Starting phenix.real_space_refine on Fri Mar 6 16:00:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nih_12359/03_2026/7nih_12359.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nih_12359/03_2026/7nih_12359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nih_12359/03_2026/7nih_12359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nih_12359/03_2026/7nih_12359.map" model { file = "/net/cci-nas-00/data/ceres_data/7nih_12359/03_2026/7nih_12359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nih_12359/03_2026/7nih_12359.cif" } resolution = 2.6 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= 0.006 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 104 5.16 5 C 20752 2.51 5 N 5456 2.21 5 O 6128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32464 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 4.51, per 1000 atoms: 0.14 Number of scatterers: 32464 At special positions: 0 Unit cell: (159.997, 159.997, 135.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 16 15.00 Mg 8 11.99 O 6128 8.00 N 5456 7.00 C 20752 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: 2.42 Conformation dependent library (CDL) restraints added in 1.7 seconds 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7712 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 32 sheets defined 46.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.768A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 240 through 260 removed outlier: 3.917A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 452 Processing helix chain 'A' and resid 457 through 464 removed outlier: 4.092A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.593A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.536A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.268A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 685 Processing helix chain 'A' and resid 701 through 708 removed outlier: 3.594A pdb=" N TYR A 705 " --> pdb=" O LYS A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.769A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 240 through 260 removed outlier: 3.916A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 452 Processing helix chain 'B' and resid 457 through 464 removed outlier: 4.092A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.593A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.536A pdb=" N ILE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 636 removed outlier: 4.268A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 685 Processing helix chain 'B' and resid 701 through 708 removed outlier: 3.595A pdb=" N TYR B 705 " --> pdb=" O LYS B 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.768A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 240 through 260 removed outlier: 3.916A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 452 Processing helix chain 'C' and resid 457 through 464 removed outlier: 4.092A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.595A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.535A pdb=" N ILE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 636 removed outlier: 4.267A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 685 Processing helix chain 'C' and resid 701 through 708 removed outlier: 3.594A pdb=" N TYR C 705 " --> pdb=" O LYS C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.769A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 240 through 260 removed outlier: 3.916A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 452 Processing helix chain 'D' and resid 457 through 464 removed outlier: 4.092A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.595A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.535A pdb=" N ILE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 595' Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.268A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 685 Processing helix chain 'D' and resid 701 through 708 removed outlier: 3.595A pdb=" N TYR D 705 " --> pdb=" O LYS D 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.769A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 240 through 260 removed outlier: 3.916A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 452 Processing helix chain 'E' and resid 457 through 464 removed outlier: 4.092A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.593A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.536A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 595' Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.268A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 672 through 685 Processing helix chain 'E' and resid 701 through 708 removed outlier: 3.595A pdb=" N TYR E 705 " --> pdb=" O LYS E 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.768A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 Processing helix chain 'F' and resid 240 through 260 removed outlier: 3.916A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 452 Processing helix chain 'F' and resid 457 through 464 removed outlier: 4.092A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.593A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'F' and resid 581 through 587 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.536A pdb=" N ILE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 591 through 595' Processing helix chain 'F' and resid 615 through 620 Processing helix chain 'F' and resid 622 through 636 removed outlier: 4.268A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 685 Processing helix chain 'F' and resid 701 through 708 removed outlier: 3.595A pdb=" N TYR F 705 " --> pdb=" O LYS F 701 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.769A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 240 through 260 removed outlier: 3.917A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 452 Processing helix chain 'G' and resid 457 through 464 removed outlier: 4.092A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.593A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 Processing helix chain 'G' and resid 591 through 595 removed outlier: 3.536A pdb=" N ILE G 595 " --> pdb=" O ALA G 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 595' Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 622 through 636 removed outlier: 4.268A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 685 Processing helix chain 'G' and resid 701 through 708 removed outlier: 3.594A pdb=" N TYR G 705 " --> pdb=" O LYS G 701 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.769A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 240 through 260 removed outlier: 3.916A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 452 Processing helix chain 'H' and resid 457 through 464 removed outlier: 4.093A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 removed outlier: 3.594A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 587 Processing helix chain 'H' and resid 591 through 595 removed outlier: 3.536A pdb=" N ILE H 595 " --> pdb=" O ALA H 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 591 through 595' Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 636 removed outlier: 4.268A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN H 635 " --> pdb=" O TRP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 685 Processing helix chain 'H' and resid 701 through 708 removed outlier: 3.595A pdb=" N TYR H 705 " --> pdb=" O LYS H 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 8.537A pdb=" N ILE A 54 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP A 418 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 141 removed outlier: 6.929A pdb=" N ILE A 135 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE A 194 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A 137 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 192 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 139 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS A 693 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 470 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 559 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP A 642 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 