Starting phenix.real_space_refine on Fri Mar 6 15:08:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nhs_12339/03_2026/7nhs_12339.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nhs_12339/03_2026/7nhs_12339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nhs_12339/03_2026/7nhs_12339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nhs_12339/03_2026/7nhs_12339.map" model { file = "/net/cci-nas-00/data/ceres_data/7nhs_12339/03_2026/7nhs_12339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nhs_12339/03_2026/7nhs_12339.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 20672 2.51 5 N 5416 2.21 5 O 6048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 32240 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 4.41, per 1000 atoms: 0.14 Number of scatterers: 32240 At special positions: 0 Unit cell: (159.168, 159.997, 137.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 6048 8.00 N 5416 7.00 C 20672 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: 2.35 Conformation dependent library (CDL) restraints added in 1.0 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 47.3% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 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: 3.553A 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: 3.747A 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: 4.186A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.873A 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 522 removed outlier: 3.618A pdb=" N MET A 522 " --> pdb=" O HIS A 518 " (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 588 Processing helix chain 'A' and resid 591 through 595 Processing helix chain 'A' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.519A 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 686 Processing helix chain 'A' and resid 701 through 708 removed outlier: 3.659A 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: 3.553A 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: 3.748A 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: 4.185A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.874A 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 522 removed outlier: 3.618A pdb=" N MET B 522 " --> pdb=" O HIS B 518 " (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 588 Processing helix chain 'B' and resid 591 through 595 Processing helix chain 'B' and resid 615 through 621 removed outlier: 3.524A pdb=" N MET B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.519A 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 686 Processing helix chain 'B' and resid 701 through 708 removed outlier: 3.660A 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: 3.553A 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: 3.749A 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: 4.185A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.873A 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 522 removed outlier: 3.618A pdb=" N MET C 522 " --> pdb=" O HIS C 518 " (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 588 Processing helix chain 'C' and resid 591 through 595 Processing helix chain 'C' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.519A 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 686 Processing helix chain 'C' and resid 701 through 708 removed outlier: 3.660A 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: 3.553A 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: 3.748A 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: 4.185A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.873A 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 522 removed outlier: 3.618A pdb=" N MET D 522 " --> pdb=" O HIS D 518 " (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 588 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'D' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET D 621 " --> pdb=" O ALA D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.519A 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 686 Processing helix chain 'D' and resid 701 through 708 removed outlier: 3.660A 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: 3.553A 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: 3.747A 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: 4.186A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.873A 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 522 removed outlier: 3.617A pdb=" N MET E 522 " --> pdb=" O HIS E 518 " (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 588 Processing helix chain 'E' and resid 591 through 595 Processing helix chain 'E' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET E 621 " --> pdb=" O ALA E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.366A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.519A 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 686 Processing helix chain 'E' and resid 701 through 708 removed outlier: 3.660A 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: 3.554A 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: 3.748A 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: 4.186A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.873A 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 522 removed outlier: 3.618A pdb=" N MET F 522 " --> pdb=" O HIS F 518 " (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 588 Processing helix chain 'F' and resid 591 through 595 Processing helix chain 'F' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.520A 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 686 Processing helix chain 'F' and resid 701 through 708 removed outlier: 3.660A 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: 3.554A 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: 3.748A 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: 4.185A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.872A 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 522 removed outlier: 3.618A pdb=" N MET G 522 " --> pdb=" O HIS G 518 " (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 588 Processing helix chain 'G' and resid 591 through 595 Processing helix chain 'G' and resid 615 through 621 removed outlier: 3.522A pdb=" N MET G 621 " --> pdb=" O ALA G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.519A 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 686 Processing helix chain 'G' and resid 701 through 708 removed outlier: 3.660A 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: 3.553A 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: 3.747A 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: 4.185A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.873A 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 522 removed outlier: 3.618A pdb=" N MET H 522 " --> pdb=" O HIS H 518 " (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 588 Processing helix chain 'H' and resid 591 through 595 Processing helix chain 'H' and resid 615 through 621 removed outlier: 3.523A pdb=" N MET H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) Processing helix chain 'H' and resid 622 through 636 removed outlier: 4.367A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.519A 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 686 Processing helix chain 'H' and resid 701 through 708 removed outlier: 3.660A 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: 6.874A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.379A 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: 7.398A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS A 693 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 470 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 558 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE A 607 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.873A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.378A 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: 7.398A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS B 693 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 470 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 558 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE B 607 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE B 560 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 223 removed outlier: 8.447A pdb=" N ILE C 54 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ASP C 418 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.379A 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: 7.398A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 6.591A pdb=" N CYS C 693 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA C 470 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 558 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE C 607 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE C 560 " --> pdb=" O ILE C 607 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.378A 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: 7.399A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS D 693 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA D 470 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL D 558 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE D 607 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE D 560 " --> pdb=" O ILE D 607 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.378A 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: 7.399A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS E 693 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA E 470 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.378A 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: 7.398A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 6.592A pdb=" N CYS F 693 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA F 470 " --> pdb=" O CYS F 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 223 removed outlier: 6.873A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.378A 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: 7.399A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 6.591A pdb=" N CYS G 693 " --> pdb=" O VAL G 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA G 470 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY G 533 " --> pdb=" O THR G 643 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 223 removed outlier: 6.874A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.378A 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: 7.399A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 6.591A pdb=" N CYS H 693 " --> pdb=" O VAL H 468 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA H 470 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL H 558 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE H 607 " --> pdb=" O VAL H 558 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE H 560 " --> pdb=" O ILE H 607 " (cutoff:3.500A) 1704 hydrogen bonds defined for protein. 4995 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: 6.51 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10536 1.34 - 1.46: 6209 1.46 - 1.58: 15815 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 32752 Sorted by residual: bond pdb=" C PHE A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C PHE B 117 " pdb=" N PRO B 118 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C PHE D 117 " pdb=" N PRO D 118 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 bond pdb=" C PHE C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 bond pdb=" C PHE G 117 " pdb=" N PRO G 118 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.05e+00 ... (remaining 32747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 43786 1.49 - 2.97: 427 2.97 - 4.46: 123 4.46 - 5.95: 24 5.95 - 7.43: 16 Bond angle restraints: 44376 Sorted by residual: angle pdb=" N ILE D 260 " pdb=" CA ILE D 260 " pdb=" C ILE D 260 " ideal model delta sigma weight residual 112.80 109.37 3.43 1.15e+00 7.56e-01 8.92e+00 angle pdb=" N ILE A 260 " pdb=" CA ILE A 260 " pdb=" C ILE A 260 " ideal model delta sigma weight residual 112.80 109.37 3.43 1.15e+00 7.56e-01 8.88e+00 angle pdb=" N ILE E 260 " pdb=" CA ILE E 260 " pdb=" C ILE E 260 " ideal model delta sigma weight residual 112.80 109.38 3.42 1.15e+00 7.56e-01 8.84e+00 angle pdb=" N ILE B 260 " pdb=" CA ILE B 260 " pdb=" C ILE B 260 " ideal model delta sigma weight residual 112.80 109.38 3.42 1.15e+00 7.56e-01 8.82e+00 angle pdb=" N ILE F 260 " pdb=" CA ILE F 260 " pdb=" C ILE F 260 " ideal model delta sigma weight residual 112.80 109.38 3.42 1.15e+00 7.56e-01 8.82e+00 ... (remaining 44371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 19216 17.62 - 35.25: 520 35.25 - 52.87: 136 52.87 - 70.49: 32 70.49 - 88.12: 8 Dihedral angle restraints: 19912 sinusoidal: 7912 harmonic: 12000 Sorted by residual: dihedral pdb=" CA HIS G 576 " pdb=" C HIS G 576 " pdb=" N LYS G 577 " pdb=" CA LYS G 577 " ideal model delta harmonic sigma weight residual 180.00 154.12 25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA HIS A 576 " pdb=" C HIS A 576 " pdb=" N LYS A 577 " pdb=" CA LYS A 577 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA HIS H 576 " pdb=" C HIS H 576 " pdb=" N LYS H 577 " pdb=" CA LYS H 577 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 19909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3274 0.027 - 0.055: 1210 0.055 - 0.082: 355 0.082 - 0.110: 324 0.110 - 0.137: 133 Chirality restraints: 5296 Sorted by residual: chirality pdb=" CA ILE C 167 " pdb=" N ILE C 167 " pdb=" C ILE C 167 " pdb=" CB ILE C 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE E 167 " pdb=" N ILE E 167 " pdb=" C ILE E 167 " pdb=" CB ILE E 