Starting phenix.real_space_refine on Thu May 29 07:55:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exp_50043/05_2025/9exp_50043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exp_50043/05_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_50043/05_2025/9exp_50043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exp_50043/05_2025/9exp_50043.map" model { file = "/net/cci-nas-00/data/ceres_data/9exp_50043/05_2025/9exp_50043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exp_50043/05_2025/9exp_50043.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, H Time building chain proxies: 10.69, per 1000 atoms: 0.33 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: 7.47 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 3.92 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: 12.43 Time building geometry restraints manager: 8.76 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: 0.27 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 59.840 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP B 477 HIS 0.003 0.001 HIS E 622 PHE 0.013 0.002 PHE F 220 TYR 0.007 0.001 TYR B 116 ARG 0.003 0.001 ARG H 657 Details of bonding type rmsd hydrogen bonds : bond 0.11497 ( 1640) hydrogen bonds : angle 5.30688 ( 4824) covalent geometry : bond 0.00866 (32568) covalent geometry : angle 0.70038 (44184) *********************** 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 : 3.422 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: 1.2836 time to fit residues: 582.1531 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 : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 370 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.195209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136873 restraints weight = 33346.085| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.07 r_work: 0.3448 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 32568 Z= 0.185 Angle : 0.614 7.804 44184 Z= 0.296 Chirality : 0.046 0.160 5288 Planarity : 0.004 0.034 5584 Dihedral : 9.679 130.778 4488 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.85 % Allowed : 6.44 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4072 helix: 1.30 (0.12), residues: 1840 sheet: 1.04 (0.18), residues: 664 loop : -1.65 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 477 HIS 0.003 0.001 HIS C 622 PHE 0.015 0.002 PHE H 604 TYR 0.008 0.001 TYR D 606 ARG 0.003 0.000 ARG E 657 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 1640) hydrogen bonds : angle 4.44696 ( 4824) covalent geometry : bond 0.00454 (32568) covalent geometry : angle 0.61429 (44184) *********************** 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 359 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 329 time to evaluate : 3.375 Fit side-chains REVERT: A 594 MET cc_start: 0.7719 (mtp) cc_final: 0.7466 (mpp) REVERT: A 657 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7238 (mtt-85) REVERT: B 109 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: B 462 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: B 657 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7319 (mtm-85) REVERT: C 450 PHE cc_start: 0.7986 (m-10) cc_final: 0.7781 (m-80) REVERT: C 594 MET cc_start: 0.7754 (mtp) cc_final: 0.7508 (mpp) REVERT: C 657 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7286 (mtt-85) REVERT: D 109 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: D 136 ASP cc_start: 0.7240 (t70) cc_final: 0.6916 (t0) REVERT: D 462 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: D 657 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7306 (mtm-85) REVERT: E 594 MET cc_start: 0.7735 (mtp) cc_final: 0.7482 (mpp) REVERT: E 657 ARG cc_start: 0.8172 (mmm160) cc_final: 0.7243 (mtt-85) REVERT: F 109 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: F 462 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: F 657 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7326 (mtm-85) REVERT: G 450 PHE cc_start: 0.7975 (m-10) cc_final: 0.7771 (m-80) REVERT: G 594 MET cc_start: 0.7795 (mtp) cc_final: 0.7547 (mpp) REVERT: G 657 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7291 (mtt-85) REVERT: H 109 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: H 462 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: H 657 ARG cc_start: 0.8162 (mmm160) cc_final: 0.7310 (mtm-85) outliers start: 30 outliers final: 13 residues processed: 346 average time/residue: 1.2267 time to fit residues: 516.0743 Evaluate side-chains 328 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 307 time to evaluate : 3.376 ------------------------------------------------------------------------------- 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 B residue 109 GLN Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 594 MET 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 D residue 594 MET 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 462 GLU Chi-restraints excluded: chain F residue 594 MET 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 Chi-restraints excluded: chain H residue 594 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 234 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 276 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.198221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145661 restraints weight = 33622.427| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.99 r_work: 0.3559 