561 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 8.537A pdb=" N ILE B 54 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP B 418 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 60 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 141 removed outlier: 6.930A pdb=" N ILE B 135 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE B 194 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE B 137 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 192 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 139 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS B 693 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 470 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 559 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP B 642 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 561 " --> pdb=" O ASP B 642 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 223 removed outlier: 8.538A pdb=" N ILE C 54 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP C 418 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU C 60 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 141 removed outlier: 6.930A pdb=" N ILE C 135 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE C 194 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE C 137 " --> pdb=" O ASN C 192 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN C 192 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 139 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS C 693 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA C 470 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU C 559 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP C 642 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 561 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 8.536A pdb=" N ILE D 54 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP D 418 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 141 removed outlier: 6.930A pdb=" N ILE D 135 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE D 194 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE D 137 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN D 192 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D 139 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS D 693 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA D 470 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 559 " --> pdb=" O ILE D 640 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP D 642 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 561 " --> pdb=" O ASP D 642 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 8.538A pdb=" N ILE E 54 " --> pdb=" O ASP E 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP E 418 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU E 60 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 141 removed outlier: 6.930A pdb=" N ILE E 135 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE E 194 " --> pdb=" O ILE E 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE E 137 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 192 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG E 139 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS E 693 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 470 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 559 " --> pdb=" O ILE E 640 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP E 642 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 561 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 8.537A pdb=" N ILE F 54 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP F 418 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F 60 " --> pdb=" O ILE F 412 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 141 removed outlier: 6.929A pdb=" N ILE F 135 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE F 194 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE F 137 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN F 192 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 139 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS F 693 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA F 470 " --> pdb=" O CYS F 693 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 559 " --> pdb=" O ILE F 640 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP F 642 " --> pdb=" O LEU F 559 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE F 561 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 223 removed outlier: 8.537A pdb=" N ILE G 54 " --> pdb=" O ASP G 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP G 418 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 141 removed outlier: 6.930A pdb=" N ILE G 135 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE G 194 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE G 137 " --> pdb=" O ASN G 192 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN G 192 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG G 139 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS G 693 " --> pdb=" O VAL G 468 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA G 470 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU G 559 " --> pdb=" O ILE G 640 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP G 642 " --> pdb=" O LEU G 559 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE G 561 " --> pdb=" O ASP G 642 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 223 removed outlier: 8.537A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 134 through 141 removed outlier: 6.930A pdb=" N ILE H 135 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE H 194 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE H 137 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN H 192 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG H 139 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 6.227A pdb=" N CYS H 693 " --> pdb=" O VAL H 468 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA H 470 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) 1664 hydrogen bonds defined for protein. 4872 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: 6.89 Time building geometry restraints manager: 3.22 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: 10514 1.34 - 1.45: 4378 1.45 - 1.57: 17876 1.57 - 1.69: 24 1.69 - 1.81: 192 Bond restraints: 32984 Sorted by residual: bond pdb=" C6 ADP A1000 " pdb=" N6 ADP A1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C6 ADP D1000 " pdb=" N6 ADP D1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C6 ADP C1000 " pdb=" N6 ADP C1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 ADP B1000 " pdb=" N6 ADP B1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 ADP H1000 " pdb=" N6 ADP H1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 32979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 44143 2.33 - 4.66: 449 4.66 - 6.99: 80 6.99 - 9.32: 32 9.32 - 11.65: 32 Bond angle restraints: 44736 Sorted by residual: angle pdb=" PA ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " ideal model delta sigma weight residual 120.50 132.15 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" PA ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " ideal model delta sigma weight residual 120.50 132.13 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" PA ADP G1000 " pdb=" O3A ADP G1000 " pdb=" PB ADP G1000 " ideal model delta sigma weight residual 120.50 132.12 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" PA ADP B1000 " pdb=" O3A ADP B1000 " pdb=" PB ADP B1000 " ideal model delta sigma weight residual 120.50 132.11 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" PA ADP F1000 " pdb=" O3A ADP F1000 " pdb=" PB ADP F1000 " ideal model delta sigma weight residual 120.50 132.10 -11.60 3.00e+00 1.11e-01 1.50e+01 ... (remaining 44731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 19680 32.87 - 65.74: 272 65.74 - 98.61: 24 98.61 - 131.48: 8 131.48 - 164.35: 16 Dihedral angle restraints: 20000 sinusoidal: 8000 harmonic: 12000 Sorted by residual: dihedral pdb=" O1B ADP G1000 " pdb=" O3A ADP G1000 " pdb=" PB ADP G1000 " pdb=" PA ADP G1000 " ideal model delta sinusoidal sigma