Starting phenix.real_space_refine on Tue Aug 26 00:07:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exp_50043/08_2025/9exp_50043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exp_50043/08_2025/9exp_50043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9exp_50043/08_2025/9exp_50043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exp_50043/08_2025/9exp_50043.map" model { file = "/net/cci-nas-00/data/ceres_data/9exp_50043/08_2025/9exp_50043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exp_50043/08_2025/9exp_50043.cif" } resolution = 2.85 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= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 104 5.16 5 C 20480 2.51 5 N 5400 2.21 5 O 6056 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32064 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3980 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 3.78, per 1000 atoms: 0.12 Number of scatterers: 32064 At special positions: 0 Unit cell: (158.455, 158.455, 139.293, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 16 15.00 Mg 8 11.99 O 6056 8.00 N 5400 7.00 C 20480 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7632 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 32 sheets defined 45.8% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 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: 3.997A 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: 3.591A 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 465 removed outlier: 4.015A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 622 through 633 removed outlier: 4.237A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.589A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 708 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: 3.997A 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: 3.592A 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 465 removed outlier: 4.015A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 633 removed outlier: 4.237A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.588A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 708 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: 3.997A 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: 3.591A 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 465 removed outlier: 4.014A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 633 removed outlier: 4.237A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.589A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 708 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: 3.997A 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: 3.591A 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 465 removed outlier: 4.014A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 633 removed outlier: 4.237A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.588A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 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: 3.997A 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: 3.591A 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 465 removed outlier: 4.015A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 633 removed outlier: 4.237A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 672 through 686 removed outlier: 3.589A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 708 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: 3.996A 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: 3.592A 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 465 removed outlier: 4.015A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY F 465 " --> pdb=" O LEU F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'F' and resid 581 through 587 Processing helix chain 'F' and resid 615 through 620 Processing helix chain 'F' and resid 622 through 633 removed outlier: 4.237A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.588A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 708 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: 3.996A 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: 3.591A 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 465 removed outlier: 4.015A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY G 465 " --> pdb=" O LEU G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 622 through 633 removed outlier: 4.237A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.588A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 708 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: 3.996A 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: 3.591A 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 465 removed outlier: 4.015A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 removed outlier: 3.793A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 587 Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 633 removed outlier: 4.236A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.588A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 701 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 8.533A pdb=" N ILE A 54 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP A 418 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.487A 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: 7.373A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.512A 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: 7.395A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 692 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 559 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP A 642 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 561 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 558 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE A 607 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 606 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 8.533A pdb=" N ILE B 54 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP B 418 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU B 56 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 416 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 58 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN B 414 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 6.487A 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: 7.372A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.512A 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: 7.395A pdb=" N LEU B 695 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B 471 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 697 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 692 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 559 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP B 642 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 561 " --> pdb=" O ASP B 642 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 558 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE B 607 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE B 560 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 606 " --> pdb=" O ASP B 597 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 223 removed outlier: 8.532A pdb=" N ILE C 54 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP C 418 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 56 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 416 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP C 58 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN C 414 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.488A 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: 7.372A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.513A 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: 7.394A pdb=" N LEU C 695 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER C 471 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY C 697 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY C 692 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 559 