Starting phenix.real_space_refine on Wed Mar 4 13:44:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wyv_66378/03_2026/9wyv_66378.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wyv_66378/03_2026/9wyv_66378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wyv_66378/03_2026/9wyv_66378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wyv_66378/03_2026/9wyv_66378.map" model { file = "/net/cci-nas-00/data/ceres_data/9wyv_66378/03_2026/9wyv_66378.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wyv_66378/03_2026/9wyv_66378.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8718 2.51 5 N 2334 2.21 5 O 2544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13656 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 1 Chain: "B" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 1 Chain: "C" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 1 Chain: "D" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 1 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 1 Chain: "F" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2276 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 8, 'TRANS': 273} Chain breaks: 1 Time building chain proxies: 3.36, per 1000 atoms: 0.25 Number of scatterers: 13656 At special positions: 0 Unit cell: (128.02, 119.14, 91.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2544 8.00 N 2334 7.00 C 8718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 701.7 milliseconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 1 sheets defined 80.9% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.823A pdb=" N TYR A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 430 " --> pdb=" O PRO A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 430' Processing helix chain 'A' and resid 437 through 451 removed outlier: 4.077A pdb=" N VAL A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 479 removed outlier: 3.882A pdb=" N ASP A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 460 " --> pdb=" O LYS A 456 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 496 through 515 removed outlier: 3.722A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 519 through 546 removed outlier: 4.076A pdb=" N LEU A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 removed outlier: 3.557A pdb=" N PHE A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 removed outlier: 4.283A pdb=" N PHE A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 607 removed outlier: 3.642A pdb=" N LEU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 657 through 669 Processing helix chain 'A' and resid 672 through 700 removed outlier: 3.618A pdb=" N ARG A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 682 " --> pdb=" O ARG A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.686A pdb=" N TYR B 429 " --> pdb=" O PRO B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 451 removed outlier: 4.201A pdb=" N VAL B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TRP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 450 " --> pdb=" O MET B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 479 removed outlier: 3.808A pdb=" N ASP B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 493 Processing helix chain 'B' and resid 495 through 516 removed outlier: 3.709A pdb=" N THR B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 516 " --> pdb=" O GLU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 546 removed outlier: 4.045A pdb=" N LEU B 523 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 563 removed outlier: 3.557A pdb=" N PHE B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 removed outlier: 4.183A pdb=" N PHE B 567 " --> pdb=" O THR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 627 through 637 removed outlier: 3.519A pdb=" N ILE B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 657 through 669 removed outlier: 3.552A pdb=" N LEU B 667 " --> pdb=" O VAL B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 700 removed outlier: 3.594A pdb=" N ARG B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 682 " --> pdb=" O ARG B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 714 removed outlier: 3.536A pdb=" N ARG B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.715A pdb=" N TYR C 429 " --> pdb=" O PRO C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 451 removed outlier: 4.338A pdb=" N VAL C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE C 450 " --> pdb=" O MET C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 479 removed outlier: 3.898A pdb=" N ASP C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 460 " --> pdb=" O LYS C 456 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP C 479 " --> pdb=" O ASP C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 495 through 515 removed outlier: 3.508A pdb=" N ILE C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN C 501 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 513 " --> pdb=" O ARG C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 519 through 546 removed outlier: 4.041A pdb=" N LEU C 523 " --> pdb=" O ASP C 519 