weight residual 300.00 135.65 164.35 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O1B ADP H1000 " pdb=" O3A ADP H1000 " pdb=" PB ADP H1000 " pdb=" PA ADP H1000 " ideal model delta sinusoidal sigma weight residual 300.00 135.67 164.33 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual 300.00 135.68 164.32 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 19997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2582 0.030 - 0.060: 1713 0.060 - 0.090: 647 0.090 - 0.120: 324 0.120 - 0.149: 62 Chirality restraints: 5328 Sorted by residual: chirality pdb=" CA HIS H 712 " pdb=" N HIS H 712 " pdb=" C HIS H 712 " pdb=" CB HIS H 712 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA HIS B 712 " pdb=" N HIS B 712 " pdb=" C HIS B 712 " pdb=" CB HIS B 712 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA HIS C 712 " pdb=" N HIS C 712 " pdb=" C HIS C 712 " pdb=" CB HIS C 712 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 5325 not shown) Planarity restraints: 5648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 602 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C GLY B 602 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY B 602 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 603 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 602 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLY A 602 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY A 602 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 603 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 602 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C GLY E 602 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY E 602 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY E 603 " -0.008 2.00e-02 2.50e+03 ... (remaining 5645 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 291 2.58 - 3.16: 27633 3.16 - 3.74: 50254 3.74 - 4.32: 76332 4.32 - 4.90: 121346 Nonbonded interactions: 275856 Sorted by model distance: nonbonded pdb=" O2B ADP D1000 " pdb="MG MG D1001 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP C1000 " pdb="MG MG C1001 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP F1000 " pdb="MG MG F1001 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP B1000 " pdb="MG MG B1001 " model vdw 2.000 2.170 nonbonded pdb=" O2B ADP A1000 " pdb="MG MG A1001 " model vdw 2.000 2.170 ... (remaining 275851 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: 0.10 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.210 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.008 0.105 32984 Z= 0.381 Angle : 0.734 11.647 44736 Z= 0.362 Chirality : 0.047 0.149 5328 Planarity : 0.004 0.033 5648 Dihedral : 12.987 164.350 12288 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.10), residues: 4112 helix: -2.17 (0.09), residues: 1808 sheet: -0.52 (0.17), residues: 616 loop : -2.19 (0.12), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 682 TYR 0.015 0.002 TYR A 708 PHE 0.012 0.002 PHE F 604 TRP 0.005 0.002 TRP G 477 HIS 0.005 0.001 HIS E 710 Details of bonding type rmsd covalent geometry : bond 0.00837 (32984) covalent geometry : angle 0.73424 (44736) hydrogen bonds : bond 0.19465 ( 1664) hydrogen bonds : angle 7.83208 ( 4872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 621 MET cc_start: 0.8832 (mtp) cc_final: 0.8490 (mtp) REVERT: A 680 MET cc_start: 0.8183 (mtp) cc_final: 0.7710 (mtt) REVERT: B 231 MET cc_start: 0.7532 (mmt) cc_final: 0.6804 (mmt) REVERT: B 621 MET cc_start: 0.8979 (mtp) cc_final: 0.8670 (mtp) REVERT: B 680 MET cc_start: 0.8195 (mtp) cc_final: 0.7895 (mtp) REVERT: C 680 MET cc_start: 0.8215 (mtp) cc_final: 0.7725 (mtt) REVERT: D 621 MET cc_start: 0.8885 (mtp) cc_final: 0.8369 (mtp) REVERT: D 680 MET cc_start: 0.8127 (mtp) cc_final: 0.7875 (mtp) REVERT: E 243 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7603 (ttt180) REVERT: E 680 MET cc_start: 0.8187 (mtp) cc_final: 0.7714 (mtt) REVERT: F 621 MET cc_start: 0.8796 (mtp) cc_final: 0.8449 (mtp) REVERT: F 680 MET cc_start: 0.8188 (mtp) cc_final: 0.7917 (mtp) REVERT: G 255 TYR cc_start: 0.8332 (t80) cc_final: 0.8131 (t80) REVERT: G 680 MET cc_start: 0.8226 (mtp) cc_final: 0.7726 (mtt) REVERT: H 231 MET cc_start: 0.7740 (mmt) cc_final: 0.7096 (mmt) REVERT: H 255 TYR cc_start: 0.8330 (t80) cc_final: 0.8107 (t80) REVERT: H 621 MET cc_start: 0.8965 (mtp) cc_final: 0.8631 (mtp) REVERT: H 680 MET cc_start: 0.8223 (mtp) cc_final: 0.7931 (mtp) outliers start: 0 outliers final: 0 residues processed: 629 average time/residue: 0.6274 time to fit residues: 470.1931 Evaluate side-chains 445 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.0570 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 173 GLN A 254 ASN A 571 HIS A 576 HIS A 611 GLN A 671 ASN B 29 HIS B 111 GLN B 173 GLN B 254 ASN B 518 HIS B 571 HIS B 576 HIS B 671 ASN C 29 HIS C 111 GLN C 173 GLN C 206 GLN C 254 ASN C 518 HIS C 571 HIS C 576 HIS C 611 GLN C 671 ASN D 29 HIS D 111 GLN D 173 GLN D 206 GLN D 254 ASN D 571 HIS D 576 HIS D 589 GLN D 611 GLN D 671 ASN E 29 HIS E 173 GLN E 254 ASN E 571 HIS E 576 HIS E 589 GLN E 611 GLN E 671 ASN F 29 HIS F 111 GLN F 173 GLN F 246 HIS F 254 ASN F 571 HIS F 576 HIS F 589 GLN F 611 GLN F 671 ASN G 29 HIS G 111 GLN G 173 GLN G 254 ASN G 571 HIS G 576 HIS G 611 GLN G 671 ASN H 29 HIS H 111 GLN H 173 GLN H 254 ASN H 518 HIS H 571 HIS H 576 HIS H 671 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.184850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140113 restraints weight = 32281.007| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.14 r_work: 0.3168 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32984 Z= 0.130 Angle : 0.594 9.856 44736 Z= 0.292 Chirality : 0.044 0.154 5328 Planarity : 0.004 0.029 5648 Dihedral : 9.779 141.885 4544 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.59 % Allowed : 12.02 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 4112 helix: -0.10 (0.11), residues: 1856 sheet: 0.06 (0.17), residues: 664 loop : -1.50 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 514 TYR 0.008 0.001 TYR F 255 PHE 0.012 0.001 PHE B 542 TRP 0.005 0.001 TRP E 631 HIS 0.008 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00284 (32984) covalent geometry : angle 0.59436 (44736) hydrogen bonds : bond 0.03954 ( 1664) hydrogen bonds : angle 4.86762 ( 4872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 527 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 THR cc_start: 0.7832 (p) cc_final: 0.7473 (t) REVERT: A 164 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 231 MET cc_start: 0.7893 (mmt) cc_final: 0.6676 (mmt) REVERT: A 525 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8151 (pttt) REVERT: A 621 MET cc_start: 0.8893 (mtp) cc_final: 0.8652 (mtp) REVERT: A 680 MET cc_start: 0.9104 (mtp) cc_final: 0.8628 (mtt) REVERT: B 164 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7909 (p0) REVERT: B 231 MET cc_start: 0.7807 (mmt) cc_final: 0.7316 (mmt) REVERT: B 235 THR cc_start: 0.8564 (p) cc_final: 0.8317 (t) REVERT: B 523 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: B 580 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7310 (mmpt) REVERT: B 621 MET cc_start: 0.9003 (mtp) cc_final: 0.8595 (mtp) REVERT: B 680 MET cc_start: 0.9053 (mtp) cc_final: 0.8789 (mtp) REVERT: B 684 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: C 164 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8154 (p0) REVERT: C 413 ASP cc_start: 0.8305 (m-30) cc_final: 0.8089 (m-30) REVERT: C 598 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8050 (mtpp) REVERT: C 680 MET cc_start: 0.9104 (mtp) cc_final: 0.8620 (mtt) REVERT: D 231 MET cc_start: 0.7740 (mmt) cc_final: 0.6876 (mmt) REVERT: D 235 THR cc_start: 0.8471 (p) cc_final: 0.8244 (t) REVERT: D 621 MET cc_start: 0.8915 (mtp) cc_final: 0.8425 (mtp) REVERT: D 680 MET cc_start: 0.9032 (mtp) cc_final: 0.8780 (mtp) REVERT: E 164 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8050 (p0) REVERT: E 243 ARG cc_start: 0.8064 (ttt90) cc_final: 0.7674 (ttt180) REVERT: E 680 MET cc_start: 0.9079 (mtp) cc_final: 0.8604 (mtt) REVERT: F 164 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8207 (p0) REVERT: F 231 MET cc_start: 0.7826 (mmt) cc_final: 0.7264 (mmt) REVERT: F 522 MET cc_start: 0.7395 (ptp) cc_final: 0.7145 (ptp) REVERT: F 621 MET cc_start: 0.8900 (mtp) cc_final: 0.8482 (mtp) REVERT: F 680 MET cc_start: 0.9057 (mtp) cc_final: 0.8808 (mtp) REVERT: F 684 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: F 707 ARG cc_start: 0.8592 (tpt-90) cc_final: 0.8316 (ttt180) REVERT: G 598 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7934 (mtpp) REVERT: G 680 MET cc_start: 0.9112 (mtp) cc_final: 0.8620 (mtt) REVERT: H 164 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7988 (p0) REVERT: H 231 MET cc_start: 0.7900 (mmt) cc_final: 0.7469 (mmt) REVERT: H 580 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7380 (mmpt) REVERT: H 621 MET cc_start: 0.8980 (mtp) cc_final: 0.8568 (mtp) REVERT: H 680 MET cc_start: 0.9044 (mtp) cc_final: 0.8813 (mtp) outliers start: 92 outliers final: 21 residues processed: 577 average time/residue: 0.6364 time to fit residues: 436.1831 Evaluate side-chains 480 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 447 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 594 MET Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 405 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 280 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 354 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 406 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 246 HIS B 611 GLN C 206 GLN D 206 GLN E 253 GLN E 518 HIS G 246 HIS H 246 HIS H 253 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.180926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133631 restraints weight = 32002.435| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.04 r_work: 0.3136 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32984 Z= 0.215 Angle : 0.651 10.449 44736 Z= 0.317 Chirality : 0.046 0.146 5328 Planarity : 0.004 0.038 5648 Dihedral : 9.137 123.548 4544 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.27 % Allowed : 12.05 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.12), residues: 4112 helix: 0.48 (0.12), residues: 1848 sheet: 0.54 (0.19), residues: 576 loop : -1.37 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 682 TYR 0.015 0.002 TYR A 708 PHE 0.009 0.002 PHE E 604 TRP 0.003 0.001 TRP G 631 HIS 0.010 0.001 HIS E 518 Details of bonding type rmsd covalent geometry : bond 0.00488 (32984) covalent geometry : angle 0.65149 (44736) hydrogen bonds : bond 0.04331 ( 1664) hydrogen bonds : angle 4.76742 ( 4872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 458 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7329 (mptt) REVERT: A 52 THR cc_start: 0.7751 (p) cc_final: 0.7490 (t) REVERT: A 164 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 459 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 621 MET cc_start: 0.8897 (mtp) cc_final: 0.8596 (mtp) REVERT: A 680 MET cc_start: 0.9080 (mtp) cc_final: 0.8590 (mtt) REVERT: B 31 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7376 (mptt) REVERT: B 164 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7891 (p0) REVERT: B 214 SER cc_start: 0.8232 (t) cc_final: 0.7820 (p) REVERT: B 231 MET cc_start: 0.7836 (mmt) cc_final: 0.7318 (mmt) REVERT: B 459 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 523 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 557 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8021 (mttt) REVERT: B 580 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7414 (mmpt) REVERT: B 621 MET cc_start: 0.8923 (mtp) cc_final: 0.8559 (mtp) REVERT: B 680 MET cc_start: 0.9013 (mtp) cc_final: 0.8755 (mtp) REVERT: B 684 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: C 31 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7581 (mptt) REVERT: C 164 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8101 (p0) REVERT: C 459 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: C 680 MET cc_start: 0.9082 (mtp) cc_final: 0.8591 (mtt) REVERT: D 31 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7399 (mptt) REVERT: D 164 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8321 (p0) REVERT: D 231 MET cc_start: 0.7800 (mmt) cc_final: 0.7159 (mmt) REVERT: D 459 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: D 523 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: D 621 MET cc_start: 0.8917 (mtp) cc_final: 0.8512 (mtp) REVERT: D 680 MET cc_start: 0.9043 (mtp) cc_final: 0.8793 (mtp) REVERT: E 31 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (mptt) REVERT: E 98 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8530 (mt) REVERT: E 164 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.8043 (p0) REVERT: E 243 ARG cc_start: 0.8102 (ttt90) cc_final: 0.7735 (ttt180) REVERT: E 446 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8267 (tp) REVERT: E 525 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (ptmt) REVERT: E 680 MET cc_start: 0.9075 (mtp) cc_final: 0.8593 (mtt) REVERT: F 31 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7385 (mptt) REVERT: F 164 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8159 (p0) REVERT: F 231 MET cc_start: 0.7901 (mmt) cc_final: 0.7245 (mmt) REVERT: F 418 ASP cc_start: 0.7939 (t0) cc_final: 0.7666 (t0) REVERT: F 459 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: F 523 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: F 621 MET cc_start: 0.8906 (mtp) cc_final: 0.8515 (mtp) REVERT: F 680 MET cc_start: 0.9030 (mtp) cc_final: 0.8764 (mtp) REVERT: F 684 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: F 707 ARG cc_start: 0.8672 (tpt-90) cc_final: 0.8471 (ttt180) REVERT: G 31 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7500 (mptt) REVERT: G 459 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: G 680 MET cc_start: 0.9086 (mtp) cc_final: 0.8600 (mtt) REVERT: H 31 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7356 (mptt) REVERT: H 164 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7981 (p0) REVERT: H 231 MET cc_start: 0.7878 (mmt) cc_final: 0.7326 (mmt) REVERT: H 459 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: H 523 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: H 580 LYS cc_start: 0.7636 (mmtt) cc_final: 0.7425 (mmpt) REVERT: H 621 MET cc_start: 0.8909 (mtp) cc_final: 0.8557 (mtp) REVERT: H 680 MET cc_start: 0.9020 (mtp) cc_final: 0.8766 (mtp) REVERT: H 684 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7823 (mt-10) outliers start: 116 outliers final: 34 residues processed: 513 average time/residue: 0.6514 time to fit residues: 396.2805 Evaluate side-chains 501 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 434 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 557 LYS Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 525 LYS Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 523 GLU Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 459 GLU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 459 GLU Chi-restraints excluded: chain H residue 523 GLU Chi-restraints excluded: chain H residue 684 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 30 optimal weight: 5.9990 chunk 352 optimal weight: 0.9980 chunk 309 optimal weight: 0.6980 chunk 240 optimal weight: 0.6980 chunk 328 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 350 optimal weight: 0.0970 chunk 405 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 48 optimal weight: 0.0980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 246 HIS C 206 GLN D 206 GLN E 114 GLN E 253 GLN G 114 GLN H 246 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.184476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.127162 restraints weight = 32367.010| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.34 r_work: 0.3063 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32984 Z= 0.106 Angle : 0.546 9.070 44736 Z= 0.265 Chirality : 0.043 0.163 5328 Planarity : 0.003 0.030 5648 Dihedral : 8.398 110.064 4544 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.34 % Allowed : 12.98 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4112 helix: 1.09 (0.12), residues: 1856 sheet: 0.76 (0.19), residues: 576 loop : -1.20 