Starting phenix.real_space_refine on Fri Sep 19 09:09:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7amy_11827/09_2025/7amy_11827.cif Found real_map, /net/cci-nas-00/data/ceres_data/7amy_11827/09_2025/7amy_11827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7amy_11827/09_2025/7amy_11827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7amy_11827/09_2025/7amy_11827.map" model { file = "/net/cci-nas-00/data/ceres_data/7amy_11827/09_2025/7amy_11827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7amy_11827/09_2025/7amy_11827.cif" } resolution = 3.75 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= 0.002 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 72 5.16 5 C 15750 2.51 5 N 4320 2.21 5 O 4707 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24849 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2761 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 21, 'TRANS': 331} Restraints were copied for chains: B, C, D, E, F, G, H, I Time building chain proxies: 3.06, per 1000 atoms: 0.12 Number of scatterers: 24849 At special positions: 0 Unit cell: (187.416, 185.772, 76.446, 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 72 16.00 O 4707 8.00 N 4320 7.00 C 15750 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: 1.99 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6012 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 36 sheets defined 49.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 368 Processing helix chain 'A' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER A 380 " --> pdb=" O ALA A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 479 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 503 through 514 removed outlier: 3.541A pdb=" N ALA A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA A 520 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP A 542 " --> pdb=" O GLN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 4.148A pdb=" N THR A 555 " --> pdb=" O THR A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 Processing helix chain 'A' and resid 598 through 613 removed outlier: 3.677A pdb=" N SER A 608 " --> pdb=" O MET A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 644 Proline residue: A 638 - end of helix removed outlier: 3.695A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG A 665 " --> pdb=" O PRO A 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER B 380 " --> pdb=" O ALA B 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA B 507 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 509 " --> pdb=" O VAL B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA B 520 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 521 " --> pdb=" O PRO B 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 removed outlier: 3.735A pdb=" N LYS B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP B 542 " --> pdb=" O GLN B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 4.150A pdb=" N THR B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 Processing helix chain 'B' and resid 598 through 613 removed outlier: 3.677A pdb=" N SER B 608 " --> pdb=" O MET B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 644 Proline residue: B 638 - end of helix removed outlier: 3.695A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG B 665 " --> pdb=" O PRO B 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 368 Processing helix chain 'C' and resid 377 through 380 removed outlier: 3.763A pdb=" N SER C 380 " --> pdb=" O ALA C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 380' Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 479 through 495 Processing helix chain 'C' and resid 496 through 500 Processing helix chain 'C' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA C 507 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C 509 " --> pdb=" O VAL C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 524 removed outlier: 3.897A pdb=" N ALA C 520 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU C 521 " --> pdb=" O PRO C 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 535 " --> pdb=" O GLN C 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP C 542 " --> pdb=" O GLN C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR C 555 " --> pdb=" O THR C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 577 removed outlier: 3.566A pdb=" N ASP C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 Processing helix chain 'C' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER C 608 " --> pdb=" O MET C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 644 Proline residue: C 638 - end of helix removed outlier: 3.695A pdb=" N LEU C 644 " --> pdb=" O ILE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 647 No H-bonds generated for 'chain 'C' and resid 645 through 647' Processing helix chain 'C' and resid 659 through 670 removed outlier: 3.994A pdb=" N ARG C 665 " --> pdb=" O PRO C 661 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 365 through 368 Processing helix chain 'D' and resid 377 through 380 removed outlier: 3.763A pdb=" N SER D 380 " --> pdb=" O ALA D 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 381 through 390 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 466 through 474 Processing helix chain 'D' and resid 479 through 495 Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.543A pdb=" N ALA D 507 " --> pdb=" O ASP D 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 509 " --> pdb=" O VAL D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA D 520 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU D 521 " --> pdb=" O PRO D 517 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 535 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP D 542 " --> pdb=" O GLN D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 560 removed outlier: 4.148A pdb=" N THR D 555 " --> pdb=" O THR D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 577 removed outlier: 3.566A pdb=" N ASP D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER D 608 " --> pdb=" O MET D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 644 Proline residue: D 638 - end of helix removed outlier: 3.696A pdb=" N LEU D 644 " --> pdb=" O ILE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 647 No H-bonds generated for 'chain 'D' and resid 645 through 647' Processing helix chain 'D' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG D 665 " --> pdb=" O PRO D 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR D 666 " --> pdb=" O LEU D 662 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 368 Processing helix chain 'E' and resid 377 through 380 removed outlier: 3.763A pdb=" N SER E 380 " --> pdb=" O ALA E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 466 through 474 Processing helix chain 'E' and resid 479 through 495 Processing helix chain 'E' and resid 496 through 500 Processing helix chain 'E' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA E 507 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 509 " --> pdb=" O VAL E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA E 520 " --> pdb=" O ALA E 516 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU E 521 " --> pdb=" O PRO E 517 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 522 " --> pdb=" O LYS E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 535 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP E 542 " --> pdb=" O GLN E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 586 Processing helix chain 'E' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER E 