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 524 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C 539 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 563 Processing helix chain 'C' and resid 563 through 575 removed outlier: 4.153A pdb=" N PHE C 567 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 572 " --> pdb=" O ARG C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 607 removed outlier: 3.602A pdb=" N LEU C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 607 " --> pdb=" O TYR C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 637 Processing helix chain 'C' and resid 640 through 654 Processing helix chain 'C' and resid 657 through 669 Processing helix chain 'C' and resid 672 through 700 removed outlier: 3.586A pdb=" N ARG C 678 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 682 " --> pdb=" O ARG C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 714 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.689A pdb=" N TYR D 429 " --> pdb=" O PRO D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 451 removed outlier: 4.300A pdb=" N VAL D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 479 removed outlier: 3.889A pdb=" N ASP D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 459 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 460 " --> pdb=" O LYS D 456 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 479 " --> pdb=" O ASP D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 495 through 515 removed outlier: 3.501A pdb=" N ILE D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 501 " --> pdb=" O SER D 497 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG D 513 " --> pdb=" O ARG D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 519 through 546 removed outlier: 4.042A pdb=" N LEU D 523 " --> pdb=" O ASP D 519 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 524 " --> pdb=" O SER D 520 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET D 539 " --> pdb=" O ILE D 535 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 563 Processing helix chain 'D' and resid 563 through 575 removed outlier: 4.083A pdb=" N PHE D 567 " --> pdb=" O THR D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 605 Processing helix chain 'D' and resid 627 through 637 removed outlier: 3.505A pdb=" N HIS D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 654 Processing helix chain 'D' and resid 657 through 669 Processing helix chain 'D' and resid 672 through 700 removed outlier: 3.558A pdb=" N ARG D 678 " --> pdb=" O LEU D 674 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 682 " --> pdb=" O ARG D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 714 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.691A pdb=" N TYR E 429 " --> pdb=" O PRO E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 451 removed outlier: 4.112A pdb=" N VAL E 448 " --> pdb=" O ASP E 444 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP E 449 " --> pdb=" O ALA E 445 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 450 " --> pdb=" O MET E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 479 removed outlier: 3.797A pdb=" N ASP E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU E 459 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 460 " --> pdb=" O LYS E 456 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 471 " --> pdb=" O LEU E 467 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP E 479 " --> pdb=" O ASP E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 493 Processing helix chain 'E' and resid 495 through 516 removed outlier: 3.710A pdb=" N THR E 499 " --> pdb=" O GLY E 495 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE E 500 " --> pdb=" O LEU E 496 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN E 501 " --> pdb=" O SER E 497 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 507 " --> pdb=" O ALA E 503 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL E 508 " --> pdb=" O ASN E 504 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 513 " --> pdb=" O ARG E 509 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 546 removed outlier: 4.045A pdb=" N LEU E 523 " --> pdb=" O ASP E 519 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 524 " --> pdb=" O SER E 520 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET E 539 " --> pdb=" O ILE E 535 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 541 " --> pdb=" O GLN E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 563 Processing helix chain 'E' and resid 563 through 575 removed outlier: 4.155A pdb=" N PHE E 567 " --> pdb=" O THR E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 605 Processing helix chain 'E' and resid 627 through 637 removed outlier: 3.536A pdb=" N ILE E 631 " --> pdb=" O SER E 627 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS E 632 " --> pdb=" O LEU E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 654 Processing helix chain 'E' and resid 657 through 669 removed outlier: 3.599A pdb=" N LEU E 667 " --> pdb=" O VAL E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 700 removed outlier: 