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.015 0.001 TYR A 255 PHE 0.013 0.001 PHE D 542 TRP 0.004 0.001 TRP F 631 HIS 0.003 0.000 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00227 (32984) covalent geometry : angle 0.54647 (44736) hydrogen bonds : bond 0.03307 ( 1664) hydrogen bonds : angle 4.34425 ( 4872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 475 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7438 (mptt) REVERT: A 52 THR cc_start: 0.7875 (p) cc_final: 0.7665 (t) REVERT: A 164 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7927 (p0) REVERT: A 476 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8073 (mp0) REVERT: A 523 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: A 580 LYS cc_start: 0.7797 (mmtt) cc_final: 0.7452 (mmpt) REVERT: A 680 MET cc_start: 0.9232 (mtp) cc_final: 0.8775 (mtt) REVERT: B 31 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7456 (mptt) REVERT: B 164 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7943 (p0) REVERT: B 214 SER cc_start: 0.8222 (t) cc_final: 0.7799 (p) REVERT: B 231 MET cc_start: 0.7720 (mmt) cc_final: 0.7211 (mmt) REVERT: B 232 LEU cc_start: 0.8150 (mt) cc_final: 0.7872 (mm) REVERT: B 235 THR cc_start: 0.8577 (p) cc_final: 0.8305 (t) REVERT: B 523 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 580 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7227 (mmpt) REVERT: B 621 MET cc_start: 0.8988 (mtp) cc_final: 0.8649 (mtp) REVERT: B 680 MET cc_start: 0.9194 (mtp) cc_final: 0.8971 (mtp) REVERT: C 31 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7629 (mptt) REVERT: C 164 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8141 (p0) REVERT: C 580 LYS cc_start: 0.7509 (mmtt) cc_final: 0.7169 (mmpt) REVERT: C 680 MET cc_start: 0.9224 (mtp) cc_final: 0.8768 (mtt) REVERT: D 31 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7496 (mptt) REVERT: D 128 MET cc_start: 0.8700 (mtp) cc_final: 0.8370 (mtt) REVERT: D 164 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (p0) REVERT: D 235 THR cc_start: 0.8568 (p) cc_final: 0.8307 (t) REVERT: D 523 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: D 580 LYS cc_start: 0.7518 (mmtt) cc_final: 0.7128 (mmpt) REVERT: D 621 MET cc_start: 0.8969 (mtp) cc_final: 0.8535 (mtp) REVERT: D 680 MET cc_start: 0.9207 (mtp) cc_final: 0.8982 (mtp) REVERT: E 31 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7564 (mptt) REVERT: E 164 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8118 (p0) REVERT: E 243 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7833 (ttt180) REVERT: E 680 MET cc_start: 0.9231 (mtp) cc_final: 0.8780 (mtt) REVERT: F 31 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7499 (mptt) REVERT: F 128 MET cc_start: 0.8614 (mtp) cc_final: 0.8378 (mtt) REVERT: F 164 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8193 (p0) REVERT: F 231 MET cc_start: 0.7830 (mmt) cc_final: 0.7299 (mmt) REVERT: F 523 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: F 621 MET cc_start: 0.8978 (mtp) cc_final: 0.8644 (mtp) REVERT: F 680 MET cc_start: 0.9191 (mtp) cc_final: 0.8964 (mtp) REVERT: F 707 ARG cc_start: 0.8679 (tpt-90) cc_final: 0.8458 (ttt180) REVERT: G 31 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7573 (mptt) REVERT: G 580 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7376 (mmpt) REVERT: G 680 MET cc_start: 0.9230 (mtp) cc_final: 0.8771 (mtt) REVERT: H 31 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7472 (mptt) REVERT: H 164 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7991 (p0) REVERT: H 231 MET cc_start: 0.7777 (mmt) cc_final: 0.7304 (mmt) REVERT: H 523 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: H 580 LYS cc_start: 0.7499 (mmtt) cc_final: 0.7247 (mmpt) REVERT: H 621 MET cc_start: 0.8977 (mtp) cc_final: 0.8639 (mtp) REVERT: H 680 MET cc_start: 0.9188 (mtp) cc_final: 0.8981 (mtp) outliers start: 83 outliers final: 16 residues processed: 512 average time/residue: 0.6353 time to fit residues: 387.5005 Evaluate side-chains 470 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 523 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 523 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 344 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 411 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 246 HIS C 114 GLN C 206 GLN D 206 GLN E 114 GLN E 253 GLN G 114 GLN H 246 HIS H 611 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.183663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138826 restraints weight = 31852.706| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.12 r_work: 0.3138 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32984 Z= 0.143 Angle : 0.576 8.154 44736 Z= 0.278 Chirality : 0.044 0.161 5328 Planarity : 0.003 0.029 5648 Dihedral : 8.604 121.365 4544 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.34 % Allowed : 13.63 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 4112 helix: 1.22 (0.12), residues: 1856 sheet: 0.89 (0.20), residues: 576 loop : -1.09 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 209 TYR 0.011 0.001 TYR A 708 PHE 0.011 0.001 PHE D 542 TRP 0.003 0.001 TRP G 631 HIS 0.003 0.001 HIS E 712 Details of bonding type rmsd covalent geometry : bond 0.00318 (32984) covalent geometry : angle 0.57560 (44736) hydrogen bonds : bond 0.03597 ( 1664) hydrogen bonds : angle 4.35750 ( 4872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 436 time to evaluate : 1.195 Fit side-chains REVERT: A 31 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7382 (mptt) REVERT: A 164 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7900 (p0) REVERT: A 476 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7975 (mp0) REVERT: A 580 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7443 (mmpt) REVERT: A 680 MET cc_start: 0.9093 (mtp) cc_final: 0.8641 (mtt) REVERT: B 31 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7357 (mptt) REVERT: B 214 SER cc_start: 0.8235 (t) cc_final: 0.7846 (p) REVERT: B 231 MET cc_start: 0.7740 (mmt) cc_final: 0.7146 (mmt) REVERT: B 235 THR cc_start: 0.8577 (p) cc_final: 0.8286 (t) REVERT: B 580 LYS cc_start: 0.7472 (mmtt) cc_final: 0.7264 (mmpt) REVERT: B 621 MET cc_start: 0.8924 (mtp) cc_final: 0.8546 (mtp) REVERT: B 680 MET cc_start: 0.9058 (mtp) cc_final: 0.8787 (mtp) REVERT: C 31 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7528 (mptt) REVERT: C 680 MET cc_start: 0.9106 (mtp) cc_final: 0.8656 (mtt) REVERT: D 31 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7372 (mptt) REVERT: D 164 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8284 (p0) REVERT: D 231 MET cc_start: 0.7656 (mmt) cc_final: 0.7206 (mmt) REVERT: D 235 THR cc_start: 0.8584 (p) cc_final: 0.8291 (t) REVERT: D 580 LYS cc_start: 0.7442 (mmtt) cc_final: 0.7222 (mmpt) REVERT: D 621 MET cc_start: 0.8919 (mtp) cc_final: 0.8530 (mtp) REVERT: D 680 MET cc_start: 0.9066 (mtp) cc_final: 0.8803 (mtp) REVERT: E 31 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7521 (mptt) REVERT: E 164 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8141 (p0) REVERT: E 243 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7759 (ttt180) REVERT: E 680 MET cc_start: 0.9114 (mtp) cc_final: 0.8630 (mtt) REVERT: F 31 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7355 (mptt) REVERT: F 124 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7908 (mm) REVERT: F 164 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8158 (p0) REVERT: F 231 MET cc_start: 0.7893 (mmt) cc_final: 0.7128 (mmt) REVERT: F 621 MET cc_start: 0.8915 (mtp) cc_final: 0.8522 (mtp) REVERT: F 680 MET cc_start: 0.9068 (mtp) cc_final: 0.8786 (mtp) REVERT: F 707 ARG cc_start: 0.8648 (tpt-90) cc_final: 0.8421 (ttt180) REVERT: G 31 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7470 (mptt) REVERT: G 580 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7363 (mmpt) REVERT: G 680 MET cc_start: 0.9102 (mtp) cc_final: 0.8649 (mtt) REVERT: H 31 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7307 (mptt) REVERT: H 164 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7989 (p0) REVERT: H 231 MET cc_start: 0.7819 (mmt) cc_final: 0.7238 (mmt) REVERT: H 