608 " --> pdb=" O MET E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 629 through 644 Proline residue: E 638 - end of helix removed outlier: 3.695A pdb=" N LEU E 644 " --> pdb=" O ILE E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 647 No H-bonds generated for 'chain 'E' and resid 645 through 647' Processing helix chain 'E' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG E 665 " --> pdb=" O PRO E 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR E 666 " --> pdb=" O LEU E 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 365 through 368 Processing helix chain 'F' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER F 380 " --> pdb=" O ALA F 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 466 through 474 Processing helix chain 'F' and resid 479 through 495 Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 503 through 514 removed outlier: 3.543A pdb=" N ALA F 507 " --> pdb=" O ASP F 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 509 " --> pdb=" O VAL F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 524 removed outlier: 3.898A pdb=" N ALA F 520 " --> pdb=" O ALA F 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU F 521 " --> pdb=" O PRO F 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 522 " --> pdb=" O LYS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 542 removed outlier: 3.735A pdb=" N LYS F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 535 " --> pdb=" O GLN F 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP F 542 " --> pdb=" O GLN F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR F 555 " --> pdb=" O THR F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 586 Processing helix chain 'F' and resid 598 through 613 removed outlier: 3.677A pdb=" N SER F 608 " --> pdb=" O MET F 604 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 644 Proline residue: F 638 - end of helix removed outlier: 3.696A pdb=" N LEU F 644 " --> pdb=" O ILE F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 647 No H-bonds generated for 'chain 'F' and resid 645 through 647' Processing helix chain 'F' and resid 659 through 670 removed outlier: 3.993A pdb=" N ARG F 665 " --> pdb=" O PRO F 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR F 666 " --> pdb=" O LEU F 662 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 353 Processing helix chain 'G' and resid 365 through 368 Processing helix chain 'G' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER G 380 " --> pdb=" O ALA G 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 377 through 380' Processing helix chain 'G' and resid 381 through 390 Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 466 through 474 Processing helix chain 'G' and resid 479 through 495 Processing helix chain 'G' and resid 496 through 500 Processing helix chain 'G' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA G 507 " --> pdb=" O ASP G 503 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 524 removed outlier: 3.899A pdb=" N ALA G 520 " --> pdb=" O ALA G 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU G 521 " --> pdb=" O PRO G 517 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G 522 " --> pdb=" O LYS G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS G 534 " --> pdb=" O ALA G 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL G 535 " --> pdb=" O GLN G 531 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP G 542 " --> pdb=" O GLN G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 549 through 560 removed outlier: 4.147A pdb=" N THR G 555 " --> pdb=" O THR G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 567 through 577 removed outlier: 3.566A pdb=" N ASP G 572 " --> pdb=" O LEU G 568 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 586 Processing helix chain 'G' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER G 608 " --> pdb=" O MET G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 629 through 644 Proline residue: G 638 - end of helix removed outlier: 3.696A pdb=" N LEU G 644 " --> pdb=" O ILE G 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 645 through 647 No H-bonds generated for 'chain 'G' and resid 645 through 647' Processing helix chain 'G' and resid 659 through 670 removed outlier: 3.994A pdb=" N ARG G 665 " --> pdb=" O PRO G 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR G 666 " --> pdb=" O LEU G 662 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 353 Processing helix chain 'H' and resid 365 through 368 Processing helix chain 'H' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER H 380 " --> pdb=" O ALA H 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 377 through 380' Processing helix chain 'H' and resid 381 through 390 Processing helix chain 'H' and resid 390 through 395 Processing helix chain 'H' and resid 466 through 474 Processing helix chain 'H' and resid 479 through 495 Processing helix chain 'H' and resid 496 through 500 Processing helix chain 'H' and resid 503 through 514 removed outlier: 3.542A pdb=" N ALA H 507 " --> pdb=" O ASP H 503 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 509 " --> pdb=" O VAL H 505 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 524 removed outlier: 3.897A pdb=" N ALA H 520 " --> pdb=" O ALA H 516 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU H 521 " --> pdb=" O PRO H 517 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS H 534 " --> pdb=" O ALA H 530 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL H 535 " --> pdb=" O GLN H 531 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP H 542 " --> pdb=" O GLN H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 549 through 560 removed outlier: 4.148A pdb=" N THR H 555 " --> pdb=" O THR H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP H 572 " --> pdb=" O LEU H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 577 through 586 Processing helix chain 'H' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER H 608 " --> pdb=" O MET H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 629 through 644 Proline residue: H 638 - end of helix removed outlier: 3.696A pdb=" N LEU H 644 " --> pdb=" O ILE H 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 647 No H-bonds generated for 'chain 'H' and resid 645 through 647' Processing helix chain 'H' and resid 659 through 670 removed outlier: 3.995A pdb=" N ARG H 665 " --> pdb=" O PRO H 661 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR H 666 " --> pdb=" O LEU H 662 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 353 Processing helix chain 'I' and resid 365 through 368 Processing helix chain 'I' and resid 377 through 380 removed outlier: 3.764A pdb=" N SER I 380 " --> pdb=" O ALA I 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 377 through 380' Processing helix chain 'I' and resid 381 through 390 Processing helix chain 'I' and resid 390 through 395 Processing helix chain 'I' and resid 466 through 474 Processing helix chain 'I' and resid 479 through 495 Processing helix chain 'I' and resid 496 through 500 Processing helix chain 'I' and resid 503 through 514 removed outlier: 3.541A pdb=" N ALA I 507 " --> pdb=" O ASP I 503 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 509 " --> pdb=" O VAL I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 516 through 524 removed outlier: 3.897A pdb=" N ALA I 520 " --> pdb=" O ALA I 516 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU I 521 " --> pdb=" O PRO I 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA I 522 " --> pdb=" O LYS I 518 