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE H 167 " pdb=" N ILE H 167 " pdb=" C ILE H 167 " pdb=" CB ILE H 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 5293 not shown) Planarity restraints: 5640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 535 " 0.013 5.00e-02 4.00e+02 1.97e-02 6.22e-01 pdb=" N PRO E 536 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO E 536 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO E 536 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 535 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.16e-01 pdb=" N PRO F 536 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO F 536 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO F 536 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 535 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.15e-01 pdb=" N PRO C 536 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 536 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 536 " 0.011 5.00e-02 4.00e+02 ... (remaining 5637 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8643 2.81 - 3.33: 31251 3.33 - 3.85: 53955 3.85 - 4.38: 65462 4.38 - 4.90: 107238 Nonbonded interactions: 266549 Sorted by model distance: nonbonded pdb=" O ILE B 551 " pdb=" OG1 THR B 554 " model vdw 2.284 3.040 nonbonded pdb=" O ILE G 551 " pdb=" OG1 THR G 554 " model vdw 2.284 3.040 nonbonded pdb=" O ILE D 551 " pdb=" OG1 THR D 554 " model vdw 2.284 3.040 nonbonded pdb=" O ILE H 551 " pdb=" OG1 THR H 554 " model vdw 2.284 3.040 nonbonded pdb=" O ILE C 551 " pdb=" OG1 THR C 554 " model vdw 2.285 3.040 ... (remaining 266544 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: 0.09 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.180 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32752 Z= 0.093 Angle : 0.479 7.433 44376 Z= 0.267 Chirality : 0.041 0.137 5296 Planarity : 0.002 0.020 5640 Dihedral : 9.506 88.117 12200 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -2.35 (0.11), residues: 4112 helix: -1.53 (0.09), residues: 1864 sheet: -0.15 (0.18), residues: 696 loop : -2.10 (0.12), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 624 TYR 0.004 0.001 TYR A 255 PHE 0.007 0.001 PHE D 117 TRP 0.003 0.001 TRP D 631 HIS 0.002 0.000 HIS G 571 Details of bonding type rmsd covalent geometry : bond 0.00181 (32752) covalent geometry : angle 0.47934 (44376) hydrogen bonds : bond 0.21130 ( 1704) hydrogen bonds : angle 7.75954 ( 4995) *********************** 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 661 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 661 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 MET cc_start: 0.8745 (mtp) cc_final: 0.8534 (mtm) REVERT: D 621 MET cc_start: 0.8616 (mtp) cc_final: 0.8204 (mtp) REVERT: F 621 MET cc_start: 0.8723 (mtp) cc_final: 0.8324 (mtp) REVERT: H 621 MET cc_start: 0.8581 (mtp) cc_final: 0.8243 (mtp) outliers start: 0 outliers final: 3 residues processed: 661 average time/residue: 0.6318 time to fit residues: 497.0388 Evaluate side-chains 442 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 439 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain D residue 432 ILE Chi-restraints excluded: chain G residue 432 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 0.0270 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- 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 206 GLN A 254 ASN A 571 HIS A 622 HIS A 671 ASN A 710 HIS B 29 HIS B 173 GLN B 206 GLN B 254 ASN B 571 HIS B 671 ASN B 710 HIS C 29 HIS C 173 GLN C 206 GLN C 254 ASN C 571 HIS C 622 HIS C 671 ASN C 710 HIS D 29 HIS D 173 GLN D 254 ASN D 571 HIS D 611 GLN D 671 ASN D 710 HIS E 29 HIS E 173 GLN E 254 ASN E 571 HIS E 611 GLN E 622 HIS E 671 ASN E 710 HIS F 29 HIS F 173 GLN F 206 GLN F 254 ASN F 571 HIS F 671 ASN F 710 HIS G 29 HIS G 173 GLN G 206 GLN G 254 ASN G 571 HIS G 671 ASN G 710 HIS H 29 HIS H 173 GLN H 206 GLN H 254 ASN H 571 HIS H 671 ASN H 710 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.196329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167440 restraints weight = 29467.364| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 0.83 r_work: 0.3577 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work: 0.3334 rms_B_bonded: 4.07 restraints_weight: 0.1250 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32752 Z= 0.152 Angle : 0.580 8.563 44376 Z= 0.303 Chirality : 0.045 0.149 5296 Planarity : 0.004 0.052 5640 Dihedral : 4.418 28.493 4462 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.06 % Allowed : 8.05 % Favored : 89.89 % 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 (0.12), residues: 4112 helix: 0.70 (0.11), residues: 1904 sheet: 0.39 (0.18), residues: 704 loop : -1.42 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 243 TYR 0.014 0.001 TYR E 718 PHE 0.014 0.002 PHE G 542 TRP 0.007 0.001 TRP F 631 HIS 0.007 0.001 HIS C 622 Details of bonding type rmsd covalent geometry : bond 0.00321 (32752) covalent geometry : angle 0.58025 (44376) hydrogen bonds : bond 0.04626 ( 1704) hydrogen bonds : angle 4.91203 ( 4995) *********************** 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 562 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 489 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 447 PHE cc_start: 0.7648 (m-10) cc_final: 0.7344 (t80) REVERT: A 521 MET cc_start: 0.8457 (mtp) cc_final: 0.8198 (mtp) REVERT: A 684 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: B 443 VAL cc_start: 0.8001 (m) cc_final: 0.7744 (t) REVERT: B 447 PHE cc_start: 0.7759 (m-10) cc_final: 0.7437 (t80) REVERT: B 684 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: C 443 VAL cc_start: 0.8020 (m) cc_final: 0.7776 (t) REVERT: C 447 PHE cc_start: 0.7614 (m-10) cc_final: 0.7302 (t80) REVERT: C 598 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7161 (mtpp) REVERT: C 684 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: D 447 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7160 (t80) REVERT: D 598 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6735 (tptp) REVERT: D 621 MET cc_start: 0.9056 (mtp) cc_final: 0.8774 (mtp) REVERT: E 447 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7008 (t80) REVERT: E 521 MET cc_start: 0.8328 (mtp) cc_final: 0.8064 (mtp) REVERT: F 447 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7123 (t80) REVERT: F 598 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6757 (tptp) REVERT: F 621 MET cc_start: 0.9075 (mtp) cc_final: 0.8792 (mtp) REVERT: G 447 PHE cc_start: 0.7634 (m-10) cc_final: 0.7318 (t80) REVERT: G 521 MET cc_start: 0.8435 (mtp) cc_final: 0.8168 (mtp) REVERT: G 598 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7199 (mtpp) REVERT: H 447 PHE cc_start: 0.7729 (m-10) cc_final: 0.7363 (t80) REVERT: H 621 MET cc_start: 0.9072 (mtp) cc_final: 0.8809 (mtp) REVERT: H 708 