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP C 642 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 561 " --> pdb=" O ASP C 642 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 558 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE C 607 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE C 560 " --> pdb=" O ILE C 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR C 606 " --> pdb=" O ASP C 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 8.533A pdb=" N ILE D 54 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP D 418 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.488A 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: 7.372A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.513A 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: 7.394A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY D 692 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU D 559 " --> pdb=" O ILE D 640 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP D 642 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE D 561 " --> pdb=" O ASP D 642 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL D 558 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE D 607 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE D 560 " --> pdb=" O ILE D 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR D 606 " --> pdb=" O ASP D 597 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 8.533A pdb=" N ILE E 54 " --> pdb=" O ASP E 418 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASP E 418 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU E 56 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL E 416 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP E 58 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN E 414 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.488A 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: 7.372A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.513A 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: 7.395A pdb=" N LEU E 695 " --> pdb=" O TYR E 469 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER E 471 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY E 697 " --> pdb=" O SER E 471 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY E 692 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU E 559 " --> pdb=" O ILE E 640 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP E 642 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 561 " --> pdb=" O ASP E 642 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 558 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE E 607 " --> pdb=" O VAL E 558 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE E 560 " --> pdb=" O ILE E 607 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 606 " --> pdb=" O ASP E 597 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 8.533A pdb=" N ILE F 54 " --> pdb=" O ASP F 418 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP F 418 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU F 56 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL F 416 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP F 58 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN F 414 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 6.486A 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: 7.372A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.514A 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: 7.394A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY F 692 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU F 559 " --> pdb=" O ILE F 640 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP F 642 " --> pdb=" O LEU F 559 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE F 561 " --> pdb=" O ASP F 642 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 558 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE F 607 " --> pdb=" O VAL F 558 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE F 560 " --> pdb=" O ILE F 607 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR F 606 " --> pdb=" O ASP F 597 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 223 removed outlier: 8.533A pdb=" N ILE G 54 " --> pdb=" O ASP G 418 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP G 418 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.487A 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: 7.372A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.513A 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: 7.395A pdb=" N LEU G 695 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER G 471 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY G 697 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY G 692 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU G 559 " --> pdb=" O ILE G 640 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP G 642 " --> pdb=" O LEU G 559 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE G 561 " --> pdb=" O ASP G 642 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL G 558 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE G 607 " --> pdb=" O VAL G 558 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE G 560 " --> pdb=" O ILE G 607 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR G 606 " --> pdb=" O ASP G 597 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 223 removed outlier: 8.533A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.488A 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: 7.372A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.512A 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: 7.394A pdb=" N LEU H 695 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER H 471 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 697 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY H 692 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL H 558 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE H 607 " --> pdb=" O VAL H 558 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE H 560 " --> pdb=" O ILE H 607 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR H 606 " --> pdb=" O ASP H 597 " (cutoff:3.500A) 1640 hydrogen bonds defined for protein. 4824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10450 1.34 - 1.46: 3752 1.46 - 1.57: 18134 1.57 - 1.69: 40 1.69 - 1.81: 192 Bond restraints: 32568 Sorted by residual: bond pdb=" C3' ADP D1000 " pdb=" C4' ADP D1000 " ideal model delta sigma weight residual 1.524 1.273 0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C3' ADP C1000 " pdb=" C4' ADP C1000 " ideal model delta sigma weight residual 1.524 1.274 0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C3' ADP A1000 " pdb=" C4' ADP A1000 " ideal model delta sigma weight residual 1.524 1.274 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3' ADP H1000 " pdb=" C4' ADP H1000 " ideal model delta sigma weight residual 1.524 1.274 0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C3' ADP B1000 " pdb=" C4' ADP B1000 " ideal model delta sigma weight residual 1.524 1.274 0.250 2.00e-02 2.50e+03 1.56e+02 ... (remaining 32563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 43696 2.41 - 4.81: 360 4.81 - 7.22: 64 7.22 - 9.63: 16 9.63 - 12.03: 48 Bond angle restraints: 44184 Sorted by residual: angle pdb=" O1B ADP E1000 " pdb=" PB ADP E1000 " pdb=" O3B ADP E1000 " ideal model delta sigma weight residual 119.90 107.87 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O1B ADP F1000 " pdb=" PB ADP F1000 " pdb=" O3B ADP F1000 " ideal model delta sigma weight residual 119.90 107.87 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O1B ADP H1000 " pdb=" PB ADP H1000 " pdb=" O3B ADP H1000 " ideal model delta sigma weight residual 119.90 107.87 12.03 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O1B ADP G1000 " pdb=" PB ADP G1000 " pdb=" O3B ADP G1000 " ideal model delta sigma weight residual 119.90 107.91 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O1B ADP D1000 " pdb=" PB