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 542 removed outlier: 3.736A pdb=" N LYS I 534 " --> pdb=" O ALA I 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL I 535 " --> pdb=" O GLN I 531 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 549 through 560 removed outlier: 4.149A pdb=" N THR I 555 " --> pdb=" O THR I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 567 through 577 removed outlier: 3.565A pdb=" N ASP I 572 " --> pdb=" O LEU I 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 577 through 586 Processing helix chain 'I' and resid 598 through 613 removed outlier: 3.678A pdb=" N SER I 608 " --> pdb=" O MET I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 629 through 644 Proline residue: I 638 - end of helix removed outlier: 3.695A pdb=" N LEU I 644 " --> pdb=" O ILE I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 647 No H-bonds generated for 'chain 'I' and resid 645 through 647' Processing helix chain 'I' and resid 659 through 670 removed outlier: 3.994A pdb=" N ARG I 665 " --> pdb=" O PRO I 661 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR I 666 " --> pdb=" O LEU I 662 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 402 through 404 removed outlier: 6.660A pdb=" N LEU A 359 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG A 404 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU A 361 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 414 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A 425 " --> pdb=" O TYR A 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 416 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA A 459 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 434 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 592 through 594 Processing sheet with id=AA4, first strand: chain 'A' and resid 653 through 654 removed outlier: 5.814A pdb=" N LEU A 653 " --> pdb=" O LEU A 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 402 through 404 removed outlier: 6.661A pdb=" N LEU B 359 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ARG B 404 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU B 361 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR B 414 " --> pdb=" O GLN B 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN B 425 " --> pdb=" O TYR B 414 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 416 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 448 through 451 removed outlier: 3.811A pdb=" N ALA B 459 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 434 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 592 through 594 Processing sheet with id=AA8, first strand: chain 'B' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU B 653 " --> pdb=" O LEU B 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU C 359 " --> pdb=" O ARG C 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG C 404 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU C 361 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR C 414 " --> pdb=" O GLN C 425 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN C 425 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 416 " --> pdb=" O ILE C 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA C 459 " --> pdb=" O GLY C 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 434 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 592 through 594 Processing sheet with id=AB3, first strand: chain 'C' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU C 653 " --> pdb=" O LEU C 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 402 through 404 removed outlier: 6.660A pdb=" N LEU D 359 " --> pdb=" O ARG D 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG D 404 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU D 361 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR D 414 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN D 425 " --> pdb=" O TYR D 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 416 " --> pdb=" O ILE D 423 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 448 through 451 removed outlier: 3.811A pdb=" N ALA D 459 " --> pdb=" O GLY D 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 434 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 592 through 594 Processing sheet with id=AB7, first strand: chain 'D' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU D 653 " --> pdb=" O LEU D 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU E 359 " --> pdb=" O ARG E 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG E 404 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU E 361 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR E 414 " --> pdb=" O GLN E 425 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN E 425 " --> pdb=" O TYR E 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 416 " --> pdb=" O ILE E 423 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA E 459 " --> pdb=" O GLY E 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET E 434 " --> pdb=" O VAL E 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 592 through 594 Processing sheet with id=AC2, first strand: chain 'E' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU E 653 " --> pdb=" O LEU E 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU F 359 " --> pdb=" O ARG F 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG F 404 " --> pdb=" O LEU F 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU F 361 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR F 414 " --> pdb=" O GLN F 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN F 425 " --> pdb=" O TYR F 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 416 " --> pdb=" O ILE F 423 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA F 459 " --> pdb=" O GLY F 450 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET F 434 " --> pdb=" O VAL F 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 592 through 594 Processing sheet with id=AC6, first strand: chain 'F' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU F 653 " --> pdb=" O LEU F 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 402 through 404 removed outlier: 6.659A pdb=" N LEU G 359 " --> pdb=" O ARG G 402 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG G 404 " --> pdb=" O LEU G 359 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU G 361 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR G 414 " --> pdb=" O GLN G 425 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN G 425 " --> pdb=" O TYR G 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE G 416 " --> pdb=" O ILE G 423 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA G 459 " --> pdb=" O GLY G 450 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET G 434 " --> pdb=" O VAL G 478 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 592 through 594 Processing sheet with id=AD1, first strand: chain 'G' and resid 653 through 654 removed outlier: 5.813A pdb=" N LEU G 653 " --> pdb=" O LEU G 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'H' and resid 402 through 404 removed outlier: 6.660A pdb=" N LEU H 359 " --> pdb=" O ARG H 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG H 404 " --> pdb=" O LEU H 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU H 361 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR H 414 " --> pdb=" O GLN H 425 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN H 425 " --> pdb=" O TYR H 414 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE H 416 " --> pdb=" O ILE H 423 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 448 through 451 