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.6597 (m-80) outliers start: 73 outliers final: 12 residues processed: 535 average time/residue: 0.5937 time to fit residues: 379.8318 Evaluate side-chains 428 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 405 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 598 LYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 708 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 332 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 324 optimal weight: 5.9990 chunk 152 optimal weight: 0.0970 chunk 196 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 315 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN H 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.197811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.169761 restraints weight = 29723.319| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 0.85 r_work: 0.3597 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work: 0.3357 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32752 Z= 0.108 Angle : 0.525 7.231 44376 Z= 0.271 Chirality : 0.043 0.186 5296 Planarity : 0.003 0.045 5640 Dihedral : 4.155 28.307 4460 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.03 % Allowed : 9.43 % Favored : 88.54 % 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: 0.65 (0.13), residues: 4112 helix: 1.58 (0.12), residues: 1904 sheet: 0.74 (0.18), residues: 704 loop : -1.23 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 707 TYR 0.009 0.001 TYR D 606 PHE 0.013 0.001 PHE G 542 TRP 0.009 0.001 TRP D 631 HIS 0.002 0.000 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00227 (32752) covalent geometry : angle 0.52521 (44376) hydrogen bonds : bond 0.04016 ( 1704) hydrogen bonds : angle 4.47687 ( 4995) *********************** 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 520 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 448 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8460 (tm) REVERT: A 447 PHE cc_start: 0.7613 (m-10) cc_final: 0.7342 (t80) REVERT: A 521 MET cc_start: 0.8491 (mtp) cc_final: 0.8278 (mtp) REVERT: A 684 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: B 447 PHE cc_start: 0.7743 (m-10) cc_final: 0.7422 (t80) REVERT: B 573 MET cc_start: 0.7653 (ttp) cc_final: 0.7403 (ttm) REVERT: C 447 PHE cc_start: 0.7614 (m-10) cc_final: 0.7359 (t80) REVERT: C 521 MET cc_start: 0.8612 (mtp) cc_final: 0.8250 (mtp) REVERT: D 447 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7067 (t80) REVERT: D 598 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6747 (tptp) REVERT: D 621 MET cc_start: 0.9066 (mtp) cc_final: 0.8755 (mtp) REVERT: E 447 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7027 (t80) REVERT: E 521 MET cc_start: 0.8417 (mtp) cc_final: 0.8180 (mtp) REVERT: E 684 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: F 447 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7087 (t80) REVERT: F 621 MET cc_start: 0.9061 (mtp) cc_final: 0.8748 (mtp) REVERT: G 447 PHE cc_start: 0.7596 (m-10) cc_final: 0.7313 (t80) REVERT: G 521 MET cc_start: 0.8478 (mtp) cc_final: 0.8207 (mtp) REVERT: H 32 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8428 (tm) REVERT: H 447 PHE cc_start: 0.7741 (m-10) cc_final: 0.7385 (t80) REVERT: H 598 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6860 (tptp) REVERT: H 621 MET cc_start: 0.9050 (mtp) cc_final: 0.8755 (mtp) REVERT: H 708 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.6540 (m-80) outliers start: 72 outliers final: 11 residues processed: 492 average time/residue: 0.5953 time to fit residues: 351.2544 Evaluate side-chains 417 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 396 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 218 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 606 TYR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 598 LYS Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 708 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 105 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 359 optimal weight: 1.9990 chunk 384 optimal weight: 0.6980 chunk 217 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 216 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 204 optimal weight: 0.0870 chunk 381 optimal weight: 5.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.194643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.165215 restraints weight = 29172.038| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 0.82 r_work: 0.3552 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work: 0.3300 rms_B_bonded: 4.13 restraints_weight: 0.1250 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32752 Z= 0.156 Angle : 0.575 7.636 44376 Z= 0.299 Chirality : 0.045 0.177 5296 Planarity : 0.004 0.035 5640 Dihedral : 4.426 28.096 4458 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.08 % Allowed : 9.88 % Favored : 88.03 % 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: 0.75 (0.13), residues: 4112 helix: 1.58 (0.12), residues: 1920 sheet: 0.84 (0.18), residues: 720 loop : -1.15 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 514 TYR 0.013 0.002 TYR D 718 PHE 0.018 0.002 PHE G 542 TRP 0.011 0.001 TRP D 631 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00343 (32752) covalent geometry : angle 0.57471 (44376) hydrogen bonds : bond 0.04442 ( 1704) hydrogen bonds : angle 4.59978 ( 4995) *********************** 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 503 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 429 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (tm) REVERT: A 447 PHE cc_start: 0.7676 (m-10) cc_final: 0.7363 (t80) REVERT: A 684 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: B 447 PHE cc_start: 0.7771 (m-10) cc_final: 0.7410 (t80) REVERT: C 447 PHE cc_start: 0.7674 (m-10) cc_final: 0.7336 (t80) REVERT: C 684 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: D 447 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7161 (t80) REVERT: D 598 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6882 (tptp) REVERT: D 621 MET cc_start: 0.9086 (mtp) cc_final: 0.8804 (mtp) REVERT: D 708 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: E 447 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7123 (t80) REVERT: F 447 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7156 (t80) REVERT: F 598 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6820 (tptp) REVERT: F 621 MET cc_start: 0.9097 (mtp) cc_final: 0.8818 (mtp) REVERT: F 708 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: G 32 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8450 (tm) REVERT: G 447 PHE cc_start: 0.7682 (m-10) cc_final: 0.7372 (t80) REVERT: H 447 PHE cc_start: 0.7818 (m-10) cc_final: 0.7420 (t80) REVERT: H 621 MET cc_start: 0.9103 (mtp) cc_final: 0.8816 (mtp) REVERT: H 708 