3.529A pdb=" N THR E 677 " --> pdb=" O SER E 673 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 678 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 682 " --> pdb=" O ARG E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 714 removed outlier: 3.533A pdb=" N ARG E 714 " --> pdb=" O LEU E 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 430 removed outlier: 3.843A pdb=" N TYR F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE F 430 " --> pdb=" O PRO F 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 425 through 430' Processing helix chain 'F' and resid 437 through 451 removed outlier: 4.125A pdb=" N VAL F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TRP F 449 " --> pdb=" O ALA F 445 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE F 450 " --> pdb=" O MET F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 479 removed outlier: 3.877A pdb=" N ASP F 458 " --> pdb=" O ALA F 454 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE F 460 " --> pdb=" O LYS F 456 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP F 479 " --> pdb=" O ASP F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 493 Processing helix chain 'F' and resid 496 through 515 removed outlier: 3.720A pdb=" N ILE F 500 " --> pdb=" O LEU F 496 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN F 501 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU F 507 " --> pdb=" O ALA F 503 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG F 513 " --> pdb=" O ARG F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 518 No H-bonds generated for 'chain 'F' and resid 516 through 518' Processing helix chain 'F' and resid 519 through 546 removed outlier: 4.027A pdb=" N LEU F 523 " --> pdb=" O ASP F 519 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU F 524 " --> pdb=" O SER F 520 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET F 539 " --> pdb=" O ILE F 535 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 541 " --> pdb=" O GLN F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 563 removed outlier: 3.548A pdb=" N PHE F 556 " --> pdb=" O MET F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 575 removed outlier: 4.314A pdb=" N PHE F 567 " --> pdb=" O THR F 563 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG F 572 " --> pdb=" O ARG F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 607 removed outlier: 3.688A pdb=" N LEU F 606 " --> pdb=" O ASP F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 637 Processing helix chain 'F' and resid 640 through 654 Processing helix chain 'F' and resid 657 through 669 Processing helix chain 'F' and resid 672 through 700 removed outlier: 3.626A pdb=" N ARG F 678 " --> pdb=" O LEU F 674 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU F 681 " --> pdb=" O THR F 677 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 682 " --> pdb=" O ARG F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 714 Processing sheet with id=AA1, first strand: chain 'B' and resid 483 through 484 874 hydrogen bonds defined for protein. 2574 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: 1.73 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4393 1.34 - 1.46: 1590 1.46 - 1.57: 7805 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 13896 Sorted by residual: bond pdb=" CA ARG F 531 " pdb=" C ARG F 531 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.24e-02 6.50e+03 2.87e+00 bond pdb=" C LEU F 533 " pdb=" O LEU F 533 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.18e-02 7.18e+03 1.91e+00 bond pdb=" C ASN F 532 " pdb=" O ASN F 532 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.15e-02 7.56e+03 1.88e+00 bond pdb=" C ARG F 531 " pdb=" O ARG F 531 " ideal model delta sigma weight residual 1.236 1.221 0.015 1.15e-02 7.56e+03 1.78e+00 bond pdb=" CA LEU F 533 " pdb=" C LEU F 533 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.35e-02 5.49e+03 1.74e+00 ... (remaining 13891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18574 1.71 - 3.41: 161 3.41 - 5.12: 31 5.12 - 6.83: 3 6.83 - 8.53: 5 Bond angle restraints: 18774 Sorted by residual: angle pdb=" N LEU F 533 " pdb=" CA LEU F 533 " pdb=" C LEU F 533 " ideal model delta sigma weight residual 111.33 107.69 3.64 1.21e+00 6.83e-01 9.04e+00 angle pdb=" N ASP B 476 " pdb=" CA ASP B 476 " pdb=" C ASP B 476 " ideal model delta sigma weight residual 112.34 108.51 3.83 1.30e+00 5.92e-01 8.68e+00 angle pdb=" N ARG F 531 " pdb=" CA ARG F 531 " pdb=" C ARG F 531 " ideal model delta sigma weight residual 110.97 108.26 2.71 1.09e+00 8.42e-01 6.19e+00 angle pdb=" CA LEU B 533 " pdb=" CB LEU B 533 " pdb=" CG LEU B 533 " ideal model delta sigma weight residual 116.30 124.83 -8.53 3.50e+00 8.16e-02 5.95e+00 angle pdb=" CA LEU A 533 " pdb=" CB LEU A 533 " pdb=" CG LEU A 533 " ideal model delta sigma weight residual 116.30 124.79 -8.49 3.50e+00 8.16e-02 5.89e+00 ... (remaining 18769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 7156 17.40 - 34.81: 868 34.81 - 52.21: 299 52.21 - 69.61: 88 69.61 - 87.02: 25 Dihedral angle restraints: 8436 sinusoidal: 3486 harmonic: 