580 LYS cc_start: 0.7464 (mmtt) cc_final: 0.7264 (mmpt) REVERT: H 621 MET cc_start: 0.8911 (mtp) cc_final: 0.8537 (mtp) REVERT: H 680 MET cc_start: 0.9059 (mtp) cc_final: 0.8805 (mtp) outliers start: 83 outliers final: 29 residues processed: 484 average time/residue: 0.6745 time to fit residues: 384.8990 Evaluate side-chains 461 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 418 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 114 optimal weight: 4.9990 chunk 341 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 383 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 390 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 246 HIS C 114 GLN C 206 GLN D 206 GLN D 671 ASN E 114 GLN E 253 GLN F 107 ASN F 671 ASN G 114 GLN G 246 HIS G 671 ASN H 114 GLN H 246 HIS H 671 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.180150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.139406 restraints weight = 31674.833| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.37 r_work: 0.2965 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 32984 Z= 0.307 Angle : 0.716 12.298 44736 Z= 0.348 Chirality : 0.050 0.161 5328 Planarity : 0.004 0.043 5648 Dihedral : 9.363 130.487 4544 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.41 % Allowed : 12.92 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4112 helix: 0.80 (0.12), residues: 1856 sheet: 0.86 (0.20), residues: 592 loop : -1.09 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 682 TYR 0.017 0.002 TYR B 708 PHE 0.013 0.003 PHE D 604 TRP 0.004 0.001 TRP D 631 HIS 0.008 0.002 HIS E 712 Details of bonding type rmsd covalent geometry : bond 0.00705 (32984) covalent geometry : angle 0.71592 (44736) hydrogen bonds : bond 0.04563 ( 1664) hydrogen bonds : angle 4.71476 ( 4872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 436 time to evaluate : 1.197 Fit side-chains REVERT: A 31 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7498 (mptt) REVERT: A 113 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: A 164 ASN cc_start: 0.8179 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 428 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7909 (mt) REVERT: A 459 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 476 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8124 (mp0) REVERT: A 680 MET cc_start: 0.9255 (mtp) cc_final: 0.8800 (mtt) REVERT: B 31 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7386 (mptt) REVERT: B 214 SER cc_start: 0.8223 (t) cc_final: 0.7764 (p) REVERT: B 231 MET cc_start: 0.7629 (mmt) cc_final: 0.6925 (mmt) REVERT: B 459 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: B 580 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7375 (mmpt) REVERT: B 680 MET cc_start: 0.9221 (mtp) cc_final: 0.8990 (mtp) REVERT: C 31 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7594 (mptt) REVERT: C 418 ASP cc_start: 0.7928 (t0) cc_final: 0.7714 (t70) REVERT: C 428 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7997 (mt) REVERT: C 446 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8388 (tp) REVERT: C 459 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: C 593 GLU cc_start: 0.8239 (mp0) cc_final: 0.8026 (mp0) REVERT: C 667 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8833 (tpt-90) REVERT: C 680 MET cc_start: 0.9270 (mtp) cc_final: 0.8842 (mtt) REVERT: D 31 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7371 (mptt) REVERT: D 164 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8351 (p0) REVERT: D 231 MET cc_start: 0.7479 (mmt) cc_final: 0.7177 (mmt) REVERT: D 459 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: D 680 MET cc_start: 0.9221 (mtp) cc_final: 0.8972 (mtp) REVERT: E 31 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7551 (mptt) REVERT: E 164 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8132 (p0) REVERT: E 243 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7817 (ttt180) REVERT: E 428 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7917 (mt) REVERT: E 459 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: E 667 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8834 (tpt-90) REVERT: E 680 MET cc_start: 0.9257 (mtp) cc_final: 0.8801 (mtt) REVERT: F 31 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7373 (mptt) REVERT: F 124 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7942 (mm) REVERT: F 164 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (p0) REVERT: F 231 MET cc_start: 0.7794 (mmt) cc_final: 0.7094 (mmt) REVERT: F 418 ASP cc_start: 0.8013 (t0) cc_final: 0.7718 (t0) REVERT: F 428 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8001 (mt) REVERT: F 459 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: F 680 MET cc_start: 0.9225 (mtp) cc_final: 0.8979 (mtp) REVERT: G 31 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7524 (mptt) REVERT: G 103 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8436 (mp) REVERT: G 428 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7978 (mt) REVERT: G 459 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: G 667 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8873 (tpt170) REVERT: G 672 THR cc_start: 0.9000 (m) cc_final: 0.8785 (p) REVERT: G 680 MET cc_start: 0.9270 (mtp) cc_final: 0.8832 (mtt) REVERT: H 31 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7393 (mptt) REVERT: H 164 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7967 (p0) REVERT: H 231 MET cc_start: 0.7655 (mmt) cc_final: 0.6975 (mmt) REVERT: H 428 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8021 (mt) REVERT: H 459 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: H 680 MET cc_start: 0.9224 (mtp) cc_final: 0.8991 (mtp) outliers start: 121 outliers final: 41 residues processed: 500 average time/residue: 0.6746 time to fit residues: 398.1220 Evaluate side-chains 500 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 425 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 667 ARG Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 459 GLU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain G residue 667 ARG Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 459 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 377 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 414 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 360 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 114 GLN B 246 HIS C 114 GLN C 206 GLN D 114 GLN D 206 GLN D 671 ASN E 114 GLN E 253 GLN F 114 GLN F 671 ASN G 114 GLN H 114 GLN H 246 HIS H 671 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.183459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3402 r_free = 0.3402 target = 0.132022 restraints weight = 31895.006| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.09 r_work: 0.3095 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32984 Z= 0.131 Angle : 0.571 7.912 44736 Z= 0.277 Chirality : 0.044 0.165 5328 Planarity : 0.003 0.031 5648 Dihedral : 8.658 115.001 4544 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.03 % Allowed : 14.53 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4112 helix: 1.18 (0.12), residues: 1856 sheet: 1.09 (0.20), residues: 576 loop : -1.01 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.008 0.001 TYR A 255 PHE 0.011 0.001 PHE D 542 TRP 0.004 0.001 TRP A 631 HIS 0.003 0.001 HIS B 710 Details of bonding type rmsd covalent geometry : bond 0.00287 (32984) covalent geometry : angle 0.57129 (44736) hydrogen bonds : bond 0.03518 ( 1664) hydrogen bonds : angle 4.38182 ( 4872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 433 time to evaluate : 1.128 Fit side-chains REVERT: A 31 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7394 (mptt) REVERT: A 164 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7943 (p0) REVERT: A 476 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8049 (mp0) REVERT: A 522 MET cc_start: 0.7455 (ptp) cc_final: 0.6970 (ptp) REVERT: A 523 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 680 MET cc_start: 0.9161 (mtp) cc_final: 0.8727 (mtt) REVERT: B 31 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7302 (mptt) REVERT: B 214 SER cc_start: 0.8230 (t) cc_final: 