVERT: A 624 PHE cc_start: 0.9179 (m-80) cc_final: 0.8969 (m-80) REVERT: A 761 MET cc_start: 0.8568 (mmp) cc_final: 0.8311 (mmp) REVERT: B 482 MET cc_start: 0.7569 (mmm) cc_final: 0.7260 (mmt) REVERT: B 587 MET cc_start: 0.8924 (mtm) cc_final: 0.8674 (mtp) REVERT: B 621 TYR cc_start: 0.9349 (t80) cc_final: 0.9067 (t80) REVERT: B 624 PHE cc_start: 0.9165 (m-80) cc_final: 0.8926 (m-80) REVERT: B 710 LEU cc_start: 0.9852 (mm) cc_final: 0.9608 (mp) REVERT: B 761 MET cc_start: 0.8574 (mmp) cc_final: 0.8363 (mmp) REVERT: C 397 GLU cc_start: 0.9131 (pm20) cc_final: 0.8637 (tm-30) REVERT: C 482 MET cc_start: 0.8277 (mmm) cc_final: 0.7564 (mmt) REVERT: C 622 LEU cc_start: 0.9177 (tp) cc_final: 0.8974 (tp) REVERT: C 624 PHE cc_start: 0.9139 (m-80) cc_final: 0.8939 (m-80) REVERT: D 397 GLU cc_start: 0.9135 (pm20) cc_final: 0.8663 (tm-30) REVERT: D 482 MET cc_start: 0.8270 (mmm) cc_final: 0.7582 (mmt) REVERT: D 587 MET cc_start: 0.9029 (mtm) cc_final: 0.8759 (mtp) REVERT: D 778 PHE cc_start: 0.7344 (t80) cc_final: 0.7105 (t80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1143 time to fit residues: 42.5356 Evaluate side-chains 194 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 chunk 63 optimal weight: 0.3980 chunk 21 optimal weight: 0.0970 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 ASN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 ASN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.099474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.077638 restraints weight = 100546.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079645 restraints weight = 60478.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080994 restraints weight = 42911.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081880 restraints weight = 33792.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.082524 restraints weight = 28637.916| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20136 Z= 0.151 Angle : 0.540 5.483 27288 Z= 0.285 Chirality : 0.036 0.142 3136 Planarity : 0.004 0.036 3408 Dihedral : 4.982 29.316 2692 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 58.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.78 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -1.40 (0.17), residues: 2424 helix: 0.78 (0.14), residues: 1400 sheet: -1.11 (0.56), residues: 76 loop : -3.74 (0.18), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.016 0.001 TYR C 303 PHE 0.021 0.001 PHE C 707 TRP 0.010 0.001 TRP A 586 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (20136) covalent geometry : angle 0.53968 / 0.29 (27288) hydrogen bonds : bond 0.02980 / 1.98 ( 944) hydrogen bonds : angle 4.70164 / 3.33 ( 2784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.9129 (pm20) cc_final: 0.8619 (tm-30) REVERT: A 482 MET cc_start: 0.8295 (mmm) cc_final: 0.7631 (mmt) REVERT: A 622 LEU cc_start: 0.9233 (tp) cc_final: 0.9027 (tp) REVERT: A 624 PHE cc_start: 0.9118 (m-80) cc_final: 0.8912 (m-80) REVERT: A 761 MET cc_start: 0.8531 (mmp) cc_final: 0.8097 (mmp) REVERT: B 397 GLU cc_start: 0.9257 (pm20) cc_final: 0.8683 (tm-30) REVERT: B 482 MET cc_start: 0.7745 (mmm) cc_final: 0.7429 (mmt) REVERT: B 587 MET cc_start: 0.8855 (mtm) cc_final: 0.8587 (mtp) REVERT: B 624 PHE cc_start: 0.9116 (m-80) cc_final: 0.8893 (m-80) REVERT: B 642 MET cc_start: 0.8668 (tpt) cc_final: 0.8448 (tpp) REVERT: B 761 MET cc_start: 0.8593 (mmp) cc_final: 0.8385 (mmp) REVERT: B 778 PHE cc_start: 0.7753 (t80) cc_final: 0.7529 (t80) REVERT: C 397 GLU cc_start: 0.9143 (pm20) cc_final: 0.8656 (tm-30) REVERT: C 482 MET cc_start: 0.8329 (mmm) cc_final: 0.7675 (mmt) REVERT: C 622 LEU cc_start: 0.9147 (tp) cc_final: 0.8902 (tp) REVERT: D 176 HIS cc_start: 0.9120 (t-90) cc_final: 0.8788 (t-90) REVERT: D 397 GLU cc_start: 0.9133 (pm20) cc_final: 0.8681 (tm-30) REVERT: D 482 MET cc_start: 0.8269 (mmm) cc_final: 0.7591 (mmt) REVERT: D 587 MET cc_start: 0.8946 (mtm) cc_final: 0.8701 (mtp) REVERT: D 778 PHE cc_start: 0.7355 (t80) cc_final: 0.7085 (t80) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1122 time to fit residues: 41.7045 Evaluate side-chains 183 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 187 optimal weight: 0.4980 chunk 219 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 ASN ** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.095785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.072690 restraints weight = 91399.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.074742 restraints weight = 55122.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.076090 restraints weight = 39291.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.076991 restraints weight = 31215.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077560 restraints weight = 26658.832| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20136 Z= 0.087 Angle : 0.476 6.098 27288 Z= 0.251 Chirality : 0.035 0.112 3136 Planarity : 0.003 0.047 3408 Dihedral : 4.691 28.208 2692 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 56.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.09 % Favored : 87.75 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -0.88 (0.18), residues: 2424 helix: 1.28 (0.14), residues: 1380 sheet: -0.80 (0.56), residues: 76 loop : -3.58 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 757 TYR 0.012 0.001 TYR C 628 PHE 0.019 0.001 PHE D 624 TRP 0.011 0.001 TRP A 586 HIS 0.004 0.001 HIS D 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (20136) covalent geometry : angle 0.47635 / 0.25 (27288) hydrogen bonds : bond 0.02619 / 1.73 ( 944) hydrogen bonds : angle 4.37247 / 3.09 ( 2784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9126 (t-90) cc_final: 0.8769 (t-90) REVERT: A 397 GLU cc_start: 0.9113 (pm20) cc_final: 0.8652 (tm-30) REVERT: A 482 MET cc_start: 0.8280 (mmm) cc_final: 0.7590 (mmt) REVERT: A 622 LEU cc_start: 0.9215 (tp) cc_final: 0.8955 (tp) REVERT: A 642 MET cc_start: 0.8666 (tpt) cc_final: 0.8455 (tpp) REVERT: A 761 MET cc_start: 0.8522 (mmp) cc_final: 0.8236 (mmp) REVERT: B 176 HIS cc_start: 0.9190 (t-90) cc_final: 0.8957 (t-90) REVERT: B 397 GLU cc_start: 0.9291 (pm20) cc_final: 0.8731 (tm-30) REVERT: B 482 MET cc_start: 0.7750 (mmm) cc_final: 0.7465 (mmt) REVERT: B 587 MET cc_start: 0.8974 (mtm) cc_final: 0.8730 (mtp) REVERT: B 622 LEU cc_start: 0.9237 (tp) cc_final: 0.9010 (tp) REVERT: B 778 PHE cc_start: 0.7731 (t80) cc_final: 0.7472 (t80) REVERT: C 176 HIS cc_start: 0.9096 (t-90) cc_final: 0.8746 (t-90) REVERT: C 397 GLU cc_start: 0.9171 (pm20) cc_final: 0.8703 (tm-30) REVERT: C 482 MET cc_start: 0.8438 (mmm) cc_final: 0.7639 (mmt) REVERT: C 622 LEU cc_start: 0.9133 (tp) cc_final: 0.8799 (tp) REVERT: C 778 PHE cc_start: 0.7301 (t80) cc_final: 0.7085 (t80) REVERT: D 176 HIS cc_start: 0.9127 (t-90) cc_final: 0.8787 (t-90) REVERT: D 397 GLU cc_start: 0.9171 (pm20) cc_final: 0.8725 (tm-30) REVERT: D 482 MET cc_start: 0.8341 (mmm) cc_final: 0.7469 (mmt) REVERT: D 556 TYR cc_start: 0.9221 (t80) cc_final: 0.8916 (t80) REVERT: D 587 MET cc_start: 0.9076 (mtm) cc_final: 0.8840 (mtp) REVERT: D 778 PHE cc_start: 0.7334 (t80) cc_final: 0.7053 (t80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1145 time to fit residues: 43.2088 Evaluate side-chains 199 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 126 optimal weight: 0.6980 chunk 210 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 238 optimal weight: 6.9990 chunk 148 optimal weight: 0.0370 chunk 121 optimal weight: 10.0000 chunk 214 optimal weight: 0.4980 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 180 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064940 restraints weight = 97835.