4950 Sorted by residual: dihedral pdb=" CB GLU F 455 " pdb=" CG GLU F 455 " pdb=" CD GLU F 455 " pdb=" OE1 GLU F 455 " ideal model delta sinusoidal sigma weight residual 0.00 -87.02 87.02 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU A 455 " pdb=" CG GLU A 455 " pdb=" CD GLU A 455 " pdb=" OE1 GLU A 455 " ideal model delta sinusoidal sigma weight residual 0.00 -86.90 86.90 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU B 455 " pdb=" CG GLU B 455 " pdb=" CD GLU B 455 " pdb=" OE1 GLU B 455 " ideal model delta sinusoidal sigma weight residual 0.00 -86.87 86.87 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 8433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1420 0.027 - 0.054: 522 0.054 - 0.082: 193 0.082 - 0.109: 45 0.109 - 0.136: 16 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CA ILE B 548 " pdb=" N ILE B 548 " pdb=" C ILE B 548 " pdb=" CB ILE B 548 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE C 548 " pdb=" N ILE C 548 " pdb=" C ILE C 548 " pdb=" CB ILE C 548 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 548 " pdb=" N ILE A 548 " pdb=" C ILE A 548 " pdb=" CB ILE A 548 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 2193 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 482 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C GLU F 482 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU F 482 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU F 483 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 482 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C GLU C 482 " -0.024 2.00e-02 2.50e+03 pdb=" O GLU C 482 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU C 483 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 482 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C GLU A 482 " 0.024 2.00e-02 2.50e+03 pdb=" O GLU A 482 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 483 " -0.008 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 7424 3.01 - 3.48: 14393 3.48 - 3.96: 20395 3.96 - 4.43: 24350 4.43 - 4.90: 38903 Nonbonded interactions: 105465 Sorted by model distance: nonbonded pdb=" N ASP E 479 " pdb=" OD1 ASP E 479 " model vdw 2.539 3.120 nonbonded pdb=" N ASP B 479 " pdb=" OD1 ASP B 479 " model vdw 2.544 3.120 nonbonded pdb=" O ASN F 532 " pdb=" C LEU F 533 " model vdw 2.553 3.270 nonbonded pdb=" ND1 HIS F 557 " pdb=" OE2 GLU F 560 " model vdw 2.584 3.120 nonbonded pdb=" OD1 ASP B 475 " pdb=" N ASP B 476 " model vdw 2.591 3.120 ... (remaining 105460 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.220 Find NCS groups from input model: 0.240 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 : 0.002 0.030 13896 Z= 0.106 Angle : 0.447 8.534 18774 Z= 0.235 Chirality : 0.034 0.136 2196 Planarity : 0.003 0.027 2352 Dihedral : 18.032 87.016 5220 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.58 % Allowed : 21.27 % Favored : 78.15 % 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: 1.57 (0.21), residues: 1668 helix: 1.78 (0.15), residues: 1242 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.010 0.001 TYR D 596 PHE 0.013 0.001 PHE F 570 TRP 0.003 0.001 TRP D 650 HIS 0.002 0.000 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00215 (13896) covalent geometry : angle 0.44666 (18774) hydrogen bonds : bond 0.20850 ( 874) hydrogen bonds : angle 5.33405 ( 2574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 281 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 ARG cc_start: 0.7798 (mtm180) cc_final: 0.7416 (mtt90) REVERT: B 540 ASP cc_start: 0.9202 (t0) cc_final: 0.8915 (t0) REVERT: B 696 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 437 ARG cc_start: 0.7577 (mtm180) cc_final: 0.7298 (mtt90) REVERT: C 540 ASP cc_start: 0.9215 (t0) cc_final: 0.8986 (t0) REVERT: D 601 ASP cc_start: 0.9004 (m-30) cc_final: 0.8503 (t0) REVERT: E 540 ASP cc_start: 0.9188 (t0) cc_final: 0.8931 (t0) REVERT: E 601 ASP cc_start: 0.9053 (m-30) cc_final: 0.8775 (t70) REVERT: F 437 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7430 (mtt90) outliers start: 9 outliers final: 2 residues processed: 286 average time/residue: 0.1398 time to fit residues: 54.7094 Evaluate side-chains 216 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain D residue 701 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0050 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 645 ASN F 504 ASN ** F 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107686 restraints weight = 20942.873| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.40 r_work: 0.3209 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13896 Z= 0.115 Angle : 0.453 6.654 18774 Z= 0.241 Chirality : 0.036 0.157 2196 Planarity : 0.003 0.027 2352 Dihedral : 2.975 18.379 1838 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.75 % Allowed : 20.82 % Favored : 77.43 % 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: 2.15 (0.22), residues: 1668 helix: 2.17 (0.15), residues: 1278 sheet: None (None), residues: 0 loop : -1.15 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 437 TYR 0.012 0.001 TYR C 603 PHE 0.033 0.001 