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 32568 Z= 0.137 Angle : 0.567 7.434 44184 Z= 0.272 Chirality : 0.044 0.156 5288 Planarity : 0.004 0.031 5584 Dihedral : 8.909 118.421 4488 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.45 % Allowed : 7.89 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.13), residues: 4072 helix: 1.52 (0.13), residues: 1840 sheet: 1.13 (0.18), residues: 664 loop : -1.60 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 477 HIS 0.002 0.001 HIS C 622 PHE 0.012 0.001 PHE H 542 TYR 0.006 0.001 TYR G 705 ARG 0.002 0.000 ARG A 609 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1640) hydrogen bonds : angle 4.18917 ( 4824) covalent geometry : bond 0.00327 (32568) covalent geometry : angle 0.56686 (44184) *********************** 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 375 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 324 time to evaluate : 3.605 Fit side-chains REVERT: A 136 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7355 (m-30) REVERT: A 594 MET cc_start: 0.7596 (mtp) cc_final: 0.7338 (mpp) REVERT: A 657 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7063 (mtt-85) REVERT: B 136 ASP cc_start: 0.7317 (t70) cc_final: 0.6979 (m-30) REVERT: B 462 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: B 657 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7103 (mtm-85) REVERT: C 136 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: C 450 PHE cc_start: 0.7770 (m-10) cc_final: 0.7555 (m-80) REVERT: C 657 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7047 (mtt-85) REVERT: D 109 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: D 136 ASP cc_start: 0.6875 (t70) cc_final: 0.6391 (t0) REVERT: D 462 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: D 657 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7108 (mtm-85) REVERT: E 109 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7166 (pm20) REVERT: E 136 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: E 214 SER cc_start: 0.7465 (t) cc_final: 0.6779 (p) REVERT: E 657 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7060 (mtt-85) REVERT: F 109 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: F 136 ASP cc_start: 0.7390 (t70) cc_final: 0.7066 (m-30) REVERT: F 462 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: F 657 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7105 (mtm-85) REVERT: G 109 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: G 128 MET cc_start: 0.7327 (mtp) cc_final: 0.7120 (mtt) REVERT: G 136 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: G 450 PHE cc_start: 0.7751 (m-10) cc_final: 0.7535 (m-80) REVERT: G 594 MET cc_start: 0.7619 (mtp) cc_final: 0.7352 (mpp) REVERT: G 657 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7051 (mtt-85) REVERT: H 136 ASP cc_start: 0.7363 (t70) cc_final: 0.7056 (m-30) REVERT: H 462 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: H 657 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7118 (mtm-85) outliers start: 51 outliers final: 16 residues processed: 355 average time/residue: 1.2351 time to fit residues: 530.6819 Evaluate side-chains 337 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 309 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 217 LEU 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 462 GLU Chi-restraints excluded: chain D residue 594 MET Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 217 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 462 GLU Chi-restraints excluded: chain F residue 594 MET 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 462 GLU Chi-restraints excluded: chain H residue 594 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 307 optimal weight: 1.9990 chunk 302 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 384 optimal weight: 0.0870 chunk 372 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.198636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146212 restraints weight = 33622.665| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.90 r_work: 0.3577 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 32568 Z= 0.125 Angle : 0.546 7.323 44184 Z= 0.262 Chirality : 0.044 0.157 5288 Planarity : 0.003 0.030 5584 Dihedral : 8.555 114.553 4488 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.94 % Allowed : 8.71 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4072 helix: 1.66 (0.13), residues: 1840 sheet: 1.13 (0.18), residues: 672 loop : -1.67 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 477 HIS 0.002 0.001 HIS G 518 PHE 0.011 0.001 PHE F 542 TYR 0.006 0.001 TYR B 658 ARG 0.001 0.000 ARG G 657 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1640) hydrogen bonds : angle 4.05187 ( 4824) covalent geometry : bond 0.00295 (32568) covalent geometry : angle 0.54648 (44184) *********************** 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 397 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 329 time to evaluate : 3.774 Fit side-chains REVERT: A 109 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: A 136 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: A 657 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7169 (mtm-85) REVERT: B 109 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: B 136 ASP cc_start: 0.7316 (t70) cc_final: 0.6960 (m-30) REVERT: B 428 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6771 (tt) REVERT: B 462 