removed outlier: 3.811A pdb=" N ALA H 459 " --> pdb=" O GLY H 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET H 434 " --> pdb=" O VAL H 478 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 592 through 594 Processing sheet with id=AD5, first strand: chain 'H' and resid 653 through 654 removed outlier: 5.814A pdb=" N LEU H 653 " --> pdb=" O LEU H 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 402 through 404 removed outlier: 6.661A pdb=" N LEU I 359 " --> pdb=" O ARG I 402 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG I 404 " --> pdb=" O LEU I 359 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU I 361 " --> pdb=" O ARG I 404 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR I 414 " --> pdb=" O GLN I 425 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLN I 425 " --> pdb=" O TYR I 414 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE I 416 " --> pdb=" O ILE I 423 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 448 through 451 removed outlier: 3.810A pdb=" N ALA I 459 " --> pdb=" O GLY I 450 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET I 434 " --> pdb=" O VAL I 478 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 592 through 594 Processing sheet with id=AD9, first strand: chain 'I' and resid 653 through 654 removed outlier: 5.814A pdb=" N LEU I 653 " --> pdb=" O LEU I 677 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 972 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 2.61 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: 8485 1.34 - 1.45: 3269 1.45 - 1.57: 13365 1.57 - 1.69: 0 1.69 - 1.80: 135 Bond restraints: 25254 Sorted by residual: bond pdb=" CA ASN D 389 " pdb=" C ASN D 389 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.72e-02 3.38e+03 1.45e+01 bond pdb=" CA ASN E 389 " pdb=" C ASN E 389 " ideal model delta sigma weight residual 1.522 1.456 0.065 1.72e-02 3.38e+03 1.45e+01 bond pdb=" CA ASN H 389 " pdb=" C ASN H 389 " ideal model delta sigma weight residual 1.522 1.456 0.065 1.72e-02 3.38e+03 1.44e+01 bond pdb=" CA ASN B 389 " pdb=" C ASN B 389 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.72e-02 3.38e+03 1.43e+01 bond pdb=" CA ASN G 389 " pdb=" C ASN G 389 " ideal model delta sigma weight residual 1.522 1.457 0.065 1.72e-02 3.38e+03 1.43e+01 ... (remaining 25249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 32087 1.60 - 3.19: 1876 3.19 - 4.79: 297 4.79 - 6.38: 93 6.38 - 7.98: 18 Bond angle restraints: 34371 Sorted by residual: angle pdb=" N ASP F 345 " pdb=" CA ASP F 345 " pdb=" C ASP F 345 " ideal model delta sigma weight residual 112.97 106.14 6.83 1.06e+00 8.90e-01 4.15e+01 angle pdb=" N ASP G 345 " pdb=" CA ASP G 345 " pdb=" C ASP G 345 " ideal model delta sigma weight residual 112.97 106.14 6.83 1.06e+00 8.90e-01 4.15e+01 angle pdb=" N ASP I 345 " pdb=" CA ASP I 345 " pdb=" C ASP I 345 " ideal model delta sigma weight residual 112.97 106.17 6.80 1.06e+00 8.90e-01 4.12e+01 angle pdb=" N ASP B 345 " pdb=" CA ASP B 345 " pdb=" C ASP B 345 " ideal model delta sigma weight residual 112.97 106.17 6.80 1.06e+00 8.90e-01 4.12e+01 angle pdb=" N ASP E 345 " pdb=" CA ASP E 345 " pdb=" C ASP E 345 " ideal model delta sigma weight residual 112.97 106.19 6.78 1.06e+00 8.90e-01 4.10e+01 ... (remaining 34366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 13276 14.75 - 29.49: 1673 29.49 - 44.24: 558 44.24 - 58.99: 99 58.99 - 73.73: 45 Dihedral angle restraints: 15651 sinusoidal: 6390 harmonic: 9261 Sorted by residual: dihedral pdb=" CA GLY G 420 " pdb=" C GLY G 420 " pdb=" N GLU G 421 " pdb=" CA GLU G 421 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA GLY H 420 " pdb=" C GLY H 420 " pdb=" N GLU H 421 " pdb=" CA GLU H 421 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA GLY I 420 " pdb=" C GLY I 420 " pdb=" N GLU I 421 " pdb=" CA GLU I 421 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 15648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2082 0.035 - 0.070: 1315 0.070 - 0.106: 527 0.106 - 0.141: 126 0.141 - 0.176: 36 Chirality restraints: 4086 Sorted by residual: chirality pdb=" CA ASN E 389 " pdb=" N ASN E 389 " pdb=" C ASN E 389 " pdb=" CB ASN E 389 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CA ASN G 389 " pdb=" N ASN G 389 " pdb=" C ASN G 389 " pdb=" CB ASN G 389 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN B 389 " pdb=" N ASN B 389 " pdb=" C ASN B 389 " pdb=" CB ASN B 389 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 4083 not shown) Planarity restraints: 4509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 391 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER E 391 " -0.036 2.00e-02 2.50e+03 pdb=" O SER E 391 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU E 392 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 391 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C SER H 391 " 0.035 2.00e-02 2.50e+03 pdb=" O SER H 391 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU H 392 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 391 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C SER D 391 " -0.035 2.00e-02 2.50e+03 pdb=" O SER D 391 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D 392 " 0.012 2.00e-02 2.50e+03 ... (remaining 4506 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2627 2.72 - 3.27: 27081 3.27 - 3.81: 39793 3.81 - 4.36: 49396 4.36 - 4.90: 79948 Nonbonded interactions: 198845 Sorted by model distance: nonbonded pdb=" O HIS H 502 " pdb=" ND1 HIS H 502 " model vdw 2.177 3.120 nonbonded pdb=" O HIS I 502 " pdb=" ND1 HIS I 502 " model vdw 2.177 3.120 nonbonded pdb=" O HIS E 502 " pdb=" ND1 HIS E 502 " model vdw 2.178 3.120 nonbonded pdb=" O HIS A 502 " pdb=" ND1 HIS A 502 " model vdw 2.178 3.120 nonbonded pdb=" O HIS C 502 " pdb=" ND1 HIS C 502 " model vdw 2.178 3.120 ... (remaining 198840 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.540 Find NCS groups from input model: 0.220 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.010 0.066 25254 Z= 0.430 Angle : 0.890 7.978 34371 Z= 0.472 Chirality : 0.051 0.176 4086 Planarity : 0.005 0.040 4509 Dihedral : 14.934 73.735 9639 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.77 % Favored : 85.94 % Rotamer: Outliers : 0.66 % Allowed : 12.17 % Favored : 87.18 % 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 aren not related in a simple way. whole: -5.40 (0.11), residues: 3159 helix: -3.63 (0.09), residues: 1467 sheet: -2.85 (0.17), residues: 558 loop : -3.55 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 574 TYR 0.015 0.002 TYR G 595 PHE 0.006 0.001 PHE E 633 TRP 0.009 0.002 TRP A 350 HIS 0.004 0.001 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00956 (25254) covalent geometry : angle 0.88967 (34371) hydrogen bonds : bond 0.22981 ( 972) hydrogen bonds : angle 8.02221 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 MET cc_start: 0.6684 (mtp) cc_final: 0.6358 (tpt) REVERT: A 567 ILE cc_start: 0.9387 (mp) cc_final: 0.9127 (mt) REVERT: B 473 MET cc_start: 0.6864 (mtp) cc_final: 0.6591 (tpt) REVERT: C 473 MET cc_start: 0.6878 (mtp) cc_final: 0.6437 (tpt) REVERT: D 473 MET cc_start: 0.6843 (mtp) cc_final: 0.6393 (tpt) REVERT: D 567 ILE cc_start: 0.9382 (mp) cc_final: 0.9149 (mt) REVERT: E 473 MET cc_start: 0.6936 (mtp) cc_final: 0.6515 (tpt) REVERT: F 473 MET cc_start: 0.6741 (mtp) cc_final: 0.6254 (tpt) REVERT: G 473 MET cc_start: 0.6745 (mtp) cc_final: 0.6437 (tpt) REVERT: G 567 ILE cc_start: 0.9431 (mp) cc_final: 0.9197 (mt) REVERT: H 473 MET cc_start: 0.6789 (mtp) cc_final: 0.6481 (tpt) REVERT: I 473 MET cc_start: 0.6824 (mtp) cc_final: 0.6407 (tpt) REVERT: I 567 ILE cc_start: 0.9411 (mp) cc_final: 0.9178 (mt) outliers start: 18 outliers final: 7 residues processed: 315 average time/residue: 0.1590 time to fit residues: 79.1785 Evaluate side-chains 214 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 207 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain I residue 488 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 GLN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 543 GLN ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078995 restraints weight = 55327.