ADP D1000 " pdb=" O3B ADP D1000 " ideal model delta sigma weight residual 119.90 107.92 11.98 3.00e+00 1.11e-01 1.60e+01 ... (remaining 44179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 19264 26.07 - 52.14: 387 52.14 - 78.21: 69 78.21 - 104.29: 16 104.29 - 130.36: 16 Dihedral angle restraints: 19752 sinusoidal: 7888 harmonic: 11864 Sorted by residual: dihedral pdb=" C5' ADP H1000 " pdb=" O5' ADP H1000 " pdb=" PA ADP H1000 " pdb=" O2A ADP H1000 " ideal model delta sinusoidal sigma weight residual 300.00 169.65 130.36 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" C5' ADP F1000 " pdb=" O5' ADP F1000 " pdb=" PA ADP F1000 " pdb=" O2A ADP F1000 " ideal model delta sinusoidal sigma weight residual 300.00 169.69 130.31 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" C5' ADP B1000 " pdb=" O5' ADP B1000 " pdb=" PA ADP B1000 " pdb=" O2A ADP B1000 " ideal model delta sinusoidal sigma weight residual 300.00 169.70 130.31 1 2.00e+01 2.50e-03 3.95e+01 ... (remaining 19749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3075 0.030 - 0.060: 1396 0.060 - 0.091: 402 0.091 - 0.121: 356 0.121 - 0.151: 59 Chirality restraints: 5288 Sorted by residual: chirality pdb=" CA PHE G 117 " pdb=" N PHE G 117 " pdb=" C PHE G 117 " pdb=" CB PHE G 117 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA PHE D 117 " pdb=" N PHE D 117 " pdb=" C PHE D 117 " pdb=" CB PHE D 117 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA PHE F 117 " pdb=" N PHE F 117 " pdb=" C PHE F 117 " pdb=" CB PHE F 117 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 5285 not shown) Planarity restraints: 5584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 457 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO F 458 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO F 458 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 458 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 457 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO C 458 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 458 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 458 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 457 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO D 458 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 458 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 458 " 0.017 5.00e-02 4.00e+02 ... (remaining 5581 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 190 2.57 - 3.15: 25722 3.15 - 3.73: 47112 3.73 - 4.32: 68056 4.32 - 4.90: 116318 Nonbonded interactions: 257398 Sorted by model distance: nonbonded pdb=" O2B ADP D1000 " pdb="MG MG D1001 " model vdw 1.987 2.170 nonbonded pdb=" O2B ADP H1000 " pdb="MG MG H1001 " model vdw 1.987 2.170 nonbonded pdb=" O2B ADP C1000 " pdb="MG MG C1001 " model vdw 1.987 2.170 nonbonded pdb=" O2B ADP G1000 " pdb="MG MG G1001 " model vdw 1.988 2.170 nonbonded pdb=" O2B ADP B1000 " pdb="MG MG B1001 " model vdw 1.988 2.170 ... (remaining 257393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.160 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.009 0.251 32568 Z= 0.417 Angle : 0.700 12.032 44184 Z= 0.328 Chirality : 0.044 0.151 5288 Planarity : 0.003 0.031 5584 Dihedral : 11.966 130.357 12120 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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 aren not related in a simple way. whole: 0.27 (0.13), residues: 4072 helix: 1.28 (0.12), residues: 1840 sheet: 1.00 (0.19), residues: 672 loop : -1.59 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 657 TYR 0.007 0.001 TYR B 116 PHE 0.013 0.002 PHE F 220 TRP 0.006 0.001 TRP B 477 HIS 0.003 0.001 HIS E 622 Details of bonding type rmsd covalent geometry : bond 0.00866 (32568) covalent geometry : angle 0.70038 (44184) hydrogen bonds : bond 0.11497 ( 1640) hydrogen bonds : angle 5.30688 ( 4824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.904 Fit side-chains REVERT: A 450 PHE cc_start: 0.7939 (m-10) cc_final: 0.7734 (m-80) REVERT: A 597 ASP cc_start: 0.7266 (t0) cc_final: 0.7021 (t70) REVERT: A 657 ARG cc_start: 0.7687 (mmm160) cc_final: 0.7409 (mtt-85) REVERT: B 657 ARG cc_start: 0.7762 (mmm160) cc_final: 0.7472 (mtm-85) REVERT: C 450 PHE cc_start: 0.7947 (m-10) cc_final: 0.7717 (m-80) REVERT: C 597 ASP cc_start: 0.7243 (t0) cc_final: 0.6999 (t70) REVERT: C 657 ARG cc_start: 0.7691 (mmm160) cc_final: 0.7396 (mtt-85) REVERT: D 657 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7467 (mtm-85) REVERT: E 450 PHE cc_start: 0.7937 (m-10) cc_final: 0.7710 (m-80) REVERT: E 597 ASP cc_start: 0.7251 (t0) cc_final: 0.7023 (t70) REVERT: E 657 ARG cc_start: 0.7675 (mmm160) cc_final: 0.7439 (mtt-85) REVERT: F 657 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7461 (mtm-85) REVERT: G 450 PHE cc_start: 0.7922 (m-10) cc_final: 0.7691 (m-80) REVERT: G 597 ASP cc_start: 0.7246 (t0) cc_final: 0.7033 (t70) REVERT: G 657 ARG cc_start: 0.7679 (mmm160) cc_final: 0.7445 (mtt-85) REVERT: H 657 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7476 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.5688 time to fit residues: 256.0986 Evaluate side-chains 299 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN C 611 GLN E 611 GLN G 611 GLN H 611 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.203436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.153436 restraints weight = 33593.006| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.94 r_work: 0.3647 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 32568 Z= 0.100 Angle : 0.534 6.308 44184 Z= 0.258 Chirality : 0.043 0.154 5288 Planarity : 0.003 0.029 5584 Dihedral : 9.666 133.903 4488 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.63 % Allowed : 6.32 % Favored : 93.05 % 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 aren not related in a simple way. whole: 0.73 (0.13), residues: 4072 helix: 1.74 (0.13), residues: 1840 sheet: 1.28 (0.18), residues: 696 loop : -1.52 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 452 TYR 0.009 0.001 TYR C 705 PHE 0.010 0.001 PHE C 117 TRP 0.003 0.001 TRP C 477 HIS 0.002 0.000 HIS B 518 Details of bonding type rmsd covalent geometry : bond 0.00213 (32568) covalent geometry : angle 0.53439 (44184) hydrogen bonds : bond 0.03504 ( 1640) hydrogen bonds : angle 4.22756 ( 4824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 348 time to evaluate : 1.287 Fit side-chains REVERT: A 109 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: A 136 ASP cc_start: 0.7586 (t0) cc_final: 0.7289 (m-30) REVERT: A 214 SER cc_start: 0.7689 (t) cc_final: 0.7020 (p) REVERT: A 594 MET cc_start: 0.7703 (mtp) cc_final: 0.7464 (mpp) REVERT: A 597 ASP cc_start: 0.7509 (t0) cc_final: 0.7272 (t70) REVERT: A 657 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7204 (mtt-85) REVERT: B 594 MET cc_start: 0.7534 (mtp) cc_final: 0.7262 (mpp) REVERT: B 657 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7217 (mtm-85) REVERT: C 109 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7378 (pm20) REVERT: C 136 ASP cc_start: 0.7580 (t0) cc_final: 0.7269 (m-30) REVERT: C 214 SER cc_start: 0.7708 (t) cc_final: 0.7033 (p) REVERT: C 450 PHE cc_start: 0.7861 (m-10) cc_final: 0.7645 (m-80) REVERT: C 594 MET cc_start: 0.7674 (mtp) cc_final: 0.7442 (mpp) REVERT: C 597 ASP cc_start: 0.7477 (t0) cc_final: 0.7256 (t70) REVERT: C 657 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7175 (mtt-85) REVERT: D 136 ASP cc_start: 0.7142 (t70) cc_final: 0.6713 (t0) REVERT: D 447 PHE cc_start: 0.6742 (m-10) cc_final: 0.6029 (t80) REVERT: D 594 MET cc_start: 0.7523 (mtp) cc_final: 0.7266 (mpp) REVERT: D 657 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7230 (mtm-85) REVERT: E 109 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: E 136 ASP cc_start: 0.7591 (t0) cc_final: 0.7288 (m-30) REVERT: E 214 SER cc_start: 0.7683 (t) cc_final: 0.7008 (p) REVERT: E 594 MET cc_start: 0.7671 (mtp) cc_final: 0.7432 (mpp) REVERT: E 597 ASP cc_start: 0.7489 (t0) cc_final: 0.7270 (t70) REVERT: E 657 