0.7819 (p) REVERT: B 231 MET cc_start: 0.7631 (mmt) cc_final: 0.6944 (mmt) REVERT: B 235 THR cc_start: 0.8654 (p) cc_final: 0.8353 (t) REVERT: B 418 ASP cc_start: 0.7957 (t0) cc_final: 0.7609 (t0) REVERT: B 580 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7291 (mmpt) REVERT: B 680 MET cc_start: 0.9133 (mtp) cc_final: 0.8877 (mtp) REVERT: C 31 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7466 (mptt) REVERT: C 523 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: C 593 GLU cc_start: 0.8098 (mp0) cc_final: 0.7882 (mp0) REVERT: C 680 MET cc_start: 0.9158 (mtp) cc_final: 0.8722 (mtt) REVERT: D 31 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7315 (mptt) REVERT: D 164 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8278 (p0) REVERT: D 231 MET cc_start: 0.7503 (mmt) cc_final: 0.7209 (mmt) REVERT: D 580 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7291 (mmpt) REVERT: D 680 MET cc_start: 0.9133 (mtp) cc_final: 0.8901 (mtp) REVERT: E 31 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7451 (mptt) REVERT: E 164 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8157 (p0) REVERT: E 243 ARG cc_start: 0.8120 (ttt90) cc_final: 0.7788 (ttt180) REVERT: E 680 MET cc_start: 0.9166 (mtp) cc_final: 0.8740 (mtt) REVERT: F 31 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7301 (mptt) REVERT: F 164 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8158 (p0) REVERT: F 231 MET cc_start: 0.7842 (mmt) cc_final: 0.7180 (mmt) REVERT: F 418 ASP cc_start: 0.7973 (t0) cc_final: 0.7672 (t0) REVERT: F 680 MET cc_start: 0.9133 (mtp) cc_final: 0.8896 (mtp) REVERT: G 31 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7466 (mptt) REVERT: G 680 MET cc_start: 0.9156 (mtp) cc_final: 0.8718 (mtt) REVERT: H 31 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7311 (mptt) REVERT: H 164 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7988 (p0) REVERT: H 231 MET cc_start: 0.7702 (mmt) cc_final: 0.7084 (mmt) REVERT: H 580 LYS cc_start: 0.7524 (mmtt) cc_final: 0.7297 (mmpt) REVERT: H 680 MET cc_start: 0.9131 (mtp) cc_final: 0.8873 (mtp) outliers start: 72 outliers final: 27 residues processed: 476 average time/residue: 0.6625 time to fit residues: 372.5998 Evaluate side-chains 458 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 416 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 193 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 375 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 332 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 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 253 GLN B 114 GLN B 246 HIS C 114 GLN C 206 GLN D 114 GLN D 206 GLN D 671 ASN E 114 GLN E 253 GLN F 114 GLN F 671 ASN G 114 GLN H 114 GLN H 246 HIS H 671 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.182234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.136105 restraints weight = 31781.464| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.11 r_work: 0.3138 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32984 Z= 0.155 Angle : 0.589 8.834 44736 Z= 0.285 Chirality : 0.044 0.210 5328 Planarity : 0.003 0.031 5648 Dihedral : 8.755 121.506 4544 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.97 % Allowed : 14.84 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 4112 helix: 1.25 (0.12), residues: 1856 sheet: 1.10 (0.20), residues: 576 loop : -0.98 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.011 0.001 TYR A 708 PHE 0.010 0.002 PHE D 542 TRP 0.003 0.001 TRP G 631 HIS 0.003 0.001 HIS C 712 Details of bonding type rmsd covalent geometry : bond 0.00347 (32984) covalent geometry : angle 0.58910 (44736) hydrogen bonds : bond 0.03667 ( 1664) hydrogen bonds : angle 4.39067 ( 4872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 428 time to evaluate : 0.990 Fit side-chains REVERT: A 31 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7346 (mptt) REVERT: A 164 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7944 (p0) REVERT: A 476 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7962 (mp0) REVERT: A 680 MET cc_start: 0.9082 (mtp) cc_final: 0.8626 (mtt) REVERT: B 31 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7241 (mptt) REVERT: B 214 SER cc_start: 0.8236 (t) cc_final: 0.7855 (p) REVERT: B 231 MET cc_start: 0.7674 (mmt) cc_final: 0.6867 (mmt) REVERT: B 418 ASP cc_start: 0.7909 (t0) cc_final: 0.7559 (t0) REVERT: B 680 MET cc_start: 0.9034 (mtp) cc_final: 0.8772 (mtp) REVERT: C 31 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7401 (mptt) REVERT: C 680 MET cc_start: 0.9090 (mtp) cc_final: 0.8637 (mtt) REVERT: D 31 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7245 (mptt) REVERT: D 164 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8288 (p0) REVERT: D 231 MET cc_start: 0.7418 (mmt) cc_final: 0.7056 (mmt) REVERT: D 680 MET cc_start: 0.9034 (mtp) cc_final: 0.8790 (mtp) REVERT: E 31 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7448 (mptt) REVERT: E 164 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8178 (p0) REVERT: E 243 ARG cc_start: 0.8069 (ttt90) cc_final: 0.7740 (ttt180) REVERT: E 680 MET cc_start: 0.9099 (mtp) cc_final: 0.8649 (mtt) REVERT: F 31 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7235 (mptt) REVERT: F 164 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8102 (p0) REVERT: F 231 MET cc_start: 0.7896 (mmt) cc_final: 0.7113 (mmt) REVERT: F 418 ASP cc_start: 0.7909 (t0) cc_final: 0.7624 (t0) REVERT: F 680 MET cc_start: 0.9032 (mtp) cc_final: 0.8786 (mtp) REVERT: G 31 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7402 (mptt) REVERT: G 103 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (mp) REVERT: G 680 MET cc_start: 0.9082 (mtp) cc_final: 0.8627 (mtt) REVERT: H 31 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7249 (mptt) REVERT: H 164 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7955 (p0) REVERT: H 231 MET cc_start: 0.7711 (mmt) cc_final: 0.7049 (mmt) REVERT: H 680 MET cc_start: 0.9030 (mtp) cc_final: 0.8763 (mtp) outliers start: 70 outliers final: 28 residues processed: 472 average time/residue: 0.6485 time to fit residues: 361.9145 Evaluate side-chains 458 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 416 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 416 VAL Chi-restraints excluded: chain H residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 399 optimal weight: 1.9990 chunk 368 optimal weight: 6.9990 chunk 200 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 348 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 245 optimal weight: 0.9980 chunk 226 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 253 GLN B 114 GLN B 246 HIS C 114 GLN C 206 GLN D 114 GLN D 206 GLN D 671 ASN E 114 GLN F 114 GLN F 206 GLN G 114 GLN H 114 GLN H 246 HIS H 671 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.184003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130674 restraints weight = 31827.585| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.69 r_work: 0.3106 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32984 Z= 0.124 Angle : 0.562 9.625 44736 Z= 0.271 Chirality : 0.044 0.262 5328 Planarity : 0.003 0.031 5648 Dihedral : 8.448 116.027 4544 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.77 % Allowed : 15.20 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.13), residues: 4112 helix: 1.45 (0.12), residues: 1856 sheet: 1.18 (0.20), residues: 576 loop : -0.93 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.008 0.001 TYR A 708 PHE 0.012 0.001 PHE D 542 TRP 0.003 0.001 TRP G 631 HIS 0.003 0.001 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00275 (32984) covalent geometry : angle 0.56152 (44736) hydrogen bonds : bond 0.03356 ( 1664) hydrogen bonds : angle 4.25405 ( 4872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 418 time to evaluate : 1.187 Fit side-chains REVERT: A 31 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7378 (mptt) REVERT: A 164 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7966 (p0) REVERT: A 476 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8008 (mp0) REVERT: A 680 MET cc_start: 0.9140 (mtp) cc_final: 0.8702 (mtt) REVERT: B 31 