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.6335 (m-80) outliers start: 74 outliers final: 16 residues processed: 480 average time/residue: 0.5676 time to fit residues: 328.4743 Evaluate side-chains 434 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 406 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 598 LYS Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 708 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 708 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 177 optimal weight: 5.9990 chunk 326 optimal weight: 20.0000 chunk 216 optimal weight: 2.9990 chunk 293 optimal weight: 0.2980 chunk 317 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 363 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.195119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.166438 restraints weight = 29262.674| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 0.82 r_work: 0.3556 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work: 0.3313 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32752 Z= 0.141 Angle : 0.559 6.983 44376 Z= 0.291 Chirality : 0.044 0.174 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.343 28.134 4456 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.17 % Allowed : 11.15 % Favored : 86.68 % 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: 0.85 (0.13), residues: 4112 helix: 1.65 (0.12), residues: 1920 sheet: 0.93 (0.18), residues: 720 loop : -1.10 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 514 TYR 0.011 0.001 TYR D 606 PHE 0.016 0.002 PHE H 542 TRP 0.013 0.001 TRP D 631 HIS 0.003 0.001 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00312 (32752) covalent geometry : angle 0.55936 (44376) hydrogen bonds : bond 0.04208 ( 1704) hydrogen bonds : angle 4.48292 ( 4995) *********************** 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 501 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 424 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7922 (tp) cc_final: 0.7694 (tp) REVERT: A 447 PHE cc_start: 0.7726 (m-10) cc_final: 0.7421 (t80) REVERT: A 684 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: B 447 PHE cc_start: 0.7794 (m-10) cc_final: 0.7496 (t80) REVERT: B 708 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: C 19 LEU cc_start: 0.7909 (tp) cc_final: 0.7684 (tp) REVERT: C 447 PHE cc_start: 0.7690 (m-10) cc_final: 0.7431 (t80) REVERT: C 684 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: D 439 ILE cc_start: 0.8444 (mt) cc_final: 0.8241 (mp) REVERT: D 447 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7178 (t80) REVERT: D 598 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6934 (tptp) REVERT: D 621 MET cc_start: 0.9098 (mtp) cc_final: 0.8822 (mtp) REVERT: D 708 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: E 19 LEU cc_start: 0.7911 (tp) cc_final: 0.7662 (tp) REVERT: E 410 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6927 (ttt180) REVERT: E 447 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7123 (t80) REVERT: E 684 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: F 447 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7141 (t80) REVERT: F 598 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6892 (tptp) REVERT: F 621 MET cc_start: 0.9094 (mtp) cc_final: 0.8825 (mtp) REVERT: F 708 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: G 19 LEU cc_start: 0.7905 (tp) cc_final: 0.7665 (tp) REVERT: G 32 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8441 (tm) REVERT: G 447 PHE cc_start: 0.7665 (m-10) cc_final: 0.7392 (t80) REVERT: G 598 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7250 (mtpp) REVERT: H 447 PHE cc_start: 0.7790 (m-10) cc_final: 0.7476 (t80) REVERT: H 598 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6880 (tptp) REVERT: H 621 MET cc_start: 0.9106 (mtp) cc_final: 0.8834 (mtp) outliers start: 77 outliers final: 25 residues processed: 475 average time/residue: 0.5874 time to fit residues: 335.3711 Evaluate side-chains 427 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 387 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 708 TYR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 598 LYS Chi-restraints excluded: chain F residue 606 TYR Chi-restraints excluded: chain F residue 708 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 598 LYS Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 642 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 43 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 345 optimal weight: 0.6980 chunk 251 optimal weight: 0.7980 chunk 351 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN B 467 ASN D 467 ASN F 467 ASN H 467 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.195568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.167079 restraints weight = 29225.274| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 0.79 r_work: 0.3567 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work: 0.3319 rms_B_bonded: 4.12 restraints_weight: 0.1250 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32752 Z= 0.132 Angle : 0.550 8.919 44376 Z= 0.286 Chirality : 0.044 0.172 5296 Planarity : 0.003 0.032 5640 Dihedral : 4.288 27.879 4456 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.70 % Allowed : 10.78 % Favored : 86.51 % 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: 1.74 (0.12), residues: 1904 sheet: 0.99 (0.18), residues: 720 loop : -1.11 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 243 TYR 0.013 0.001 TYR H 708 PHE 0.016 0.001 PHE H 542 TRP 0.017 0.001 TRP D 631 HIS 0.002 0.000 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00290 (32752) covalent geometry : angle 0.55011 (44376) hydrogen bonds : bond 0.04097 ( 1704) hydrogen bonds : angle 4.40200 ( 4995) *********************** 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 508 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 412 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8006 (tp) cc_final: 0.7771 (tp) REVERT: A 410 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6934 (ttt180) REVERT: A 447 PHE cc_start: 0.7719 (m-10) cc_final: 0.7373 (t80) REVERT: A 684 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: B 447 PHE cc_start: 0.7794 (m-10) cc_final: 0.7465 (t80) REVERT: C 19 LEU cc_start: 0.8030 (tp) cc_final: 0.7789 (tp) REVERT: C 410 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7023 (ttt180) REVERT: C 447 PHE cc_start: 0.7669 (m-10) cc_final: 0.7355 (t80) REVERT: C 521 MET cc_start: 0.8697 (mtp) cc_final: 0.8421 (mtp) REVERT: C 684 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: D 439 ILE cc_start: 0.8409 (mt) cc_final: 0.8198 (mp) REVERT: D 447 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7145 (t80) REVERT: D 598 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6861 (tptp) REVERT: D 621 MET cc_start: 0.9080 (mtp) cc_final: 0.8806 (mtp) REVERT: D 708 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: E 19 LEU cc_start: 0.7904 (tp) cc_final: 0.7655 (tp) REVERT: E 410 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6928 (ttt180) REVERT: E 447 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7079 (t80) REVERT: E 684 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: F 447 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7106 (t80) REVERT: F 598 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6851 (tptp) REVERT: F 621 MET cc_start: 0.9083 (mtp) cc_final: 0.8824 (mtp) REVERT: G 19 LEU cc_start: 0.7994 (tp) cc_final: 0.7744 (tp) REVERT: G 32 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8468 (tm) REVERT: G 447 PHE cc_start: 0.7688 (m-10) cc_final: 0.7368 (t80) REVERT: G 598 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7241 (mtpp) REVERT: G 684 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: H 447 PHE cc_start: 0.7757 (m-10) cc_final: 0.7421 (t80) REVERT: H 598 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.6867 (tptp) REVERT: H 621 MET cc_start: 0.9100 (mtp) cc_final: 0.8839 (mtp) outliers start: 96 outliers final: 24 residues processed: 470 average time/residue: 0.5565 time to fit residues: 316.9419 Evaluate side-chains 441 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 401 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 410 ARG Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 708 TYR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 598 LYS Chi-restraints excluded: chain F residue 606 TYR Chi-restraints excluded: chain F residue 708 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 598 LYS Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 642 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 402 optimal weight: 5.9990 chunk 374 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 408 optimal weight: 0.1980 chunk 195 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 chunk 343 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN B 467 ASN C 467 ASN D 467 ASN E 467 ASN F 467 ASN G 467 ASN H 467 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.195158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166432 restraints weight = 29342.479| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 0.82 r_work: 0.3559 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work: 0.3307 rms_B_bonded: 4.12 restraints_weight: 0.1250 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32752 Z= 0.144 Angle : 0.570 8.513 44376 Z= 0.297 Chirality : 0.045 0.170 5296 Planarity : 0.003 0.031 5640 Dihedral : 4.330 27.982 4456 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.31 % Allowed : 11.37 % Favored : 86.32 % 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: 0.93 (0.13), residues: 4112 helix: 1.71 (0.12), residues: 1904 sheet: 1.03 (0.18), residues: 720 loop : -1.06 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 243 TYR 0.014 0.002 TYR H 708 PHE 0.017 0.002 PHE H 542 TRP 0.021 0.001 TRP D 631 HIS 0.002 0.000 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00320 (32752) covalent geometry : angle 0.57037 (44376) hydrogen bonds : bond 0.04227 ( 1704) hydrogen bonds : angle 4.41801 ( 4995) *********************** 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 484 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 402 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8007 (tp) cc_final: 0.7767 (tp) REVERT: A 32 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8336 (tm) REVERT: A 410 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6969 (ttt180) REVERT: A 447 PHE cc_start: 0.7723 (m-10) cc_final: 0.7363 (t80) REVERT: A 684 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: B 447 PHE cc_start: 0.7789 (m-10) cc_final: 0.7438 (t80) REVERT: C 19 LEU cc_start: 0.8019 (tp) cc_final: 0.7783 (tp) REVERT: C 410 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7081 (ttt180) REVERT: C 447 PHE cc_start: 0.7676 (m-10) cc_final: 0.7349 (t80) REVERT: C 521 MET cc_start: 0.8702 (mtp) cc_final: 0.8412 (mtp) REVERT: C 684 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: D 447 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7112 (t80) REVERT: D 598 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6868 (tptp) REVERT: D 621 MET cc_start: 0.9097 (mtp) cc_final: 0.8824 (mtp) REVERT: E 19 LEU cc_start: 0.7898 (tp) cc_final: 0.7644 (tp) REVERT: E 447 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7057 (t80) REVERT: E 598 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7205 (mtpp) REVERT: E 684 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: F 447 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7092 (t80) REVERT: F 598 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6803 (tptp) REVERT: F 621 MET cc_start: 0.9094 (mtp) cc_final: 0.8833 (mtp) REVERT: G 19 LEU cc_start: 0.7998 (tp) cc_final: 0.7754 (tp) REVERT: G 32 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8451 (tm) REVERT: G 231 MET cc_start: 0.7783 (mmt) cc_final: 0.7577 (mmt) REVERT: G 447 PHE cc_start: 0.7724 (m-10) cc_final: 0.7361 (t80) REVERT: G 598 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7234 (mtpp) REVERT: G 684 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: H 38 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7918 (m) REVERT: H 447 PHE cc_start: 0.7787 (m-10) cc_final: 0.7419 (t80) REVERT: H 573 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7369 (ptm) REVERT: H 598 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6886 (tptp) REVERT: H 621 MET cc_start: 0.9109 (mtp) cc_final: 0.8839 (mtp) outliers start: 82 outliers final: 28 residues processed: 452 average time/residue: 0.5869 time to fit residues: 320.0257 Evaluate side-chains 444 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 398 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 606 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 708 TYR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 598 LYS Chi-restraints excluded: chain F residue 606 TYR Chi-restraints excluded: chain F residue 708 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 573 MET Chi-restraints excluded: chain H residue 598 LYS Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 642 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 280 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 379 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 385 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN B 467 ASN C 467 ASN D 467 ASN E 467 ASN F 467 ASN G 467 ASN H 467 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.194101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164970 restraints weight = 29187.236| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 0.80 r_work: 0.3548 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work: 