PHE E 570 TRP 0.008 0.001 TRP B 543 HIS 0.002 0.000 HIS E 491 Details of bonding type rmsd covalent geometry : bond 0.00245 (13896) covalent geometry : angle 0.45260 (18774) hydrogen bonds : bond 0.04698 ( 874) hydrogen bonds : angle 3.50897 ( 2574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.402 Fit side-chains REVERT: A 440 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7556 (mp0) REVERT: A 540 ASP cc_start: 0.9013 (t0) cc_final: 0.8655 (t0) REVERT: B 440 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7529 (mp0) REVERT: B 696 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7566 (tm-30) REVERT: D 440 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7606 (mp0) REVERT: E 440 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7463 (mp0) REVERT: F 440 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7524 (mp0) REVERT: F 540 ASP cc_start: 0.9006 (t0) cc_final: 0.8636 (t0) outliers start: 27 outliers final: 9 residues processed: 212 average time/residue: 0.1168 time to fit residues: 36.5569 Evaluate side-chains 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 658 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 GLN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3582 r_free = 0.3582 target = 0.125594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104348 restraints weight = 21046.117| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.37 r_work: 0.3190 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13896 Z= 0.122 Angle : 0.431 6.715 18774 Z= 0.230 Chirality : 0.036 0.153 2196 Planarity : 0.003 0.026 2352 Dihedral : 2.899 13.015 1836 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.82 % Allowed : 20.75 % Favored : 77.43 % 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: 2.29 (0.22), residues: 1668 helix: 2.25 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -1.10 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 451 TYR 0.012 0.001 TYR A 685 PHE 0.030 0.001 PHE E 570 TRP 0.005 0.001 TRP F 543 HIS 0.003 0.000 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00285 (13896) covalent geometry : angle 0.43129 (18774) hydrogen bonds : bond 0.04340 ( 874) hydrogen bonds : angle 3.29370 ( 2574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.537 Fit side-chains REVERT: A 440 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 474 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7507 (mm) REVERT: A 540 ASP cc_start: 0.9021 (t0) cc_final: 0.8649 (t0) REVERT: B 440 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7556 (mp0) REVERT: B 696 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 539 MET cc_start: 0.8771 (mmt) cc_final: 0.8499 (mmt) REVERT: D 440 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7636 (mp0) REVERT: D 539 MET cc_start: 0.8791 (mmt) cc_final: 0.8548 (mmt) REVERT: E 440 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7467 (mp0) REVERT: F 440 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7510 (mp0) REVERT: F 474 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7512 (mm) REVERT: F 540 ASP cc_start: 0.9035 (t0) cc_final: 0.8715 (t0) outliers start: 28 outliers final: 17 residues processed: 202 average time/residue: 0.1235 time to fit residues: 36.4929 Evaluate side-chains 185 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 431 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 431 THR Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 593 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 115 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 120 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106620 restraints weight = 20990.353| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.41 r_work: 0.3193 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13896 Z= 0.100 Angle : 0.403 4.791 18774 Z= 0.215 Chirality : 0.035 0.146 2196 Planarity : 0.003 0.026 2352 Dihedral : 2.872 12.621 1836 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.49 % Allowed : 21.53 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.22), residues: 1668 helix: 2.39 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.010 0.001 TYR C 685 PHE 0.029 0.001 PHE E 570 TRP 0.004 0.001 TRP E 543 HIS 0.002 0.000 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00223 (13896) covalent geometry : angle 0.40271 (18774) hydrogen bonds : bond 0.03593 ( 874) hydrogen bonds : angle 3.13520 ( 2574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.556 Fit side-chains REVERT: A 440 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7512 (mp0) REVERT: A 540 ASP cc_start: 0.9002 (t0) cc_final: 0.8584 (t0) REVERT: B 440 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7529 (mp0) REVERT: B 696 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 474 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7083 (mm) REVERT: C 539 MET cc_start: 0.8668 (mmt) cc_final: 0.8348 (mmt) REVERT: D 440 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7613 (mp0) REVERT: D 539 MET cc_start: 0.8698 (mmt) cc_final: 0.8396 (mmt) REVERT: E 440 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7471 (mp0) REVERT: F 440 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7488 (mp0) REVERT: F 540 ASP cc_start: 0.9019 (t0) cc_final: 0.8642 (t0) outliers start: 23 outliers final: 17 residues processed: 189 average time/residue: 0.1252 time to fit residues: 34.2491 Evaluate side-chains 185 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 658 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.125102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103962 restraints weight = 21083.523| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.35 r_work: 0.3169 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13896 Z= 0.120 Angle : 0.415 4.873 18774 Z= 0.222 Chirality : 0.036 0.149 2196 Planarity : 0.003 0.027 2352 Dihedral : 2.909 13.630 1836 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.62 % Allowed : 21.85 % Favored : 76.52 % 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: 2.53 (0.22), residues: 1668 helix: 2.43 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -1.05 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.013 0.001 TYR A 685 PHE 0.028 0.001 PHE E 570 TRP 0.005 0.001 TRP D 449 HIS 0.002 0.000 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00280 (13896) covalent geometry : angle 0.41502 (18774) hydrogen bonds : bond 0.04017 ( 874) hydrogen bonds : angle 3.17695 ( 2574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.535 Fit side-chains REVERT: A 440 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7521 (mp0) REVERT: A 540 ASP cc_start: 0.9052 (t0) cc_final: 0.8641 (t0) REVERT: B 440 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7524 (mp0) REVERT: B 696 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7677 (tm-30) REVERT: C 474 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7220 (mm) REVERT: C 539 MET cc_start: 0.8684 (mmt) cc_final: 0.8401 (mmt) REVERT: D 440 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7606 (mp0) REVERT: D 539 MET cc_start: 0.8705 (mmt) cc_final: 0.8406 (mmt) REVERT: E 440 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7447 (mp0) REVERT: F 440 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7479 (mp0) REVERT: F 482 GLU cc_start: 0.8609 (pm20) cc_final: 0.8386 (pm20) REVERT: F 540 ASP cc_start: 0.9016 (t0) cc_final: 0.8621 (t0) outliers start: 25 outliers final: 15 residues processed: 183 average time/residue: 0.1289 time to fit residues: 34.0248 Evaluate side-chains 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 560 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 31 optimal weight: 0.0570 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3600 r_free = 0.3600 target = 0.127228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106250 restraints weight = 21061.768| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.35 r_work: 0.3208 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13896 Z= 0.096 Angle : 0.395 5.507 18774 Z= 0.211 Chirality : 0.035 0.138 2196 Planarity : 0.003 0.027 2352 Dihedral : 2.860 12.743 1836 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.04 % Allowed : 22.70 % Favored : 76.26 % 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: 2.72 (0.22), residues: 1668 helix: 2.56 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -0.98 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 451 TYR 0.011 0.001 TYR D 685 PHE 0.027 0.001 PHE E 570 TRP 0.004 0.001 TRP C 449 HIS 0.001 0.000 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00214 (13896) covalent geometry : angle 0.39488 (18774) hydrogen bonds : bond 0.03390 ( 874) hydrogen bonds : angle 3.05403 ( 2574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.596 Fit side-chains REVERT: A 440 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7525 (mp0) REVERT: A 540 ASP cc_start: 0.8980 (t0) cc_final: 0.8581 (t0) REVERT: B 440 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7573 (mp0) REVERT: B 696 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7675 (tm-30) REVERT: C 474 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7076 (mm) REVERT: C 539 MET cc_start: 0.8665 (mmt) cc_final: 0.8373 (mmt) REVERT: D 440 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7607 (mp0) REVERT: D 539 MET cc_start: 0.8715 (mmt) cc_final: 0.8452 (mmt) REVERT: E 440 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7488 (mp0) REVERT: F 440 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7470 (mp0) REVERT: F 482 GLU cc_start: 0.8596 (pm20) cc_final: 0.8382 (pm20) REVERT: F 540 ASP cc_start: 0.9002 (t0) cc_final: 0.8565 (t0) outliers start: 16 outliers final: 12 residues processed: 176 average time/residue: 0.1274 time to fit residues: 32.2490 Evaluate side-chains 172 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 ASN ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.126670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105196 restraints weight = 21086.893| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.38 r_work: 0.3176 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13896 Z= 0.113 Angle : 0.411 5.191 18774 Z= 0.218 Chirality : 0.036 0.144 