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081279 restraints weight = 31957.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082682 restraints weight = 22992.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083349 restraints weight = 19122.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.083884 restraints weight = 17446.484| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25254 Z= 0.148 Angle : 0.733 8.617 34371 Z= 0.364 Chirality : 0.047 0.225 4086 Planarity : 0.005 0.039 4509 Dihedral : 5.681 30.120 3416 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.10 % Favored : 91.61 % Rotamer: Outliers : 2.62 % Allowed : 14.97 % Favored : 82.40 % 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 aren not related in a simple way. whole: -3.40 (0.14), residues: 3159 helix: -2.09 (0.12), residues: 1548 sheet: -2.08 (0.21), residues: 558 loop : -2.21 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 432 TYR 0.006 0.001 TYR D 414 PHE 0.006 0.001 PHE B 396 TRP 0.005 0.001 TRP C 461 HIS 0.002 0.001 HIS F 464 Details of bonding type rmsd covalent geometry : bond 0.00332 (25254) covalent geometry : angle 0.73282 (34371) hydrogen bonds : bond 0.04724 ( 972) hydrogen bonds : angle 5.09518 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 275 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7958 (ttp80) REVERT: B 519 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9075 (tt) REVERT: B 543 GLN cc_start: 0.8280 (tt0) cc_final: 0.8055 (mt0) REVERT: B 665 ARG cc_start: 0.8242 (ttp80) cc_final: 0.8014 (ttp80) REVERT: D 367 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7197 (pp) REVERT: D 665 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8030 (ttp80) REVERT: E 455 TYR cc_start: 0.7483 (m-10) cc_final: 0.7239 (m-10) REVERT: E 665 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7947 (ttp80) REVERT: F 455 TYR cc_start: 0.7337 (m-10) cc_final: 0.7105 (m-10) REVERT: F 665 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7882 (ttp80) REVERT: G 519 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9022 (tt) REVERT: G 665 ARG cc_start: 0.8361 (ttp80) cc_final: 0.7754 (ttp80) REVERT: H 519 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9042 (tt) REVERT: H 665 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8116 (ttp-110) REVERT: I 665 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7640 (ttp80) outliers start: 72 outliers final: 24 residues processed: 333 average time/residue: 0.1637 time to fit residues: 86.5821 Evaluate side-chains 236 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 519 LEU Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 519 LEU Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 491 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 271 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 543 GLN ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 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 = 0.3569 r_free = 0.3569 target = 0.108542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.079127 restraints weight = 55230.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.081378 restraints weight = 32005.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082786 restraints weight = 23093.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.083589 restraints weight = 19198.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083949 restraints weight = 17390.140| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25254 Z= 0.148 Angle : 0.669 6.937 34371 Z= 0.331 Chirality : 0.045 0.145 4086 Planarity : 0.004 0.041 4509 Dihedral : 5.465 29.488 3416 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.77 % Favored : 92.94 % Rotamer: Outliers : 2.81 % Allowed : 17.49 % Favored : 79.71 % 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 aren not related in a simple way. whole: -2.84 (0.15), residues: 3159 helix: -1.60 (0.12), residues: 1548 sheet: -1.91 (0.22), residues: 558 loop : -1.94 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 660 TYR 0.014 0.001 TYR D 455 PHE 0.003 0.001 PHE C 500 TRP 0.006 0.001 TRP I 461 HIS 0.002 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00345 (25254) covalent geometry : angle 0.66928 (34371) hydrogen bonds : bond 0.04114 ( 972) hydrogen bonds : angle 4.86140 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 665 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7996 (ttp80) REVERT: B 519 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9013 (tt) REVERT: D 367 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7181 (pp) REVERT: E 434 MET cc_start: 0.8087 (tmm) cc_final: 0.7877 (tmm) REVERT: G 533 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9098 (tt) REVERT: G 665 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8081 (ttp80) REVERT: H 665 ARG cc_start: 0.8252 (ttp80) cc_final: 0.8002 (ttp80) REVERT: I 665 ARG cc_start: 0.8215 (ttp80) cc_final: 0.8012 (ttp80) outliers start: 77 outliers final: 45 residues processed: 299 average time/residue: 0.1648 time to fit residues: 77.5710 Evaluate side-chains 243 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 209 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 242 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 280 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 286 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 ASN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 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 = 0.3583 r_free = 0.3583 target = 0.109367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080099 restraints weight = 55119.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082353 restraints weight = 31910.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083772 restraints weight = 23039.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084597 restraints weight = 19117.