0.3303 rms_B_bonded: 3.92 restraints_weight: 0.1250 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32752 Z= 0.168 Angle : 0.599 8.673 44376 Z= 0.312 Chirality : 0.046 0.175 5296 Planarity : 0.004 0.031 5640 Dihedral : 4.481 28.086 4456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.89 % Allowed : 12.30 % Favored : 85.81 % 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: 0.84 (0.13), residues: 4112 helix: 1.58 (0.12), residues: 1904 sheet: 1.08 (0.18), residues: 712 loop : -1.07 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 243 TYR 0.016 0.002 TYR H 708 PHE 0.018 0.002 PHE H 542 TRP 0.023 0.001 TRP F 631 HIS 0.003 0.001 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00377 (32752) covalent geometry : angle 0.59911 (44376) hydrogen bonds : bond 0.04500 ( 1704) hydrogen bonds : angle 4.54576 ( 4995) *********************** 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 473 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 406 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.8034 (tp) cc_final: 0.7784 (tp) REVERT: A 32 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8385 (tm) REVERT: A 410 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.7015 (ttt180) REVERT: A 447 PHE cc_start: 0.7715 (m-10) cc_final: 0.7380 (t80) REVERT: A 684 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: B 32 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8472 (tm) REVERT: B 447 PHE cc_start: 0.7784 (m-10) cc_final: 0.7465 (t80) REVERT: C 19 LEU cc_start: 0.8053 (tp) cc_final: 0.7808 (tp) REVERT: C 447 PHE cc_start: 0.7673 (m-10) cc_final: 0.7366 (t80) REVERT: C 684 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: D 447 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7090 (t80) REVERT: D 598 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6936 (tptp) REVERT: D 621 MET cc_start: 0.9100 (mtp) cc_final: 0.8835 (mtp) REVERT: E 19 LEU cc_start: 0.7932 (tp) cc_final: 0.7676 (tp) REVERT: E 447 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7136 (t80) REVERT: E 598 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7367 (mtpp) REVERT: E 684 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: F 447 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7051 (t80) REVERT: F 522 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7022 (mmm) REVERT: F 621 MET cc_start: 0.9100 (mtp) cc_final: 0.8845 (mtp) REVERT: G 19 LEU cc_start: 0.7923 (tp) cc_final: 0.7673 (tp) REVERT: G 32 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8432 (tm) REVERT: G 447 PHE cc_start: 0.7678 (m-10) cc_final: 0.7379 (t80) REVERT: G 598 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7371 (mtpp) REVERT: G 684 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: H 38 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7902 (m) REVERT: H 447 PHE cc_start: 0.7785 (m-10) cc_final: 0.7423 (t80) REVERT: H 598 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.6909 (tptp) REVERT: H 621 MET cc_start: 0.9107 (mtp) cc_final: 0.8844 (mtp) REVERT: H 708 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.6352 (m-80) outliers start: 67 outliers final: 22 residues processed: 446 average time/residue: 0.5544 time to fit residues: 300.3876 Evaluate side-chains 438 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 398 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 410 ARG Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 708 TYR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 598 LYS Chi-restraints excluded: chain H residue 642 ASP Chi-restraints excluded: chain H residue 708 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 192 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 363 optimal weight: 0.9990 chunk 270 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN B 467 ASN C 467 ASN D 467 ASN ** D 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN ** E 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 ASN G 467 ASN H 164 ASN H 467 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.194150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165550 restraints weight = 28989.441| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 0.84 r_work: 0.3542 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work: 0.3285 rms_B_bonded: 4.42 restraints_weight: 0.1250 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32752 Z= 0.169 Angle : 0.602 8.465 44376 Z= 0.313 Chirality : 0.046 0.173 5296 Planarity : 0.004 0.031 5640 Dihedral : 4.498 28.334 4456 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.60 % Allowed : 12.78 % Favored : 85.61 % 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: 0.83 (0.13), residues: 4112 helix: 1.52 (0.12), residues: 1920 sheet: 1.04 (0.18), residues: 712 loop : -1.00 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 243 TYR 0.017 0.002 TYR H 708 PHE 0.018 0.002 PHE H 542 TRP 0.022 0.001 TRP F 631 HIS 0.003 0.001 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00378 (32752) covalent geometry : angle 0.60160 (44376) hydrogen bonds : bond 0.04461 ( 1704) hydrogen bonds : angle 4.54775 ( 4995) *********************** 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 466 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 409 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7917 (tp) cc_final: 0.7677 (tp) REVERT: A 32 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8420 (tm) REVERT: A 447 PHE cc_start: 0.7728 (m-10) cc_final: 0.7452 (t80) REVERT: A 684 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 447 PHE cc_start: 0.7809 (m-10) cc_final: 0.7488 (t80) REVERT: C 19 LEU cc_start: 0.8065 (tp) cc_final: 0.7824 (tp) REVERT: C 447 PHE cc_start: 0.7688 (m-10) cc_final: 0.7363 (t80) REVERT: C 598 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7395 (mtpp) REVERT: C 684 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: D 447 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7159 (t80) REVERT: D 598 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6992 (tptp) REVERT: D 621 MET cc_start: 0.9112 (mtp) cc_final: 0.8846 (mtp) REVERT: E 19 LEU cc_start: 0.7946 (tp) cc_final: 0.7699 (tp) REVERT: E 447 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7129 (t80) REVERT: E 598 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7447 (mtpp) REVERT: E 684 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: F 447 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7140 (t80) REVERT: F 522 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7113 (mmm) REVERT: F 621 MET cc_start: 0.9102 (mtp) cc_final: 0.8846 (mtp) REVERT: G 19 LEU cc_start: 0.7918 (tp) cc_final: 0.7674 (tp) REVERT: G 32 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8463 (tm) REVERT: G 447 PHE cc_start: 0.7731 (m-10) cc_final: 0.7406 (t80) REVERT: G 598 