2196 Planarity : 0.003 0.027 2352 Dihedral : 2.887 13.596 1836 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.23 % Allowed : 22.96 % Favored : 75.81 % 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: 2.71 (0.22), residues: 1668 helix: 2.57 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -1.03 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.012 0.001 TYR D 685 PHE 0.026 0.001 PHE D 570 TRP 0.004 0.001 TRP D 449 HIS 0.002 0.000 HIS F 491 Details of bonding type rmsd covalent geometry : bond 0.00264 (13896) covalent geometry : angle 0.41088 (18774) hydrogen bonds : bond 0.03745 ( 874) hydrogen bonds : angle 3.09903 ( 2574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.546 Fit side-chains REVERT: A 440 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7525 (mp0) REVERT: A 540 ASP cc_start: 0.9032 (t0) cc_final: 0.8639 (t0) REVERT: B 440 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7567 (mp0) REVERT: B 696 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7703 (tm-30) REVERT: C 474 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7205 (mm) REVERT: C 539 MET cc_start: 0.8683 (mmt) cc_final: 0.8393 (mmt) REVERT: D 440 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7647 (mp0) REVERT: D 539 MET cc_start: 0.8704 (mmt) cc_final: 0.8434 (mmt) REVERT: E 440 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7473 (mp0) REVERT: E 474 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7142 (mm) REVERT: F 440 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7488 (mp0) REVERT: F 482 GLU cc_start: 0.8645 (pm20) cc_final: 0.8439 (pm20) REVERT: F 540 ASP cc_start: 0.9035 (t0) cc_final: 0.8637 (t0) outliers start: 19 outliers final: 14 residues processed: 170 average time/residue: 0.1296 time to fit residues: 31.5748 Evaluate side-chains 173 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 127 optimal weight: 0.4980 chunk 110 optimal weight: 0.0050 chunk 76 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3604 r_free = 0.3604 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.106525 restraints weight = 20908.522| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.34 r_work: 0.3209 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13896 Z= 0.098 Angle : 0.404 6.430 18774 Z= 0.213 Chirality : 0.035 0.136 2196 Planarity : 0.003 0.027 2352 Dihedral : 2.850 12.783 1836 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.30 % Allowed : 22.76 % Favored : 75.94 % 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: 2.84 (0.22), residues: 1668 helix: 2.66 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -0.96 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.011 0.001 TYR D 685 PHE 0.025 0.001 PHE D 570 TRP 0.004 0.001 TRP C 449 HIS 0.001 0.000 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00220 (13896) covalent geometry : angle 0.40364 (18774) hydrogen bonds : bond 0.03296 ( 874) hydrogen bonds : angle 3.01400 ( 2574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.572 Fit side-chains REVERT: A 440 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7507 (mp0) REVERT: A 540 ASP cc_start: 0.8988 (t0) cc_final: 0.8582 (t0) REVERT: B 440 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7513 (mp0) REVERT: B 604 LYS cc_start: 0.9022 (tppt) cc_final: 0.8783 (mmtp) REVERT: B 696 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7701 (tm-30) REVERT: C 474 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7068 (mm) REVERT: C 539 MET cc_start: 0.8691 (mmt) cc_final: 0.8326 (mmt) REVERT: D 440 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7627 (mp0) REVERT: D 474 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7055 (mm) REVERT: D 539 MET cc_start: 0.8702 (mmt) cc_final: 0.8351 (mmt) REVERT: E 440 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7458 (mp0) REVERT: F 440 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7463 (mp0) REVERT: F 540 ASP cc_start: 0.8988 (t0) cc_final: 0.8575 (t0) outliers start: 20 outliers final: 14 residues processed: 172 average time/residue: 0.1307 time to fit residues: 32.1858 Evaluate side-chains 176 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3592 r_free = 0.3592 target = 0.126604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105560 restraints weight = 21086.459| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.35 r_work: 0.3195 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13896 Z= 0.105 Angle : 0.416 8.591 18774 Z= 0.218 Chirality : 0.035 0.140 2196 Planarity : 0.003 0.027 2352 Dihedral : 2.859 13.223 1836 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.43 % Allowed : 22.76 % Favored : 75.81 % 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: 2.84 (0.22), residues: 1668 helix: 2.66 (0.15), residues: 1284 sheet: None (None), residues: 0 loop : -0.97 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.013 0.001 TYR D 685 PHE 0.026 0.001 PHE D 570 TRP 0.004 0.001 TRP C 449 HIS 0.002 0.000 HIS F 491 Details of bonding type rmsd covalent geometry : bond 0.00242 (13896) covalent geometry : angle 0.41602 (18774) hydrogen bonds : bond 