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7199 (mtt-85) REVERT: F 447 PHE cc_start: 0.6699 (m-10) cc_final: 0.5965 (t80) REVERT: F 462 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: F 657 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7234 (mtm-85) REVERT: G 109 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: G 136 ASP cc_start: 0.7609 (t0) cc_final: 0.7308 (m-30) REVERT: G 214 SER cc_start: 0.7688 (t) cc_final: 0.7009 (p) REVERT: G 450 PHE cc_start: 0.7717 (m-10) cc_final: 0.7498 (m-80) REVERT: G 594 MET cc_start: 0.7693 (mtp) cc_final: 0.7454 (mpp) REVERT: G 597 ASP cc_start: 0.7465 (t0) cc_final: 0.7246 (t70) REVERT: G 657 ARG cc_start: 0.8063 (mmm160) cc_final: 0.7192 (mtt-85) REVERT: H 447 PHE cc_start: 0.6689 (m-10) cc_final: 0.5960 (t80) REVERT: H 657 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7228 (mtm-85) outliers start: 22 outliers final: 5 residues processed: 361 average time/residue: 0.4901 time to fit residues: 218.6769 Evaluate side-chains 321 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 311 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 680 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 396 optimal weight: 0.5980 chunk 236 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 398 optimal weight: 2.9990 chunk 407 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 97 optimal weight: 4.9990 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 167 optimal weight: 0.0670 chunk 356 optimal weight: 6.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 611 GLN D 634 GLN G 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.203686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153300 restraints weight = 33451.396| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.92 r_work: 0.3654 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32568 Z= 0.099 Angle : 0.524 6.700 44184 Z= 0.251 Chirality : 0.043 0.178 5288 Planarity : 0.003 0.028 5584 Dihedral : 8.695 118.406 4488 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.97 % Allowed : 7.83 % Favored : 91.20 % 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 aren not related in a simple way. whole: 0.84 (0.13), residues: 4072 helix: 1.91 (0.13), residues: 1848 sheet: 1.37 (0.19), residues: 664 loop : -1.57 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 609 TYR 0.008 0.001 TYR G 705 PHE 0.012 0.001 PHE F 542 TRP 0.003 0.001 TRP C 477 HIS 0.002 0.000 HIS A 518 Details of bonding type rmsd covalent geometry : bond 0.00218 (32568) covalent geometry : angle 0.52370 (44184) hydrogen bonds : bond 0.03355 ( 1640) hydrogen bonds : angle 3.96390 ( 4824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 0.943 Fit side-chains REVERT: A 109 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: A 136 ASP cc_start: 0.7516 (t0) cc_final: 0.6996 (m-30) REVERT: A 214 SER cc_start: 0.7621 (t) cc_final: 0.6938 (p) REVERT: A 594 MET cc_start: 0.7593 (mtp) cc_final: 0.7344 (mpp) REVERT: A 597 ASP cc_start: 0.7403 (t0) cc_final: 0.7149 (t70) REVERT: A 657 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7079 (mtt-85) REVERT: B 92 LEU cc_start: 0.7688 (tp) cc_final: 0.7471 (tt) REVERT: B 109 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: B 136 ASP cc_start: 0.7375 (t70) cc_final: 0.7048 (m-30) REVERT: B 447 PHE cc_start: 0.6628 (m-10) cc_final: 0.5923 (t80) REVERT: B 462 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: B 657 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7139 (mtm-85) REVERT: C 109 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: C 136 ASP cc_start: 0.7508 (t0) cc_final: 0.7009 (m-30) REVERT: C 214 SER cc_start: 0.7643 (t) cc_final: 0.6966 (p) REVERT: C 450 PHE cc_start: 0.7739 (m-10) cc_final: 0.7527 (m-80) REVERT: C 594 MET cc_start: 0.7583 (mtp) cc_final: 0.7335 (mpp) REVERT: C 597 ASP cc_start: 0.7398 (t0) cc_final: 0.7158 (t70) REVERT: C 657 ARG cc_start: 0.8026 (mmm160) cc_final: 0.7086 (mtt-85) REVERT: D 92 LEU cc_start: 0.7652 (tp) cc_final: 0.7437 (tt) REVERT: D 109 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: D 136 ASP cc_start: 0.6886 (t70) cc_final: 0.6331 (t70) REVERT: D 447 PHE cc_start: 0.6624 (m-10) cc_final: 0.5929 (t80) REVERT: D 462 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: D 594 MET cc_start: 0.7426 (mtp) cc_final: 0.7162 (mpp) REVERT: D 657 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7145 (mtm-85) REVERT: E 109 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7036 (pm20) REVERT: E 136 ASP cc_start: 0.7534 (t0) cc_final: 0.7098 (m-30) REVERT: E 214 SER cc_start: 0.7622 (t) cc_final: 0.6949 (p) REVERT: E 594 MET cc_start: 0.7580 (mtp) cc_final: 0.7328 (mpp) REVERT: E 597 ASP cc_start: 0.7403 (t0) cc_final: 0.7169 (t70) REVERT: E 657 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7080 (mtt-85) REVERT: F 92 LEU cc_start: 0.7673 (tp) cc_final: 0.7457 (tt) REVERT: F 109 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: F 136 ASP cc_start: 0.7067 (t70) cc_final: 0.6420 (t70) REVERT: F 447 PHE cc_start: 0.6626 (m-10) cc_final: 0.5914 (t80) REVERT: F 657 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7141 (mtm-85) REVERT: G 109 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7037 (pm20) REVERT: G 136 ASP cc_start: 0.7526 (t0) cc_final: 0.7085 (m-30) REVERT: G 214 SER cc_start: 0.7602 (t) cc_final: 0.6921 (p) REVERT: G 450 PHE cc_start: 0.7648 (m-10) cc_final: 0.7438 (m-80) REVERT: G 594 MET cc_start: 0.7597 (mtp) cc_final: 0.7343 (mpp) REVERT: G 597 ASP cc_start: 0.7388 (t0) cc_final: 0.7167 (t70) REVERT: G 657 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7085 (mtt-85) REVERT: H 92 LEU cc_start: 0.7674 (tp) cc_final: 0.7454 (tt) REVERT: H 109 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: H 136 ASP cc_start: 0.7412 (t70) cc_final: 0.7152 (m-30) REVERT: H 447 PHE cc_start: 0.6627 (m-10) cc_final: 0.5917 (t80) REVERT: H 462 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: H 657 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7141 (mtm-85) outliers start: 34 outliers final: 4 residues processed: 353 average time/residue: 0.5111 time to fit residues: 219.8644 Evaluate side-chains 323 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 308 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 295 optimal weight: 0.9990 chunk 317 optimal weight: 2.9990 chunk 400 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 349 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 406 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 GLN D 634 GLN H 634 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.202867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.152001 restraints weight = 33356.273| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.90 r_work: 0.3635 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 32568 Z= 0.110 Angle : 0.525 7.058 44184 Z= 0.251 Chirality : 0.043 0.156 5288 Planarity : 0.003 0.028 5584 Dihedral : 8.423 114.276 4488 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.51 % Allowed : 8.14 % Favored : 90.35 % 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 aren not related in a simple way. whole: 0.86 (0.13), residues: 4072 helix: 1.91 (0.13), residues: 1848 sheet: 1.49 (0.18), residues: 656 loop : -1.57 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 657 TYR 0.005 0.001 TYR D 606 PHE 0.013 0.001 PHE H 542 TRP 0.004 0.001 TRP A 477 HIS 0.002 0.001 HIS C 622 Details of bonding type rmsd covalent geometry : bond 0.00253 (32568) covalent geometry : angle 0.52453 (44184) hydrogen bonds : bond 0.03402 ( 1640) hydrogen bonds : angle 3.91124 ( 4824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.917 Fit side-chains REVERT: A 109 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: A 136 ASP cc_start: 0.7536 (t0) cc_final: 0.7063 (m-30) REVERT: A 214 SER cc_start: 0.7651 (t) cc_final: 0.6972 (p) REVERT: A 594 MET cc_start: 0.7608 (mtp) cc_final: 0.7347 (mpp) REVERT: A 657 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7089 (mtt-85) REVERT: B 92 LEU cc_start: 0.7748 (tp) cc_final: 0.7518 (tt) REVERT: B 109 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: B 136 ASP cc_start: 0.7360 (t70) cc_final: 0.6787 (m-30) REVERT: B 428 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6817 (tt) REVERT: B 447 PHE cc_start: 0.6634 (m-10) cc_final: 0.5919 (t80) REVERT: B 462 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: B 657 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7151 (mtm-85) REVERT: C 109 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: C 136 ASP cc_start: 0.7530 (t0) cc_final: 0.7059 (m-30) REVERT: C 214 SER cc_start: 0.7651 (t) cc_final: 0.6972 (p) REVERT: C 450 PHE cc_start: 0.7785 (m-10) cc_final: 0.7572 (m-80) REVERT: C 594 MET cc_start: 0.7578 (mtp) cc_final: 0.7320 (mpp) REVERT: C 657 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7098 (mtt-85) REVERT: D 92 LEU cc_start: 0.7689 (tp) cc_final: 0.7462 (tt) REVERT: D 109 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: D 136 ASP cc_start: 0.6866 (t70) cc_final: 0.6263 (t70) REVERT: D 428 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6817 (tt) REVERT: D 447 PHE cc_start: 0.6620 (m-10) cc_final: 0.5916 (t80) REVERT: D 462 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: D 657 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7155 (mtm-85) REVERT: E 109 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: E 136 ASP cc_start: 0.7543 (t0) cc_final: 0.7138 (m-30) REVERT: E 214 SER cc_start: 0.7642 (t) cc_final: 0.6965 (p) REVERT: E 594 MET cc_start: 0.7583 (mtp) cc_final: 0.7321 (mpp) REVERT: E 657 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7088 (mtt-85) REVERT: F 92 LEU cc_start: 0.7728 (tp) cc_final: 0.7504 (tt) REVERT: F 109 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: F 136 ASP cc_start: 0.7006 (t70) cc_final: 0.6789 (m-30) REVERT: F 428 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6851 (tt) REVERT: F 447 PHE cc_start: 0.6613 (m-10) cc_final: 0.5894 (t80) REVERT: F 462 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: F 657 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7154 (mtm-85) REVERT: G 109 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: G 136 ASP cc_start: 0.7555 (t0) cc_final: 0.7138 (m-30) REVERT: G 214 SER cc_start: 0.7630 (t) cc_final: 0.6950 (p) REVERT: G 450 PHE cc_start: 0.7707 (m-10) cc_final: 0.7487 (m-80) REVERT: G 594 MET cc_start: 0.7614 (mtp) cc_final: 0.7348 (mpp) REVERT: G 657 ARG cc_start: 0.8037 (mmm160) cc_final: 0.7094 (mtt-85) REVERT: H 92 LEU cc_start: 0.7681 (tp) cc_final: 0.7454 (tt) REVERT: H 109 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: H 136 ASP cc_start: 0.7379 (t70) cc_final: 0.7052 (m-30) REVERT: H 428 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6840 (tt) REVERT: H 447 PHE cc_start: 0.6618 (m-10) cc_final: 0.5901 (t80) REVERT: H 462 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: H 657 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7149 (mtm-85) outliers start: 53 outliers final: 14 residues processed: 359 average time/residue: 0.5118 time to fit residues: 225.3454 Evaluate side-chains 331 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 594 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 203 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 336 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 185 optimal weight: 0.0270 chunk 126 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 365 optimal weight: 2.9990 chunk 307 optimal weight: 0.7980 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 GLN D 634 GLN H 634 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.203389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153949 restraints weight = 33539.789| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.09 r_work: 0.3635 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32568 Z= 0.104 Angle : 0.517 7.013 44184 Z= 0.247 Chirality : 0.043 0.157 5288 Planarity : 0.003 0.027 5584 Dihedral : 8.146 110.545 4488 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.48 % Allowed : 8.74 % Favored : 89.78 % 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 aren not related in a simple way. whole: 0.97 (0.13), residues: 4072 helix: 2.00 (0.13), residues: 1840 sheet: 1.44 (0.18), residues: 696 loop : -1.51 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 566 TYR 0.017 0.001 TYR F 705 PHE 0.013 0.001 PHE F 542 TRP 0.003 0.001 TRP H 477 HIS 0.001 0.000 HIS G 622 Details of bonding type rmsd covalent geometry : bond 0.00236 (32568) covalent geometry : angle 0.51688 (44184) hydrogen bonds : bond 0.03311 ( 1640) hydrogen bonds : angle 3.86468 ( 4824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 1.197 Fit side-chains REVERT: A 109 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7273 (pm20) REVERT: A 131 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8540 (mtpp) REVERT: A 214 SER cc_start: 0.7645 (t) cc_final: 0.7026 (p) REVERT: A 594 MET cc_start: 0.7595 (mtp) cc_final: 0.7332 (mpp) REVERT: A 657 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7127 (mtt-85) REVERT: B 92 LEU cc_start: 0.7672 (tp) cc_final: 0.7425 (tt) REVERT: B 109 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: B 136 ASP cc_start: 0.7228 (t70) cc_final: 0.6706 (m-30) REVERT: B 428 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6825 (tt) REVERT: B 447 PHE cc_start: 0.6637 (m-10) cc_final: 0.5926 (t80) REVERT: B 462 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: B 657 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7155 (mtm-85) REVERT: C 109 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: C 136 ASP cc_start: 0.7504 (t0) cc_final: 0.7077 (m-30) REVERT: C 214 SER cc_start: 0.7678 (t) cc_final: 0.7004 (p) REVERT: C 450 PHE cc_start: 0.7771 (m-10) cc_final: 0.7551 (m-80) REVERT: C 594 MET cc_start: 0.7580 (mtp) cc_final: 0.7320 (mpp) REVERT: C 657 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7149 (mtt-85) REVERT: D 92 LEU cc_start: 0.7600 (tp) cc_final: 0.7348 (tt) REVERT: D 109 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: D 136 ASP cc_start: 0.6834 (t70) cc_final: 0.6258 (t70) REVERT: D 428 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6810 (tt) REVERT: D 447 PHE cc_start: 0.6639 (m-10) cc_final: 0.5938 (t80) REVERT: D 462 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: D 657 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7166 (mtm-85) REVERT: E 214 SER cc_start: 0.7642 (t) cc_final: 0.7022 (p) REVERT: E 594 MET cc_start: 0.7577 (mtp) cc_final: 0.7313 (mpp) REVERT: E 657 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7128 (mtt-85) REVERT: F 92 LEU cc_start: 0.7640 (tp) cc_final: 0.7391 (tt) REVERT: F 109 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: F 428 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6846 (tt) REVERT: F 447 PHE cc_start: 0.6637 (m-10) cc_final: 0.5918 (t80) REVERT: F 462 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: F 657 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7161 (mtm-85) REVERT: G 214 SER cc_start: 0.7625 (t) cc_final: 0.6979 (p) REVERT: G 450 PHE cc_start: 0.7761 (m-10) cc_final: 0.7540 (m-80) REVERT: G 594 MET cc_start: 0.7609 (mtp) cc_final: 0.7339 (mpp) REVERT: G 657 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7131 (mtt-85) REVERT: H 92 LEU cc_start: 0.7627 (tp) cc_final: 0.7369 (tt) REVERT: H 109 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7393 (pm20) REVERT: H 136 ASP cc_start: 0.7246 (t70) cc_final: 0.6768 (m-30) REVERT: H 428 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6827 (tt) REVERT: H 447 PHE cc_start: 0.6641 (m-10) cc_final: 0.5928 (t80) REVERT: H 462 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: H 657 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7158 (mtm-85) outliers start: 52 outliers final: 15 residues processed: 344 average time/residue: 0.5341 time to fit residues: 222.9975 Evaluate