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085049 restraints weight = 17262.765| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25254 Z= 0.135 Angle : 0.633 5.837 34371 Z= 0.313 Chirality : 0.044 0.165 4086 Planarity : 0.004 0.046 4509 Dihedral : 5.270 26.820 3414 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.09 % Favored : 92.62 % Rotamer: Outliers : 3.10 % Allowed : 19.64 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.15), residues: 3159 helix: -1.00 (0.13), residues: 1458 sheet: -1.75 (0.22), residues: 558 loop : -1.94 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 382 TYR 0.017 0.001 TYR B 414 PHE 0.004 0.001 PHE A 396 TRP 0.006 0.001 TRP I 461 HIS 0.003 0.001 HIS E 502 Details of bonding type rmsd covalent geometry : bond 0.00315 (25254) covalent geometry : angle 0.63344 (34371) hydrogen bonds : bond 0.03668 ( 972) hydrogen bonds : angle 4.63244 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 245 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 498 GLU cc_start: 0.8479 (mp0) cc_final: 0.8213 (mt-10) REVERT: B 514 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8319 (mp10) REVERT: B 519 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8940 (tt) REVERT: D 367 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7205 (pp) REVERT: E 434 MET cc_start: 0.8122 (tmm) cc_final: 0.7922 (tmm) REVERT: G 533 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9088 (tt) REVERT: G 619 VAL cc_start: 0.2656 (OUTLIER) cc_final: 0.2329 (t) REVERT: G 665 ARG cc_start: 0.8286 (ttp80) cc_final: 0.8022 (ttp80) REVERT: H 665 ARG cc_start: 0.8227 (ttp80) cc_final: 0.8009 (ttp80) REVERT: I 665 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7971 (ttp80) outliers start: 85 outliers final: 48 residues processed: 308 average time/residue: 0.1590 time to fit residues: 79.0239 Evaluate side-chains 268 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 575 CYS Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 CYS Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 148 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 295 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 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 = 0.3513 r_free = 0.3513 target = 0.104904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.074893 restraints weight = 56527.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.077089 restraints weight = 33375.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.078457 restraints weight = 24136.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.079268 restraints weight = 20021.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079733 restraints weight = 18055.440| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 25254 Z= 0.369 Angle : 0.800 7.302 34371 Z= 0.388 Chirality : 0.050 0.164 4086 Planarity : 0.005 0.036 4509 Dihedral : 5.600 31.819 3404 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.50 % Favored : 92.21 % Rotamer: Outliers : 4.59 % Allowed : 20.77 % Favored : 74.64 % 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 aren not related in a simple way. whole: -2.54 (0.15), residues: 3159 helix: -1.25 (0.13), residues: 1494 sheet: -1.66 (0.22), residues: 558 loop : -2.05 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 382 TYR 0.019 0.002 TYR I 455 PHE 0.016 0.002 PHE D 670 TRP 0.010 0.002 TRP B 350 HIS 0.007 0.002 HIS G 502 Details of bonding type rmsd covalent geometry : bond 0.00864 (25254) covalent geometry : angle 0.80038 (34371) hydrogen bonds : bond 0.04402 ( 972) hydrogen bonds : angle 5.11845 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 206 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 367 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7304 (pp) REVERT: E 630 LEU cc_start: 0.8206 (mm) cc_final: 0.7958 (tp) REVERT: F 619 VAL cc_start: 0.3212 (OUTLIER) cc_final: 0.2930 (t) REVERT: G 619 VAL cc_start: 0.3180 (OUTLIER) cc_final: 0.2837 (t) REVERT: G 630 LEU cc_start: 0.8043 (mm) cc_final: 0.7820 (tp) REVERT: G 665 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8067 (ttp80) REVERT: H 475 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.6537 (m-10) REVERT: H 619 VAL cc_start: 0.3186 (OUTLIER) cc_final: 0.2891 (t) REVERT: H 665 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7634 (ttp80) REVERT: I 619 VAL cc_start: 0.3009 (OUTLIER) cc_final: 0.2723 (t) REVERT: I 665 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7918 (ttp80) outliers start: 126 outliers final: 81 residues processed: 302 average time/residue: 0.1447 time to fit residues: 72.9780 Evaluate side-chains 275 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 188 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 475 TYR Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 491 ILE Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 619 VAL Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 365 TYR Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 491 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 619 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 3 optimal weight: 8.9990 chunk 224 optimal weight: 0.8980 chunk 149 optimal weight: 20.0000 chunk 287 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 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 = 0.3586 r_free = 0.3586 target = 0.109492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080012 restraints weight = 55120.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082389 restraints weight = 31283.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.083849 restraints weight = 22317.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.084700 restraints weight = 18419.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.085016 restraints weight = 16611.337| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25254 Z= 0.122 Angle : 0.640 11.301 34371 Z= 0.314 Chirality : 0.044 0.261 4086 Planarity : 0.004 0.042 4509 Dihedral : 5.211 28.292 3404 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.43 % Favored : 93.29 % Rotamer: Outliers : 3.39 % Allowed : 21.53 % Favored : 75.08 % 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 aren not related in a simple way. whole: -2.11 (0.15), residues: 3159 helix: -0.83 (0.13), residues: 1485 sheet: -1.65 (0.22), residues: 558 loop : -1.81 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 382 TYR 0.018 0.001 TYR B 414 PHE 0.020 0.001 PHE C 670 TRP 0.005 0.001 TRP I 461 HIS 0.002 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00279 (25254) covalent geometry : angle 0.64002 (34371) hydrogen bonds : bond 0.03500 ( 972) hydrogen bonds : angle 4.66250 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 235 time to evaluate : 0.998 Fit side-chains REVERT: A 498 GLU cc_start: 0.8394 (mp0) cc_final: 0.7985 (mt-10) REVERT: B 498 GLU cc_start: 0.8487 (mp0) cc_final: 0.8232 (mt-10) REVERT: B 506 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7090 (tp30) REVERT: C 665 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7689 (ttp80) REVERT: C 672 GLN cc_start: 0.7566 (pm20) cc_final: 0.7054 (mp10) REVERT: D 367 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7173 (pp) REVERT: E 506 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7215 (tp30) REVERT: F 619 VAL cc_start: 0.2770 (OUTLIER) cc_final: 0.2460 (t) REVERT: G 619 VAL cc_start: 0.2499 (OUTLIER) cc_final: 0.2138 (t) REVERT: G 665 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8003 (ttp80) REVERT: H 619 VAL cc_start: 0.2921 (OUTLIER) cc_final: 0.2612 (t) REVERT: H 665 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7948 (ttp80) REVERT: I 619 VAL cc_start: 0.2685 (OUTLIER) cc_final: 0.2398 (t) REVERT: I 665 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7881 (ttp80) outliers start: 93 outliers final: 69 residues processed: 302 average time/residue: 0.1440 time to fit residues: 72.0887 Evaluate side-chains 281 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 207 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain F residue 619 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 575 CYS Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 619 VAL Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 365 TYR Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 575 CYS Chi-restraints excluded: chain I residue 595 TYR Chi-restraints excluded: chain I residue 619 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 208 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 213 optimal weight: 0.0010 chunk 7 optimal weight: 0.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.079412 restraints weight = 55368.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081753 restraints weight = 31591.