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7282 (mptt) REVERT: B 214 SER cc_start: 0.8240 (t) cc_final: 0.7832 (p) REVERT: B 231 MET cc_start: 0.7627 (mmt) cc_final: 0.6818 (mmt) REVERT: B 235 THR cc_start: 0.8520 (p) cc_final: 0.8255 (t) REVERT: B 680 MET cc_start: 0.9091 (mtp) cc_final: 0.8854 (mtp) REVERT: C 31 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7450 (mptt) REVERT: C 680 MET cc_start: 0.9145 (mtp) cc_final: 0.8709 (mtt) REVERT: D 31 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7283 (mptt) REVERT: D 164 ASN cc_start: 0.8589 (OUTLIER) cc_final: 0.8265 (p0) REVERT: D 231 MET cc_start: 0.7345 (mmt) cc_final: 0.6953 (mmt) REVERT: D 235 THR cc_start: 0.8588 (p) cc_final: 0.8296 (t) REVERT: D 680 MET cc_start: 0.9096 (mtp) cc_final: 0.8870 (mtp) REVERT: E 31 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7436 (mptt) REVERT: E 164 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8184 (p0) REVERT: E 243 ARG cc_start: 0.8126 (ttt90) cc_final: 0.7778 (ttt180) REVERT: E 680 MET cc_start: 0.9157 (mtp) cc_final: 0.8718 (mtt) REVERT: F 31 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7271 (mptt) REVERT: F 164 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8170 (p0) REVERT: F 206 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: F 231 MET cc_start: 0.7835 (mmt) cc_final: 0.7124 (mmt) REVERT: F 680 MET cc_start: 0.9094 (mtp) cc_final: 0.8863 (mtp) REVERT: G 31 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7435 (mptt) REVERT: G 428 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7881 (mt) REVERT: G 580 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7404 (mmpt) REVERT: G 680 MET cc_start: 0.9132 (mtp) cc_final: 0.8694 (mtt) REVERT: H 31 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7286 (mptt) REVERT: H 164 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7966 (p0) REVERT: H 231 MET cc_start: 0.7714 (mmt) cc_final: 0.7056 (mmt) REVERT: H 680 MET cc_start: 0.9090 (mtp) cc_final: 0.8840 (mtp) outliers start: 63 outliers final: 21 residues processed: 455 average time/residue: 0.6824 time to fit residues: 366.2260 Evaluate side-chains 438 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 402 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 323 optimal weight: 4.9990 chunk 249 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 314 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 404 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 253 GLN B 114 GLN B 246 HIS C 114 GLN D 114 GLN D 206 GLN D 253 GLN E 114 GLN F 114 GLN F 206 GLN F 671 ASN G 114 GLN H 114 GLN H 246 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.183602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137196 restraints weight = 31927.648| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.08 r_work: 0.3155 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32984 Z= 0.146 Angle : 0.581 8.436 44736 Z= 0.280 Chirality : 0.044 0.212 5328 Planarity : 0.003 0.031 5648 Dihedral : 8.600 120.927 4544 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.44 % Allowed : 15.91 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.13), residues: 4112 helix: 1.43 (0.12), residues: 1856 sheet: 1.20 (0.20), residues: 576 loop : -0.91 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.011 0.001 TYR H 708 PHE 0.011 0.001 PHE H 542 TRP 0.005 0.001 TRP G 477 HIS 0.003 0.001 HIS D 710 Details of bonding type rmsd covalent geometry : bond 0.00326 (32984) covalent geometry : angle 0.58051 (44736) hydrogen bonds : bond 0.03532 ( 1664) hydrogen bonds : angle 4.30672 ( 4872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 415 time to evaluate : 1.062 Fit side-chains REVERT: A 31 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7361 (mptt) REVERT: A 164 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7941 (p0) REVERT: A 476 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7920 (mp0) REVERT: A 680 MET cc_start: 0.9044 (mtp) cc_final: 0.8583 (mtt) REVERT: B 31 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7212 (mptt) REVERT: B 214 SER cc_start: 0.8262 (t) cc_final: 0.7890 (p) REVERT: B 231 MET cc_start: 0.7655 (mmt) cc_final: 0.6813 (mmt) REVERT: B 235 THR cc_start: 0.8580 (p) cc_final: 0.8296 (t) REVERT: B 680 MET cc_start: 0.8997 (mtp) cc_final: 0.8733 (mtp) REVERT: C 31 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7417 (mptt) REVERT: C 476 GLU cc_start: 0.7850 (mp0) cc_final: 0.7408 (mp0) REVERT: C 680 MET cc_start: 0.9042 (mtp) cc_final: 0.8585 (mtt) REVERT: D 31 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7220 (mptt) REVERT: D 164 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8247 (p0) REVERT: D 231 MET cc_start: 0.7292 (mmt) cc_final: 0.6924 (mmt) REVERT: D 235 THR cc_start: 0.8603 (p) cc_final: 0.8308 (t) REVERT: D 680 MET cc_start: 0.9009 (mtp) cc_final: 0.8767 (mtp) REVERT: E 31 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7403 (mptt) REVERT: E 243 ARG cc_start: 0.8034 (ttt90) cc_final: 0.7705 (ttt180) REVERT: E 462 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: E 680 MET cc_start: 0.9063 (mtp) cc_final: 0.8610 (mtt) REVERT: F 31 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7216 (mptt) REVERT: F 93 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8471 (tt) REVERT: F 164 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8117 (p0) REVERT: F 206 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: F 231 MET cc_start: 0.7891 (mmt) cc_final: 0.7098 (mmt) REVERT: F 680 MET cc_start: 0.8995 (mtp) cc_final: 0.8746 (mtp) REVERT: G 31 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7406 (mptt) REVERT: G 428 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7906 (mt) REVERT: G 476 GLU cc_start: 0.7890 (mp0) cc_final: 0.7449 (mp0) REVERT: G 680 MET cc_start: 0.9042 (mtp) cc_final: 0.8587 (mtt) REVERT: H 31 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7220 (mptt) REVERT: H 164 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7922 (p0) REVERT: H 231 MET cc_start: 0.7742 (mmt) cc_final: 0.7040 (mmt) REVERT: H 680 MET cc_start: 0.8995 (mtp) cc_final: 0.8726 (mtp) outliers start: 51 outliers final: 20 residues processed: 447 average time/residue: 0.6838 time to fit residues: 359.3759 Evaluate side-chains 443 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 407 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 525 LYS Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 164 ASN Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 164 ASN Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 516 SER Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 253 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 351 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 186 optimal weight: 0.5980 chunk 415 optimal weight: 1.9990 chunk 204 optimal weight: 0.3980 chunk 102 optimal weight: 0.0870 chunk 410 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 253 GLN B 114 GLN B 246 HIS C 114 GLN D 114 GLN D 206 GLN E 114 GLN F 114 GLN G 114 GLN H 114 GLN H 246 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.185827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.142710 restraints weight = 32081.763| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.10 r_work: 0.3188 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32984 Z= 0.106 Angle : 0.547 7.962 44736 Z= 0.264 Chirality : 0.043 0.188 5328 Planarity : 0.003 0.032 5648 Dihedral : 8.204 112.266 4544 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.24 % Allowed : 16.08 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.13), residues: 4112 helix: 1.69 (0.12), residues: 1856 sheet: 1.26 (0.20), residues: 576 loop : -0.87 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 209 TYR 0.008 0.001 TYR A 255 PHE 0.013 0.001 PHE A 542 TRP 0.004 0.001 TRP B 631 HIS 0.003 0.001 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00231 (32984) covalent geometry : angle 0.54725 (44736) hydrogen bonds : bond 0.03144 ( 1664) hydrogen bonds : angle 4.16276 ( 4872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14559.65 seconds wall clock time: 247 minutes 26.43 seconds (14846.43 seconds total)