0.03478 ( 874) hydrogen bonds : angle 3.02904 ( 2574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.541 Fit side-chains REVERT: A 440 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7512 (mp0) REVERT: A 540 ASP cc_start: 0.9010 (t0) cc_final: 0.8606 (t0) REVERT: B 440 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7539 (mp0) REVERT: B 696 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 474 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7138 (mm) REVERT: C 539 MET cc_start: 0.8654 (mmt) cc_final: 0.8356 (mmt) REVERT: D 440 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7629 (mp0) REVERT: D 474 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7107 (mm) REVERT: D 539 MET cc_start: 0.8694 (mmt) cc_final: 0.8351 (mmt) REVERT: D 701 THR cc_start: 0.8197 (m) cc_final: 0.7873 (p) REVERT: E 440 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7459 (mp0) REVERT: F 440 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7476 (mp0) REVERT: F 540 ASP cc_start: 0.9012 (t0) cc_final: 0.8526 (t0) outliers start: 22 outliers final: 16 residues processed: 165 average time/residue: 0.1230 time to fit residues: 29.3162 Evaluate side-chains 172 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 668 MET Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 560 GLU Chi-restraints excluded: chain F residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 52 optimal weight: 0.7980 chunk 167 optimal weight: 0.4980 chunk 122 optimal weight: 0.0010 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 158 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3611 r_free = 0.3611 target = 0.128214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107237 restraints weight = 21131.431| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.36 r_work: 0.3214 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13896 Z= 0.093 Angle : 0.410 8.415 18774 Z= 0.214 Chirality : 0.035 0.136 2196 Planarity : 0.003 0.026 2352 Dihedral : 2.822 12.477 1836 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.30 % Allowed : 22.96 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.22), residues: 1668 helix: 2.64 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -0.86 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.012 0.001 TYR D 685 PHE 0.025 0.001 PHE D 570 TRP 0.005 0.001 TRP D 449 HIS 0.001 0.000 HIS D 491 Details of bonding type rmsd covalent geometry : bond 0.00205 (13896) covalent geometry : angle 0.41047 (18774) hydrogen bonds : bond 0.03089 ( 874) hydrogen bonds : angle 2.95598 ( 2574) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.537 Fit side-chains REVERT: A 440 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7495 (mp0) REVERT: A 540 ASP cc_start: 0.8947 (t0) cc_final: 0.8543 (t0) REVERT: B 440 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7524 (mp0) REVERT: B 696 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 474 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.7014 (mm) REVERT: C 539 MET cc_start: 0.8684 (mmt) cc_final: 0.8340 (mmt) REVERT: D 440 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7619 (mp0) REVERT: D 474 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.7009 (mm) REVERT: D 701 THR cc_start: 0.8174 (m) cc_final: 0.7846 (p) REVERT: E 440 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7492 (mp0) REVERT: E 604 LYS cc_start: 0.8981 (tppt) cc_final: 0.8780 (mmtp) REVERT: F 440 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7475 (mp0) REVERT: F 540 ASP cc_start: 0.8964 (t0) cc_final: 0.8467 (t0) outliers start: 20 outliers final: 13 residues processed: 179 average time/residue: 0.1185 time to fit residues: 30.9488 Evaluate side-chains 174 residues out of total 1542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 601 ASP Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 chunk 161 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 160 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 GLN ** 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 = 0.3608 r_free = 0.3608 target = 0.127965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106985 restraints weight = 21294.793| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.37 r_work: 0.3218 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13896 Z= 0.098 Angle : 0.436 8.855 18774 Z= 0.223 Chirality : 0.035 0.183 2196 Planarity : 0.003 0.026 2352 Dihedral : 2.819 12.564 1836 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.04 % Allowed : 23.48 % Favored : 75.49 % 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: 2.98 (0.22), residues: 1668 helix: 2.65 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 437 TYR 0.011 0.001 TYR D 685 PHE 0.025 0.001 PHE D 570 TRP 0.004 0.001 TRP D 449 HIS 0.002 0.000 HIS F 491 Details of bonding type rmsd covalent geometry : bond 0.00222 (13896) covalent geometry : angle 0.43629 (18774) hydrogen bonds : bond 0.03143 ( 874) hydrogen bonds : angle 2.96490 ( 2574) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2669.83 seconds wall clock time: 46 minutes 44.96 seconds (2804.96 seconds total)