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083206 restraints weight = 22597.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084027 restraints weight = 18640.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.084502 restraints weight = 16827.116| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25254 Z= 0.148 Angle : 0.642 12.471 34371 Z= 0.309 Chirality : 0.044 0.267 4086 Planarity : 0.004 0.039 4509 Dihedral : 5.076 27.220 3404 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.00 % Favored : 92.72 % Rotamer: Outliers : 3.53 % Allowed : 21.97 % Favored : 74.50 % 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 aren not related in a simple way. whole: -1.92 (0.15), residues: 3159 helix: -0.64 (0.14), residues: 1485 sheet: -1.61 (0.21), residues: 558 loop : -1.75 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 382 TYR 0.015 0.001 TYR B 414 PHE 0.015 0.001 PHE E 670 TRP 0.008 0.001 TRP C 461 HIS 0.003 0.001 HIS G 502 Details of bonding type rmsd covalent geometry : bond 0.00351 (25254) covalent geometry : angle 0.64169 (34371) hydrogen bonds : bond 0.03420 ( 972) hydrogen bonds : angle 4.64480 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 219 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 GLU cc_start: 0.8392 (mp0) cc_final: 0.7959 (mt-10) REVERT: B 498 GLU cc_start: 0.8470 (mp0) cc_final: 0.8200 (mt-10) REVERT: C 665 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7608 (ttp80) REVERT: C 672 GLN cc_start: 0.7567 (pm20) cc_final: 0.6971 (mp10) REVERT: D 367 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7182 (pp) REVERT: G 665 ARG cc_start: 0.8253 (ttp80) cc_final: 0.8020 (ttp80) REVERT: H 475 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6461 (m-10) REVERT: H 665 ARG cc_start: 0.8220 (ttp80) cc_final: 0.8008 (ttp80) REVERT: I 630 LEU cc_start: 0.7879 (mm) cc_final: 0.7671 (tp) outliers start: 97 outliers final: 76 residues processed: 287 average time/residue: 0.1426 time to fit residues: 67.8538 Evaluate side-chains 276 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 198 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 475 TYR Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 475 TYR Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 488 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 475 TYR Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 521 GLU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 433 LEU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 171 optimal weight: 0.9980 chunk 297 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 291 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 265 optimal weight: 0.0010 chunk 135 optimal weight: 0.4980 chunk 152 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 628 ASN ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084394 restraints weight = 54984.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084752 restraints weight = 31558.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.084713 restraints weight = 29032.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085394 restraints weight = 24858.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085515 restraints weight = 22357.065| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25254 Z= 0.107 Angle : 0.622 11.734 34371 Z= 0.304 Chirality : 0.043 0.193 4086 Planarity : 0.004 0.062 4509 Dihedral : 4.877 24.052 3404 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.87 % Favored : 92.85 % Rotamer: Outliers : 3.17 % Allowed : 22.30 % Favored : 74.54 % 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 aren not related in a simple way. whole: -1.70 (0.15), residues: 3159 helix: -0.38 (0.14), residues: 1485 sheet: -1.58 (0.21), residues: 558 loop : -1.69 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 665 TYR 0.017 0.001 TYR B 414 PHE 0.020 0.001 PHE I 670 TRP 0.007 0.001 TRP C 461 HIS 0.002 0.001 HIS H 357 Details of bonding type rmsd covalent geometry : bond 0.00244 (25254) covalent geometry : angle 0.62245 (34371) hydrogen bonds : bond 0.03187 ( 972) hydrogen bonds : angle 4.57408 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 218 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLU cc_start: 0.8320 (mp0) cc_final: 0.7921 (mt-10) REVERT: B 472 ASN cc_start: 0.7958 (m110) cc_final: 0.7682 (m-40) REVERT: B 498 GLU cc_start: 0.8417 (mp0) cc_final: 0.8171 (mt-10) REVERT: C 672 GLN cc_start: 0.7600 (pm20) cc_final: 0.7136 (mp10) REVERT: D 367 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7061 (pp) REVERT: D 506 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6997 (tp30) REVERT: D 630 LEU cc_start: 0.7909 (mm) cc_final: 0.7639 (tp) REVERT: H 475 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.6464 (m-10) REVERT: H 488 ILE cc_start: 0.9181 (mt) cc_final: 0.8966 (tt) REVERT: H 514 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: H 665 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7915 (ttp80) REVERT: I 512 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8745 (tt) REVERT: I 630 LEU cc_start: 0.7955 (mm) cc_final: 0.7741 (tp) outliers start: 87 outliers final: 62 residues processed: 284 average time/residue: 0.1426 time to fit residues: 68.5419 Evaluate side-chains 263 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 639 LEU Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 475 TYR Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 514 GLN Chi-restraints excluded: chain H residue 521 GLU Chi-restraints excluded: chain H residue 563 THR Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 521 GLU Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 277 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 236 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 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 = 0.3603 r_free = 0.3603 target = 0.110571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084012 restraints weight = 55388.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.083961 restraints weight = 31219.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084238 restraints weight = 26107.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084718 restraints weight = 24205.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084851 restraints weight = 22883.199| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25254 Z= 0.126 Angle : 0.638 11.655 34371 Z= 0.310 Chirality : 0.044 0.284 4086 Planarity : 0.004 0.060 4509 Dihedral : 4.760 20.310 3402 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.55 % Favored : 93.16 % Rotamer: Outliers : 2.99 % Allowed : 22.77 % Favored : 74.24 % 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 aren not related in a simple way. whole: -1.53 (0.15), residues: 3159 helix: -0.16 (0.14), residues: 1476 sheet: -1.56 (0.21), residues: 558 loop : -1.70 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 665 TYR 0.020 0.001 TYR E 414 PHE 0.015 0.001 PHE G 670 TRP 0.010 0.001 TRP C 461 HIS 0.002 0.000 HIS D 502 Details of bonding type rmsd covalent geometry : bond 0.00296 (25254) covalent geometry : angle 0.63838 (34371) hydrogen bonds : bond 0.03168 ( 972) hydrogen bonds : angle 4.57404 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 218 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLU cc_start: 0.8325 (mp0) cc_final: 0.7918 (mt-10) REVERT: B 472 ASN cc_start: 0.7930 (m110) cc_final: 0.7676 (m-40) REVERT: B 498 GLU cc_start: 0.8423 (mp0) cc_final: 0.8185 (mt-10) REVERT: C 472 ASN cc_start: 0.8041 (m110) cc_final: 