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.067099 restraints weight = 55518.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068541 restraints weight = 37675.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.069503 restraints weight = 28658.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.070154 restraints weight = 23621.955| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20136 Z= 0.078 Angle : 0.459 5.412 27288 Z= 0.243 Chirality : 0.034 0.129 3136 Planarity : 0.003 0.039 3408 Dihedral : 4.416 26.641 2692 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 53.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.26 % Favored : 88.57 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.18), residues: 2424 helix: 1.61 (0.14), residues: 1396 sheet: -0.47 (0.59), residues: 76 loop : -3.35 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 400 TYR 0.012 0.001 TYR A 628 PHE 0.020 0.001 PHE C 624 TRP 0.012 0.001 TRP C 586 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.08 (20136) covalent geometry : angle 0.45945 / 0.24 (27288) hydrogen bonds : bond 0.02420 / 1.61 ( 944) hydrogen bonds : angle 4.10139 / 2.90 ( 2784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9077 (t-90) cc_final: 0.8743 (t-90) REVERT: A 397 GLU cc_start: 0.8985 (pm20) cc_final: 0.8632 (tm-30) REVERT: A 482 MET cc_start: 0.8291 (mmm) cc_final: 0.7641 (mmt) REVERT: A 622 LEU cc_start: 0.9184 (tp) cc_final: 0.8942 (tp) REVERT: A 704 ILE cc_start: 0.9756 (mm) cc_final: 0.9525 (tp) REVERT: B 176 HIS cc_start: 0.9153 (t-90) cc_final: 0.8922 (t-90) REVERT: B 397 GLU cc_start: 0.9142 (pm20) cc_final: 0.8677 (tm-30) REVERT: B 482 MET cc_start: 0.7726 (mmm) cc_final: 0.7278 (mmt) REVERT: B 622 LEU cc_start: 0.9210 (tp) cc_final: 0.8974 (tp) REVERT: B 761 MET cc_start: 0.8379 (mmp) cc_final: 0.8161 (mmp) REVERT: C 176 HIS cc_start: 0.9081 (t-90) cc_final: 0.8737 (t-90) REVERT: C 397 GLU cc_start: 0.9013 (pm20) cc_final: 0.8657 (tm-30) REVERT: C 482 MET cc_start: 0.8329 (mmm) cc_final: 0.7693 (mmt) REVERT: C 622 LEU cc_start: 0.9123 (tp) cc_final: 0.8832 (tp) REVERT: C 710 LEU cc_start: 0.9861 (mm) cc_final: 0.9623 (mp) REVERT: D 176 HIS cc_start: 0.9085 (t-90) cc_final: 0.8776 (t-90) REVERT: D 397 GLU cc_start: 0.8999 (pm20) cc_final: 0.8689 (tm-30) REVERT: D 482 MET cc_start: 0.8296 (mmm) cc_final: 0.7439 (mmt) REVERT: D 556 TYR cc_start: 0.9166 (t80) cc_final: 0.8907 (t80) REVERT: D 778 PHE cc_start: 0.7305 (t80) cc_final: 0.7103 (t80) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1099 time to fit residues: 43.3464 Evaluate side-chains 199 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 183 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 186 optimal weight: 0.1980 chunk 114 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.095891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072172 restraints weight = 91202.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074005 restraints weight = 57628.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075233 restraints weight = 42862.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076044 restraints weight = 35149.