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7444 (mtpp) REVERT: G 684 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: H 38 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7922 (m) REVERT: H 447 PHE cc_start: 0.7811 (m-10) cc_final: 0.7484 (t80) REVERT: H 598 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6958 (tptp) REVERT: H 621 MET cc_start: 0.9125 (mtp) cc_final: 0.8865 (mtp) REVERT: H 708 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.6373 (m-80) outliers start: 57 outliers final: 26 residues processed: 447 average time/residue: 0.5671 time to fit residues: 307.1560 Evaluate side-chains 439 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 396 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 42 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 517 LEU Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 708 TYR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 598 LYS Chi-restraints excluded: chain H residue 642 ASP Chi-restraints excluded: chain H residue 708 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 92 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 405 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 chunk 285 optimal weight: 0.5980 chunk 120 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN B 467 ASN C 467 ASN D 467 ASN E 467 ASN F 467 ASN G 467 ASN H 164 ASN H 467 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.196307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.167762 restraints weight = 29441.300| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 0.82 r_work: 0.3570 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work: 0.3326 rms_B_bonded: 4.29 restraints_weight: 0.1250 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 32752 Z= 0.121 Angle : 0.551 7.514 44376 Z= 0.285 Chirality : 0.044 0.170 5296 Planarity : 0.003 0.033 5640 Dihedral : 4.237 28.218 4456 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.99 % Allowed : 13.37 % Favored : 85.64 % 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: 1.00 (0.13), residues: 4112 helix: 1.76 (0.12), residues: 1904 sheet: 1.11 (0.18), residues: 712 loop : -1.03 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 243 TYR 0.013 0.001 TYR H 708 PHE 0.016 0.001 PHE H 542 TRP 0.019 0.001 TRP F 631 HIS 0.001 0.000 HIS H 518 Details of bonding type rmsd covalent geometry : bond 0.00265 (32752) covalent geometry : angle 0.55051 (44376) hydrogen bonds : bond 0.03908 ( 1704) hydrogen bonds : angle 4.32221 ( 4995) ********************** 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 448 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 413 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7950 (tp) cc_final: 0.7732 (tp) REVERT: A 32 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8453 (tm) REVERT: A 447 PHE cc_start: 0.7684 (m-10) cc_final: 0.7361 (t80) REVERT: B 439 ILE cc_start: 0.8346 (mt) cc_final: 0.8052 (mp) REVERT: B 447 PHE cc_start: 0.7778 (m-10) cc_final: 0.7461 (t80) REVERT: C 19 LEU cc_start: 0.8021 (tp) cc_final: 0.7806 (tp) REVERT: C 447 PHE cc_start: 0.7641 (m-10) cc_final: 0.7361 (t80) REVERT: C 521 MET cc_start: 0.8738 (mtp) cc_final: 0.8446 (mtp) REVERT: C 598 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7232 (mtpp) REVERT: C 684 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: D 447 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7123 (t80) REVERT: D 598 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.6913 (tptp) REVERT: D 621 MET cc_start: 0.9085 (mtp) cc_final: 0.8812 (mtp) REVERT: E 19 LEU cc_start: 0.8033 (tp) cc_final: 0.7805 (tp) REVERT: E 447 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7050 (t80) REVERT: E 598 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7122 (mtpp) REVERT: E 684 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: F 447 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7083 (t80) REVERT: F 621 MET cc_start: 0.9083 (mtp) cc_final: 0.8814 (mtp) REVERT: G 19 LEU cc_start: 0.7955 (tp) cc_final: 0.7727 (tp) REVERT: G 32 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8493 (tm) REVERT: G 447 PHE cc_start: 0.7694 (m-10) cc_final: 0.7377 (t80) REVERT: G 598 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7094 (mtpp) REVERT: G 684 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: H 38 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7950 (m) REVERT: H 447 PHE cc_start: 0.7772 (m-10) cc_final: 0.7440 (t80) REVERT: H 598 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6856 (tptp) REVERT: H 621 MET cc_start: 0.9107 (mtp) cc_final: 0.8843 (mtp) REVERT: H 708 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.6286 (m-80) outliers start: 35 outliers final: 14 residues processed: 437 average time/residue: 0.5796 time to fit residues: 307.5707 Evaluate side-chains 422 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 393 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 447 PHE Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 708 TYR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 447 PHE Chi-restraints excluded: chain F residue 517 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 598 LYS Chi-restraints excluded: chain H residue 708 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 157 optimal weight: 3.9990 chunk 382 optimal weight: 7.9990 chunk 257 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 376 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 241 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN B 467 ASN C 467 ASN D 467 ASN E 467 ASN F 467 ASN G 467 ASN H 164 ASN H 467 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.194459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165033 restraints weight = 29142.024| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 0.81 r_work: 0.3550 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work: 0.3290 rms_B_bonded: 4.22 restraints_weight: 0.1250 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32752 Z= 0.161 Angle : 0.599 9.409 44376 Z= 0.310 Chirality : 0.045 0.170 5296 Planarity : 0.004 0.032 5640 Dihedral : 4.428 28.176 4456 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.30 % Allowed : 13.43 % Favored : 85.28 % 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: 0.90 (0.13), residues: 4112 helix: 1.62 (0.12), residues: 1904 sheet: 1.08 (0.18), residues: 712 loop : -1.01 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 243 TYR 0.016 0.002 TYR H 708 PHE 0.018 0.002 PHE H 542 TRP 0.021 0.001 TRP F 631 HIS 0.003 0.001 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00362 (32752) covalent geometry : angle 0.59921 (44376) hydrogen bonds : bond 0.04353 ( 1704) hydrogen bonds : angle 4.48570 ( 4995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16662.59 seconds wall clock time: 282 minutes 33.75 seconds (16953.75 seconds total)