side-chains 325 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 594 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 165 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 113 optimal weight: 0.0870 chunk 369 optimal weight: 20.0000 chunk 206 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 GLN D 634 GLN H 634 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.202246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152062 restraints weight = 33390.079| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.99 r_work: 0.3623 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32568 Z= 0.127 Angle : 0.537 7.255 44184 Z= 0.257 Chirality : 0.044 0.165 5288 Planarity : 0.003 0.027 5584 Dihedral : 8.181 108.023 4488 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.28 % Allowed : 9.85 % Favored : 88.87 % 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 aren not related in a simple way. whole: 0.87 (0.13), residues: 4072 helix: 1.91 (0.13), residues: 1840 sheet: 1.52 (0.18), residues: 656 loop : -1.56 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 566 TYR 0.006 0.001 TYR D 606 PHE 0.014 0.001 PHE F 542 TRP 0.004 0.001 TRP B 477 HIS 0.002 0.001 HIS G 622 Details of bonding type rmsd covalent geometry : bond 0.00304 (32568) covalent geometry : angle 0.53652 (44184) hydrogen bonds : bond 0.03565 ( 1640) hydrogen bonds : angle 3.91306 ( 4824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 1.268 Fit side-chains REVERT: A 109 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: A 131 LYS cc_start: 0.8739 (ptmm) cc_final: 0.8536 (mtpp) REVERT: A 214 SER cc_start: 0.7651 (t) cc_final: 0.7000 (p) REVERT: A 594 MET cc_start: 0.7591 (mtp) cc_final: 0.7328 (mpp) REVERT: A 657 ARG cc_start: 0.8063 (mmm160) cc_final: 0.7105 (mtt-85) REVERT: B 92 LEU cc_start: 0.7720 (tp) cc_final: 0.7461 (tt) REVERT: B 109 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: B 136 ASP cc_start: 0.7196 (t70) cc_final: 0.6713 (m-30) REVERT: B 428 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6828 (tt) REVERT: B 462 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: B 657 ARG cc_start: 0.8122 (mmm160) cc_final: 0.7172 (mtm-85) REVERT: C 109 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: C 136 ASP cc_start: 0.7498 (t0) cc_final: 0.7090 (m-30) REVERT: C 214 SER cc_start: 0.7641 (t) cc_final: 0.6952 (p) REVERT: C 657 ARG cc_start: 0.8074 (mmm160) cc_final: 0.7145 (mtt-85) REVERT: D 92 LEU cc_start: 0.7667 (tp) cc_final: 0.7415 (tt) REVERT: D 109 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: D 136 ASP cc_start: 0.6804 (t70) cc_final: 0.6262 (t70) REVERT: D 428 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6833 (tt) REVERT: D 462 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: D 657 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7184 (mtm-85) REVERT: E 214 SER cc_start: 0.7644 (t) cc_final: 0.6997 (p) REVERT: E 657 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7106 (mtt-85) REVERT: F 92 LEU cc_start: 0.7702 (tp) cc_final: 0.7450 (tt) REVERT: F 109 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: F 428 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6868 (tt) REVERT: F 462 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: F 657 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7167 (mtm-85) REVERT: F 674 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7482 (tptp) REVERT: G 214 SER cc_start: 0.7640 (t) cc_final: 0.6988 (p) REVERT: G 657 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7100 (mtt-85) REVERT: H 92 LEU cc_start: 0.7695 (tp) cc_final: 0.7434 (tt) REVERT: H 109 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7527 (pm20) REVERT: H 136 ASP cc_start: 0.7219 (t70) cc_final: 0.6715 (m-30) REVERT: H 428 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6839 (tt) REVERT: H 462 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: H 657 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7151 (mtm-85) REVERT: H 674 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7465 (tptp) outliers start: 45 outliers final: 19 residues processed: 337 average time/residue: 0.5462 time to fit residues: 222.5698 Evaluate side-chains 333 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 594 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 674 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 203 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 267 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 GLN D 634 GLN H 634 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.204216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.154613 restraints weight = 33661.692| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.96 r_work: 0.3669 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32568 Z= 0.093 Angle : 0.506 6.958 44184 Z= 0.242 Chirality : 0.043 0.161 5288 Planarity : 0.003 0.027 5584 Dihedral : 7.776 105.925 4488 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.20 % Allowed : 10.22 % Favored : 88.58 % 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 aren not related in a simple way. whole: 1.12 (0.13), residues: 4072 helix: 2.09 (0.13), residues: 1840 sheet: 1.61 (0.18), residues: 688 loop : -1.44 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 624 TYR 0.015 0.001 TYR H 705 PHE 0.012 0.001 PHE F 542 TRP 0.003 0.000 TRP G 477 HIS 0.002 0.000 HIS H 622 Details of bonding type rmsd covalent geometry : bond 0.00206 (32568) covalent geometry : angle 0.50567 (44184) hydrogen bonds : bond 0.03086 ( 1640) hydrogen bonds : angle 3.78288 ( 4824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 305 time to evaluate : 1.065 Fit side-chains REVERT: A 131 LYS cc_start: 0.8742 (ptmm) cc_final: 0.8516 (mtpp) REVERT: A 214 SER cc_start: 0.7637 (t) cc_final: 0.7021 (p) REVERT: A 594 MET cc_start: 0.7597 (mtp) cc_final: 0.7332 (mpp) REVERT: A 634 GLN cc_start: 0.8487 (mt0) cc_final: 0.7611 (mm-40) REVERT: A 657 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7124 (mtt-85) REVERT: B 92 LEU cc_start: 0.7591 (tp) cc_final: 0.7319 (tt) REVERT: B 109 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: B 136 ASP cc_start: 0.7200 (t70) cc_final: 0.6741 (m-30) REVERT: B 428 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6811 (tt) REVERT: B 447 PHE cc_start: 0.6626 (m-10) cc_final: 0.5927 (t80) REVERT: B 462 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: B 657 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7153 (mtm-85) REVERT: C 214 SER cc_start: 0.7665 (t) cc_final: 0.7051 (p) REVERT: C 594 MET cc_start: 0.7629 (mtp) cc_final: 0.7394 (mpp) REVERT: C 634 GLN cc_start: 0.8494 (mt0) cc_final: 0.7604 (mm-40) REVERT: C 657 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7153 (mtt-85) REVERT: D 92 LEU cc_start: 0.7611 (tp) cc_final: 0.7350 (tt) REVERT: D 109 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7348 (pm20) REVERT: D 136 ASP cc_start: 0.6792 (t70) cc_final: 0.6261 (t70) REVERT: D 428 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6778 (tt) REVERT: D 447 PHE cc_start: 0.6630 (m-10) cc_final: 0.5931 (t80) REVERT: D 462 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: D 657 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7178 (mtm-85) REVERT: E 214 SER cc_start: 0.7655 (t) cc_final: 0.7042 (p) REVERT: E 594 MET cc_start: 0.7632 (mtp) cc_final: 0.7394 (mpp) REVERT: E 634 GLN cc_start: 0.8479 (mt0) cc_final: 0.7606 (mm-40) REVERT: E 657 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7126 (mtt-85) REVERT: F 92 LEU cc_start: 0.7585 (tp) cc_final: 0.7320 (tt) REVERT: F 109 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: F 428 ILE cc_start: 0.7045 (OUTLIER) cc_final: 0.6837 (tt) REVERT: F 447 PHE cc_start: 0.6619 (m-10) cc_final: 0.5916 (t80) REVERT: F 462 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: F 657 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7165 (mtm-85) REVERT: G 214 SER cc_start: 0.7647 (t) cc_final: 0.7036 (p) REVERT: G 594 MET