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076561 restraints weight = 30704.138| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20136 Z= 0.180 Angle : 0.577 6.142 27288 Z= 0.300 Chirality : 0.036 0.183 3136 Planarity : 0.004 0.035 3408 Dihedral : 4.737 25.539 2692 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 62.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.82 % Favored : 86.01 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2424 helix: 1.23 (0.14), residues: 1400 sheet: -0.75 (0.58), residues: 76 loop : -3.49 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 757 TYR 0.020 0.001 TYR C 303 PHE 0.026 0.002 PHE B 624 TRP 0.008 0.001 TRP C 586 HIS 0.006 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.18 (20136) covalent geometry : angle 0.57653 / 0.30 (27288) hydrogen bonds : bond 0.02876 / 1.89 ( 944) hydrogen bonds : angle 4.58128 / 3.26 ( 2784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9142 (t-90) cc_final: 0.8913 (t-90) REVERT: A 397 GLU cc_start: 0.9112 (pm20) cc_final: 0.8667 (tm-30) REVERT: A 482 MET cc_start: 0.8268 (mmm) cc_final: 0.7601 (mmt) REVERT: A 578 MET cc_start: 0.4509 (mtt) cc_final: 0.4205 (tpp) REVERT: A 622 LEU cc_start: 0.9209 (tp) cc_final: 0.8900 (tp) REVERT: A 761 MET cc_start: 0.8555 (mmp) cc_final: 0.8198 (mmp) REVERT: B 176 HIS cc_start: 0.9143 (t-90) cc_final: 0.8890 (t-90) REVERT: B 397 GLU cc_start: 0.9318 (pm20) cc_final: 0.8771 (tm-30) REVERT: B 482 MET cc_start: 0.7746 (mmm) cc_final: 0.7372 (mmt) REVERT: B 587 MET cc_start: 0.8953 (mtm) cc_final: 0.8727 (mtp) REVERT: B 622 LEU cc_start: 0.9188 (tp) cc_final: 0.8879 (tp) REVERT: C 176 HIS cc_start: 0.9249 (t-90) cc_final: 0.9009 (t-90) REVERT: C 397 GLU cc_start: 0.9056 (pm20) cc_final: 0.8680 (tm-30) REVERT: C 482 MET cc_start: 0.8341 (mmm) cc_final: 0.7709 (mmt) REVERT: C 622 LEU cc_start: 0.9119 (tp) cc_final: 0.8780 (tp) REVERT: D 176 HIS cc_start: 0.9131 (t-90) cc_final: 0.8902 (t-90) REVERT: D 397 GLU cc_start: 0.9106 (pm20) cc_final: 0.8707 (tm-30) REVERT: D 482 MET cc_start: 0.8245 (mmm) cc_final: 0.7625 (mmt) REVERT: D 625 MET cc_start: 0.8883 (ptp) cc_final: 0.8450 (ptp) REVERT: D 778 PHE cc_start: 0.7366 (t80) cc_final: 0.7142 (t80) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1050 time to fit residues: 37.8735 Evaluate side-chains 185 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 11 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 175 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.085318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063579 restraints weight = 96688.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065706 restraints weight = 54894.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067109 restraints weight = 37415.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068018 restraints weight = 28591.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068648 restraints weight = 23719.212| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20136 Z= 0.083 Angle : 0.467 5.495 27288 Z= 0.247 Chirality : 0.035 0.132 3136 Planarity : 0.003 0.031 3408 Dihedral : 4.428 25.598 2692 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 56.