0.7797 (m-40) REVERT: C 672 GLN cc_start: 0.7617 (pm20) cc_final: 0.7197 (mp10) REVERT: D 367 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7106 (pp) REVERT: D 506 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7051 (tp30) REVERT: D 630 LEU cc_start: 0.7937 (mm) cc_final: 0.7691 (tp) REVERT: E 506 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7220 (tp30) REVERT: F 472 ASN cc_start: 0.7984 (m110) cc_final: 0.7686 (m-40) REVERT: I 512 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8867 (tt) REVERT: I 630 LEU cc_start: 0.8042 (mm) cc_final: 0.7810 (tp) outliers start: 82 outliers final: 70 residues processed: 277 average time/residue: 0.1459 time to fit residues: 68.5417 Evaluate side-chains 273 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 201 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 478 VAL Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 521 GLU Chi-restraints excluded: chain H residue 563 THR Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 433 LEU Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 521 GLU Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 72 optimal weight: 8.9990 chunk 92 optimal weight: 0.0980 chunk 314 optimal weight: 9.9990 chunk 240 optimal weight: 0.0270 chunk 224 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 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 = 0.3637 r_free = 0.3637 target = 0.112506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.084312 restraints weight = 55724.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.085977 restraints weight = 34982.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086204 restraints weight = 26544.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086679 restraints weight = 24696.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.086786 restraints weight = 22844.488| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25254 Z= 0.109 Angle : 0.637 13.730 34371 Z= 0.308 Chirality : 0.044 0.216 4086 Planarity : 0.004 0.043 4509 Dihedral : 4.618 20.466 3402 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.84 % Favored : 92.88 % Rotamer: Outliers : 2.55 % Allowed : 23.57 % Favored : 73.88 % 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 aren not related in a simple way. whole: -1.42 (0.15), residues: 3159 helix: -0.09 (0.14), residues: 1485 sheet: -1.51 (0.21), residues: 558 loop : -1.62 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 665 TYR 0.020 0.001 TYR C 414 PHE 0.015 0.001 PHE H 670 TRP 0.009 0.001 TRP G 461 HIS 0.003 0.000 HIS C 487 Details of bonding type rmsd covalent geometry : bond 0.00252 (25254) covalent geometry : angle 0.63740 (34371) hydrogen bonds : bond 0.03049 ( 972) hydrogen bonds : angle 4.55882 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6318 Ramachandran restraints generated. 3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 GLU cc_start: 0.8140 (mp0) cc_final: 0.7807 (mt-10) REVERT: B 472 ASN cc_start: 0.7924 (m110) cc_final: 0.7684 (m-40) REVERT: C 472 ASN cc_start: 0.8003 (m110) cc_final: 0.7748 (m-40) REVERT: C 672 GLN cc_start: 0.7447 (pm20) cc_final: 0.7016 (mp10) REVERT: D 367 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7130 (pp) REVERT: E 472 ASN cc_start: 0.7799 (m110) cc_final: 0.7548 (m-40) REVERT: E 630 LEU cc_start: 0.8127 (mm) cc_final: 0.7919 (tp) REVERT: F 472 ASN cc_start: 0.7844 (m110) cc_final: 0.7604 (m110) REVERT: G 434 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7758 (ppp) REVERT: H 472 ASN cc_start: 0.8247 (m-40) cc_final: 0.8038 (m110) REVERT: H 488 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9024 (tt) REVERT: I 512 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8804 (tt) REVERT: I 630 LEU cc_start: 0.8001 (mm) cc_final: 0.7799 (tp) outliers start: 70 outliers final: 62 residues processed: 274 average time/residue: 0.1346 time to fit residues: 63.7093 Evaluate side-chains 263 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 595 TYR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain B residue 595 TYR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 595 TYR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 409 LEU Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 595 TYR Chi-restraints excluded: chain D residue 656 MET Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 367 LEU Chi-restraints excluded: chain E residue 409 LEU Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 563 THR Chi-restraints excluded: chain E residue 595 TYR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 488 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 563 THR Chi-restraints excluded: chain F residue 575 CYS Chi-restraints excluded: chain F residue 595 TYR Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 563 THR Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 656 MET Chi-restraints excluded: chain H residue 346 THR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 367 LEU Chi-restraints excluded: chain H residue 488 ILE Chi-restraints excluded: chain H residue 521 GLU Chi-restraints excluded: chain H residue 563 THR Chi-restraints excluded: chain H residue 581 LEU Chi-restraints excluded: chain H residue 595 TYR Chi-restraints excluded: chain H residue 656 MET Chi-restraints excluded: chain I residue 346 THR Chi-restraints excluded: chain I residue 356 VAL Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 488 ILE Chi-restraints excluded: chain I residue 512 LEU Chi-restraints excluded: chain I residue 521 GLU Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 581 LEU Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 79 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 259 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 3 optimal weight: 0.0060 chunk 199 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN ** E 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 628 ASN ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 472 ASN ** H 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 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 = 0.3638 r_free = 0.3638 target = 0.112576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.085527 restraints weight = 55673.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085669 restraints weight = 37056.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086006 restraints weight = 30736.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086266 restraints weight = 28122.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.086458 restraints weight = 26052.719| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25254 Z= 0.112 Angle : 0.636 12.171 34371 Z= 0.307 Chirality : 0.044 0.175 4086 Planarity : 0.004 0.042 4509 Dihedral : 4.535 19.921 3402 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.65 % Favored : 93.07 % Rotamer: Outliers : 2.66 % Allowed : 24.15 % Favored : 73.19 % 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 aren not related in a simple way. whole: -1.33 (0.15), residues: 3159 helix: 0.04 (0.14), residues: 1467 sheet: -1.47 (0.21), residues: 558 loop : -1.66 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 665 TYR 0.019 0.001 TYR E 414 PHE 0.015 0.001 PHE G 670 TRP 0.010 0.001 TRP G 461 HIS 0.002 0.000 HIS F 487 Details of bonding type rmsd covalent geometry : bond 0.00260 (25254) covalent geometry : angle 0.63560 (34371) hydrogen bonds : bond 0.02980 ( 972) hydrogen bonds : angle 4.55238 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3566.33 seconds wall clock time: 62 minutes 46.92 seconds (3766.92 seconds total)