cc_start: 0.7633 (mtp) cc_final: 0.7392 (mpp) REVERT: G 634 GLN cc_start: 0.8473 (mt0) cc_final: 0.7543 (mm-40) REVERT: G 657 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7114 (mtt-85) REVERT: H 92 LEU cc_start: 0.7596 (tp) cc_final: 0.7331 (tt) REVERT: H 105 ASP cc_start: 0.7819 (m-30) cc_final: 0.7304 (m-30) REVERT: H 109 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: H 136 ASP cc_start: 0.7226 (t70) cc_final: 0.6764 (m-30) REVERT: H 428 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6814 (tt) REVERT: H 447 PHE cc_start: 0.6626 (m-10) cc_final: 0.5922 (t80) REVERT: H 462 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: H 657 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7154 (mtm-85) outliers start: 42 outliers final: 10 residues processed: 335 average time/residue: 0.4973 time to fit residues: 202.6117 Evaluate side-chains 323 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 301 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 387 optimal weight: 0.4980 chunk 317 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 292 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 373 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.199841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148677 restraints weight = 33584.147| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.94 r_work: 0.3600 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 32568 Z= 0.120 Angle : 0.530 7.067 44184 Z= 0.253 Chirality : 0.043 0.159 5288 Planarity : 0.003 0.027 5584 Dihedral : 7.881 106.060 4488 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.00 % Allowed : 10.31 % Favored : 88.70 % 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 aren not related in a simple way. whole: 1.03 (0.13), residues: 4072 helix: 2.00 (0.13), residues: 1840 sheet: 1.55 (0.18), residues: 688 loop : -1.44 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 624 TYR 0.006 0.001 TYR D 606 PHE 0.014 0.001 PHE F 542 TRP 0.004 0.001 TRP H 477 HIS 0.002 0.001 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00283 (32568) covalent geometry : angle 0.52962 (44184) hydrogen bonds : bond 0.03439 ( 1640) hydrogen bonds : angle 3.82402 ( 4824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 1.071 Fit side-chains REVERT: A 131 LYS cc_start: 0.8731 (ptmm) cc_final: 0.8509 (mtpp) REVERT: A 214 SER cc_start: 0.7560 (t) cc_final: 0.6936 (p) REVERT: A 657 ARG cc_start: 0.7998 (mmm160) cc_final: 0.7061 (mtt-85) REVERT: B 92 LEU cc_start: 0.7547 (tp) cc_final: 0.7280 (tt) REVERT: B 105 ASP cc_start: 0.7704 (m-30) cc_final: 0.7190 (m-30) REVERT: B 109 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: B 136 ASP cc_start: 0.7138 (t70) cc_final: 0.6672 (m-30) REVERT: B 428 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6827 (tt) REVERT: B 462 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: B 657 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7115 (mtm-85) REVERT: B 674 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7431 (tptp) REVERT: C 214 SER cc_start: 0.7577 (t) cc_final: 0.6944 (p) REVERT: C 657 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7116 (mtt-85) REVERT: D 92 LEU cc_start: 0.7558 (tp) cc_final: 0.7298 (tt) REVERT: D 105 ASP cc_start: 0.7708 (m-30) cc_final: 0.7193 (m-30) REVERT: D 109 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: D 136 ASP cc_start: 0.6720 (t70) cc_final: 0.6170 (t70) REVERT: D 428 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6815 (tt) REVERT: D 447 PHE cc_start: 0.6631 (m-10) cc_final: 0.5922 (t80) REVERT: D 462 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: D 657 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7136 (mtm-85) REVERT: E 136 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: E 214 SER cc_start: 0.7566 (t) cc_final: 0.6942 (p) REVERT: E 657 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7076 (mtt-85) REVERT: F 92 LEU cc_start: 0.7550 (tp) cc_final: 0.7278 (tt) REVERT: F 109 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: F 428 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6834 (tt) REVERT: F 462 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: F 657 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7127 (mtm-85) REVERT: G 136 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: G 214 SER cc_start: 0.7533 (t) cc_final: 0.6910 (p) REVERT: G 594 MET cc_start: 0.7592 (mtp) cc_final: 0.7344 (mpp) REVERT: G 657 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7061 (mtt-85) REVERT: H 92 LEU cc_start: 0.7590 (tp) cc_final: 0.7331 (tt) REVERT: H 105 ASP cc_start: 0.7751 (m-30) cc_final: 0.7242 (m-30) REVERT: H 109 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: H 136 ASP cc_start: 0.7186 (t70) cc_final: 0.6720 (m-30) REVERT: H 428 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6814 (tt) REVERT: H 462 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: H 657 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7124 (mtm-85) outliers start: 35 outliers final: 14 residues processed: 325 average time/residue: 0.5431 time to fit residues: 214.0506 Evaluate side-chains 319 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 392 optimal weight: 1.9990 chunk 356 optimal weight: 0.8980 chunk 390 optimal weight: 0.0020 chunk 270 optimal weight: 20.0000 chunk 48 optimal weight: 0.5980 chunk 308 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 369 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 360 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.202234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151905 restraints weight = 33483.805| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.95 r_work: 0.3640 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32568 Z= 0.088 Angle : 0.500 6.862 44184 Z= 0.239 Chirality : 0.043 0.156 5288 Planarity : 0.003 0.027 5584 Dihedral : 7.476 101.368 4488 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.97 % Allowed : 10.56 % Favored : 88.47 % 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 aren not related in a simple way. whole: 1.27 (0.13), residues: 4072 helix: 2.21 (0.13), residues: 1840 sheet: 1.59 (0.18), residues: 680 loop : -1.29 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 209 TYR 0.015 0.001 TYR C 705 PHE 0.011 0.001 PHE F 542 TRP 0.002 0.000 TRP C 477 HIS 0.002 0.000 HIS D 622 Details of bonding type rmsd covalent geometry : bond 0.00188 (32568) covalent geometry : angle 0.50046 (44184) hydrogen bonds : bond 0.02958 ( 1640) hydrogen bonds : angle 3.72297 ( 4824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 313 time to evaluate : 1.097 Fit side-chains REVERT: A 131 LYS cc_start: 0.8720 (ptmm) cc_final: 0.8512 (mtpp) REVERT: A 214 SER cc_start: 0.7537 (t) cc_final: 0.6925 (p) REVERT: A 594 MET cc_start: 0.7518 (mtp) cc_final: 0.7279 (mpp) REVERT: A 634 GLN cc_start: 0.8500 (mt0) cc_final: 0.7561 (mm-40) REVERT: A 657 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7077 (mtt-85) REVERT: B 105 ASP cc_start: 0.7690 (m-30) cc_final: 0.7168 (m-30) REVERT: B 109 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7285 (pm20) REVERT: B 136 ASP cc_start: 0.7109 (t70) cc_final: 0.6704 (m-30) REVERT: B 428 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6723 (tt) REVERT: B 447 PHE cc_start: 0.6580 (m-10) cc_final: 0.5862 (t80) REVERT: B 462 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: B 657 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7110 (mtm-85) REVERT: C 131 LYS cc_start: 0.8672 (ptmm) cc_final: 0.8469 (mtpp) REVERT: C 214 SER cc_start: 0.7554 (t) cc_final: 0.6941 (p) REVERT: C 594 MET cc_start: 0.7524 (mtp) cc_final: 0.7283 (mpp) REVERT: C 634 GLN cc_start: 0.8502 (mt0) cc_final: 0.7584 (mm-40) REVERT: C 657 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7113 (mtt-85) REVERT: D 92 LEU cc_start: 0.7409 (tp) cc_final: 0.7136 (tt) REVERT: D 105 ASP cc_start: 0.7680 (m-30) cc_final: 0.7170 (m-30) REVERT: D 109 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: D 136 ASP cc_start: 0.6697 (t70) cc_final: 0.6165 (t70) REVERT: D 428 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6715 (tt) REVERT: D 447 PHE cc_start: 0.6604 (m-10) cc_final: 0.5878 (t80) REVERT: D 462 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: D 657 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7129 (mtm-85) REVERT: E 214 SER cc_start: 0.7540 (t) cc_final: 0.6927 (p) REVERT: E 594 MET cc_start: 0.7550 (mtp) cc_final: 0.7307 (mpp) REVERT: E 634 GLN cc_start: 0.8508 (mt0) cc_final: 0.7573 (mm-40) REVERT: E 657 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7074 (mtt-85) REVERT: F 109 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: F 428 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6743 (tt) REVERT: F 447 PHE cc_start: 0.6588 (m-10) cc_final: 0.5861 (t80) REVERT: F 462 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: F 657 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7131 (mtm-85) REVERT: G 214 SER cc_start: 0.7531 (t) cc_final: 0.6919 (p) REVERT: G 594 MET cc_start: 0.7570 (mtp) cc_final: 0.7321 (mpp) REVERT: G 634 GLN cc_start: 0.8482 (mt0) cc_final: 0.7532 (mm-40) REVERT: G 657 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7048 (mtt-85) REVERT: H 92 LEU cc_start: 0.7452 (tp) cc_final: 0.7178 (tt) REVERT: H 105 ASP cc_start: 0.7754 (m-30) cc_final: 0.7231 (m-30) REVERT: H 109 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: H 136 ASP cc_start: 0.7132 (t70) cc_final: 0.6728 (m-30) REVERT: H 428 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6720 (tt) REVERT: H 447 PHE cc_start: 0.6595 (m-10) cc_final: 0.5869 (t80) REVERT: H 462 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: H 657 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7118 (mtm-85) outliers start: 34 outliers final: 14 residues processed: 341 average time/residue: 0.5005 time to fit residues: 207.7786 Evaluate side-chains 332 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 306 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 109 GLN Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 5 optimal weight: 0.6980 chunk 404 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 241 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 401 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 335 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.202499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152361 restraints weight = 33631.829| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.99 r_work: 0.3633 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32568 Z= 0.091 Angle : 0.503 6.607 44184 Z= 0.240 Chirality : 0.042 0.154 5288 Planarity : 0.003 0.027 5584 Dihedral : 7.190 97.504 4488 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.85 % Allowed : 10.59 % Favored : 88.55 % 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 aren not related in a simple way. whole: 1.36 (0.13), residues: 4072 helix: 2.28 (0.13), residues: 1840 sheet: 1.63 (0.18), residues: 680 loop : -1.23 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 209 TYR 0.014 0.001 TYR B 705 PHE 0.012 0.001 PHE F 542 TRP 0.003 0.000 TRP B 477 HIS 0.001 0.000 HIS E 622 Details of bonding type rmsd covalent geometry : bond 0.00198 (32568) covalent geometry : angle 0.50306 (44184) hydrogen bonds : bond 0.02988 ( 1640) hydrogen bonds : angle 3.67880 ( 4824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8144 Ramachandran restraints generated. 4072 Oldfield, 0 Emsley, 4072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 326 time to evaluate : 1.174 Fit side-chains REVERT: A 214 SER cc_start: 0.7542 (t) cc_final: 0.6938 (p) REVERT: A 580 LYS cc_start: 0.6887 (mmtt) cc_final: 0.6180 (mmpt) REVERT: A 594 MET cc_start: 0.7519 (mtp) cc_final: 0.7261 (mpp) REVERT: A 634 GLN cc_start: 0.8512 (mt0) cc_final: 0.7588 (mm-40) REVERT: A 657 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7058 (mtt-85) REVERT: B 105 ASP cc_start: 0.7682 (m-30) cc_final: 0.7170 (m-30) REVERT: B 109 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: B 136 ASP cc_start: 0.7123 (t70) cc_final: 0.6736 (m-30) REVERT: B 447 PHE cc_start: 0.6618 (m-10) cc_final: 0.5896 (t80) REVERT: B 462 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: B 657 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7137 (mtm-85) REVERT: B 674 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7393 (tptp) REVERT: C 131 LYS cc_start: 0.8706 (ptmm) cc_final: 0.8494 (mtpp) REVERT: C 214 SER cc_start: 0.7561 (t) cc_final: 0.6959 (p) REVERT: C 462 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8033 (mt-10) REVERT: C 594 MET cc_start: 0.7535 (mtp) cc_final: 0.7298 (mpp) REVERT: C 634 GLN cc_start: 0.8510 (mt0) cc_final: 0.7586 (mm-40) REVERT: C 657 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7132 (mtt-85) REVERT: D 105 ASP cc_start: 0.7692 (m-30) cc_final: 0.7180 (m-30) REVERT: D 109 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: D 136 ASP cc_start: 0.6670 (t70) cc_final: 0.6152 (t70) REVERT: D 447 PHE cc_start: 0.6615 (m-10) cc_final: 0.5900 (t80) REVERT: D 462 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: D 657 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7157 (mtm-85) REVERT: E 214 SER cc_start: 0.7576 (t) cc_final: 0.6973 (p) REVERT: E 594 MET cc_start: 0.7536 (mtp) cc_final: 0.7299 (mpp) REVERT: E 634 GLN cc_start: 0.8515 (mt0) cc_final: 0.7593 (mm-40) REVERT: E 657 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7060 (mtt-85) REVERT: F 447 PHE cc_start: 0.6579 (m-10) cc_final: 0.5866 (t80) REVERT: F 462 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: F 657 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7153 (mtm-85) REVERT: G 97 MET cc_start: 0.7294 (ptm) cc_final: 0.7042 (ptp) REVERT: G 214 SER cc_start: 0.7578 (t) cc_final: 0.6982 (p) REVERT: G 594 MET cc_start: 0.7580 (mtp) cc_final: 0.7338 (mpp) REVERT: G 634 GLN cc_start: 0.8496 (mt0) cc_final: 0.7577 (mm-40) REVERT: G 657 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7043 (mtt-85) REVERT: H 105 ASP cc_start: 0.7761 (m-30) cc_final: 0.7240 (m-30) REVERT: H 109 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: H 136 ASP cc_start: 0.7144 (t70) cc_final: 0.6732 (m-30) REVERT: H 447 PHE cc_start: 0.6623 (m-10) cc_final: 0.5901 (t80) REVERT: H 462 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: H 657 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7136 (mtm-85) outliers start: 30 outliers final: 11 residues processed: 352 average time/residue: 0.5565 time to fit residues: 236.3428 Evaluate side-chains 335 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 680 MET Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 383 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 232 optimal weight: 0.0670 chunk 161 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.202664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152565 restraints weight = 33631.103| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.00 r_work: 0.3636 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 32568 Z= 0.093 Angle : 0.508 6.590 44184 Z= 0.241 Chirality : 0.043 0.154 5288 Planarity : 0.003 0.027 5584 Dihedral : 7.125 98.184 4488 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.57 % Allowed : 11.62 % Favored : 87.81 % 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 aren not related in a simple way. whole: 1.39 (0.13), residues: 4072 helix: 2.29 (0.13), residues: 1840 sheet: 1.63 (0.18), residues: 680 loop : -1.20 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 209 TYR 0.016 0.001 TYR F 705 PHE 0.012 0.001 PHE F 542 TRP 0.003 0.000 TRP B 477 HIS 0.001 0.000 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00206 (32568) covalent geometry : angle 0.50790 (44184) hydrogen bonds : bond 0.03026 ( 1640) hydrogen bonds : angle 3.68923 ( 4824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10918.78 seconds wall clock time: 186 minutes 14.78 seconds (11174.78 seconds total)