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.92 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.44 (0.18), residues: 2424 helix: 1.64 (0.14), residues: 1376 sheet: -0.69 (0.58), residues: 76 loop : -3.35 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 510 TYR 0.011 0.001 TYR A 628 PHE 0.027 0.001 PHE C 707 TRP 0.012 0.001 TRP C 586 HIS 0.004 0.001 HIS C 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (20136) covalent geometry : angle 0.46729 / 0.25 (27288) hydrogen bonds : bond 0.02489 / 1.64 ( 944) hydrogen bonds : angle 4.21718 / 2.98 ( 2784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Residue SER 659 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 HIS cc_start: 0.9062 (t-90) cc_final: 0.8743 (t-90) REVERT: A 397 GLU cc_start: 0.9031 (pm20) cc_final: 0.8643 (tm-30) REVERT: A 482 MET cc_start: 0.8311 (mmm) cc_final: 0.7647 (mmt) REVERT: A 578 MET cc_start: 0.4568 (mtt) cc_final: 0.4244 (tpp) REVERT: A 622 LEU cc_start: 0.9198 (tp) cc_final: 0.8920 (tp) REVERT: A 778 PHE cc_start: 0.7371 (t80) cc_final: 0.7169 (t80) REVERT: B 176 HIS cc_start: 0.9172 (t-90) cc_final: 0.8918 (t-90) REVERT: B 397 GLU cc_start: 0.9160 (pm20) cc_final: 0.8719 (tm-30) REVERT: B 482 MET cc_start: 0.7702 (mmm) cc_final: 0.7366 (mmt) REVERT: B 587 MET cc_start: 0.8912 (mtm) cc_final: 0.8635 (mtp) REVERT: B 622 LEU cc_start: 0.9179 (tp) cc_final: 0.8939 (tp) REVERT: B 761 MET cc_start: 0.8413 (mmp) cc_final: 0.8182 (mmp) REVERT: B 778 PHE cc_start: 0.7659 (t80) cc_final: 0.7414 (t80) REVERT: C 176 HIS cc_start: 0.9094 (t-90) cc_final: 0.8746 (t-90) REVERT: C 397 GLU cc_start: 0.9053 (pm20) cc_final: 0.8697 (tm-30) REVERT: C 482 MET cc_start: 0.8441 (mmm) cc_final: 0.7670 (mmt) REVERT: C 622 LEU cc_start: 0.9157 (tp) cc_final: 0.8812 (tp) REVERT: C 778 PHE cc_start: 0.7344 (t80) cc_final: 0.7133 (t80) REVERT: D 176 HIS cc_start: 0.9088 (t-90) cc_final: 0.8775 (t-90) REVERT: D 397 GLU cc_start: 0.9033 (pm20) cc_final: 0.8697 (tm-30) REVERT: D 482 MET cc_start: 0.8324 (mmm) cc_final: 0.7396 (mmt) REVERT: D 556 TYR cc_start: 0.9172 (t80) cc_final: 0.8866 (t80) REVERT: D 587 MET cc_start: 0.9007 (mtm) cc_final: 0.8786 (mtp) REVERT: D 625 MET cc_start: 0.9027 (ptp) cc_final: 0.8583 (ptp) REVERT: D 778 PHE cc_start: 0.7375 (t80) cc_final: 0.7107 (t80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1113 time to fit residues: 42.1805 Evaluate side-chains 197 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 165 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 238 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 173 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.085730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063913 restraints weight = 96283.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066067 restraints weight = 54575.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067487 restraints weight = 37092.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068420 restraints weight = 28301.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069039 restraints weight = 23472.852| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20136 Z= 0.082 Angle : 0.463 5.334 27288 Z= 0.245 Chirality : 0.034 0.147 3136 Planarity : 0.003 0.032 3408 Dihedral : 4.346 24.789 2692 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 56.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.80 % Favored : 88.04 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -0.19 (0.18), residues: 2424 helix: 1.73 (0.14), residues: 1396 sheet: -0.39 (0.60), residues: 76 loop : -3.17 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.011 0.001 TYR A 628 PHE 0.034 0.001 PHE C 707 TRP 0.012 0.001 TRP C 586 HIS 0.003 0.001 HIS D 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (20136) covalent geometry : angle 0.46310 / 0.24 (27288) hydrogen bonds : bond 0.02396 / 1.59 ( 944) hydrogen bonds : angle 4.11516 / 2.91 ( 2784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.86 seconds wall clock time: 56 minutes 59.03 seconds (3419.03 seconds total)