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: B 657 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7124 (mtm-85) REVERT: C 109 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: C 136 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6922 (m-30) REVERT: C 214 SER cc_start: 0.7511 (t) cc_final: 0.6808 (p) REVERT: C 450 PHE cc_start: 0.7768 (m-10) cc_final: 0.7557 (m-80) REVERT: C 657 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7097 (mtt-85) REVERT: D 109 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7224 (pm20) REVERT: D 136 ASP cc_start: 0.6826 (t70) cc_final: 0.6244 (t70) REVERT: D 428 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6785 (tt) REVERT: D 447 PHE cc_start: 0.6630 (m-10) cc_final: 0.5937 (t80) REVERT: D 462 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: D 657 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7145 (mtm-85) REVERT: E 109 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: E 136 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: E 214 SER cc_start: 0.7529 (t) cc_final: 0.6830 (p) REVERT: E 657 ARG cc_start: 0.8047 (mmm160) cc_final: 0.7161 (mtm-85) REVERT: F 109 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: F 136 ASP cc_start: 0.7368 (t70) cc_final: 0.6695 (m-30) REVERT: F 428 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6818 (tt) REVERT: F 447 PHE cc_start: 0.6607 (m-10) cc_final: 0.5914 (t80) REVERT: F 462 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: F 657 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7142 (mtm-85) REVERT: G 109 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: G 136 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: G 214 SER cc_start: 0.7524 (t) cc_final: 0.6835 (p) REVERT: G 450 PHE cc_start: 0.7739 (m-10) cc_final: 0.7510 (m-80) REVERT: G 594 MET cc_start: 0.7600 (mtp) cc_final: 0.7345 (mpp) REVERT: G 657 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7123 (mtt-85) REVERT: H 109 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: H 136 ASP cc_start: 0.7341 (t70) cc_final: 0.7066 (m-30) REVERT: H 428 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6804 (tt) REVERT: H 462 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: H 657 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7153 (mtm-85) outliers start: 68 outliers final: 15 residues processed: 376 average time/residue: 1.2169 time to fit residues: 558.3720 Evaluate side-chains 345 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 ASP 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 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 ASP 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 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 119 VAL 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 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 119 VAL 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 428 ILE Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 594 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 73 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.200284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.149367 restraints weight = 33411.482| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.92 r_work: 0.3598 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 32568 Z= 0.155 Angle : 0.570 7.706 44184 Z= 0.273 Chirality : 0.044 0.182 5288 Planarity : 0.004 0.033 5584 Dihedral : 8.590 112.442 4488 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.57 % Allowed : 9.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4072 helix: 1.58 (0.13), residues: 1840 sheet: 1.10 (0.18), residues: 672 loop : -1.69 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 477 HIS 0.003 0.001 HIS E 622 PHE 0.013 0.001 PHE F 542 TYR 0.014 0.001 TYR C 705 ARG 0.002 0.000 ARG G 657 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 1640) hydrogen bonds : angle 4.09295 ( 4824) covalent geometry : bond 0.00377 (32568) covalent geometry : angle 0.57046 (44184) *********************** 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 365 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 3.869 Fit side-chains REVERT: A 136 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: A 214 SER cc_start: 0.7719 (t) cc_final: 0.7037 (p) REVERT: A 657 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7279 (mtm-85) REVERT: B 109 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: B 136 ASP cc_start: 0.7440 (t70) cc_final: 0.6768 (m-30) REVERT: B 428 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6957 (tt) REVERT: B 462 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: B 657 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7259 (mtm-85) REVERT: C 136 ASP cc_start: 0.7681 (t70) cc_final: 0.7038 (m-30) REVERT: C 450 PHE cc_start: 0.7868 (m-10) cc_final: 0.7653 (m-80) REVERT: C 657 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7233 (mtt-85) REVERT: D 109 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: D 136 ASP cc_start: 0.6988 (t70) cc_final: 0.6387 (t70) REVERT: D 428 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6971 (tt) REVERT: D 462 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: D 657 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7261 (mtm-85) REVERT: E 109 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: E 136 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7120 (m-30) REVERT: E 657 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7277 (mtm-85) REVERT: F 109 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: F 136 ASP cc_start: 0.7518 (t70) cc_final: 0.6858 (m-30) REVERT: F 428 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6973 (tt) REVERT: F 462 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: F 657 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7249 (mtm-85) REVERT: G 109 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: G 136 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: G 450 PHE cc_start: 0.7846 (m-10) cc_final: 0.7631 (m-80) REVERT: G 657 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7237 (mtt-85) REVERT: H 109 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: H 136 ASP cc_start: 0.7465 (t70) cc_final: 0.6818 (m-30) REVERT: H 428 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6951 (tt) REVERT: H 462 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: H 657 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7253 (mtm-85) outliers start: 55 outliers final: 21 residues processed: 348 average time/residue: 1.2320 time to fit residues: 518.5993 Evaluate side-chains 342 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 3.394 ------------------------------------------------------------------------------- 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 119 VAL Chi-restraints excluded: chain A residue 136 ASP 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 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 119 VAL 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 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 119 VAL 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 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 119 VAL 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 428 ILE Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 594 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 401 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 369 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 169 optimal weight: 0.0670 chunk 315 optimal weight: 9.9990 chunk 56 optimal weight: 0.0370 chunk 374 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.6000 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.200654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.149694 restraints weight = 33540.827| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.91 r_work: 0.3608 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 32568 Z= 0.137 Angle : 0.551 7.492 44184 Z= 0.264 Chirality : 0.044 0.160 5288 Planarity : 0.003 0.031 5584 Dihedral : 8.466 111.461 4488 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.54 % Allowed : 10.42 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4072 helix: 1.65 (0.13), residues: 1840 sheet: 1.24 (0.19), residues: 664 loop : -1.69 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 477 HIS 0.002 0.001 HIS C 622 PHE 0.013 0.001 PHE H 542 TYR 0.006 0.001 TYR D 606 ARG 0.002 0.000 ARG D 609 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 1640) hydrogen bonds : angle 4.02484 ( 4824) covalent geometry : bond 0.00328 (32568) covalent geometry : angle 0.55112 (44184) *********************** 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 375 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 3.635 Fit side-chains REVERT: A 109 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: A 136 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7062 (m-30) REVERT: A 657 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7203 (mtm-85) REVERT: B 92 LEU cc_start: 0.7780 (tp) cc_final: 0.7517 (tt) REVERT: B 109 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 136 ASP cc_start: 0.7411 (t70) cc_final: 0.6753 (m-30) REVERT: B 428 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6849 (tt) REVERT: B 462 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: B 657 ARG cc_start: 0.8112 (mmm160) cc_final: 0.7178 (mtm-85) REVERT: C 136 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7081 (m-30) REVERT: C 450 PHE cc_start: 0.7778 (m-10) cc_final: 0.7569 (m-80) REVERT: C 657 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7171 (mtt-85) REVERT: D 92 LEU cc_start: 0.7746 (tp) cc_final: 0.7483 (tt) REVERT: D 109 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7242 (pm20) REVERT: D 136 ASP cc_start: 0.6958 (t70) cc_final: 0.6359 (t70) REVERT: D 428 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6847 (tt) REVERT: D 462 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: D 657 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7186 (mtm-85) REVERT: E 109 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: E 136 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: E 657 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7216 (mtm-85) REVERT: F 109 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: F 136 ASP cc_start: 0.7490 (t70) cc_final: 0.7187 (m-30) REVERT: F 428 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6862 (tt) REVERT: F 462 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: F 657 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7173 (mtm-85) REVERT: G 109 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: G 136 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: G 450 PHE cc_start: 0.7759 (m-10) cc_final: 0.7546 (m-80) REVERT: G 657 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7178 (mtt-85) REVERT: H 92 LEU cc_start: 0.7751 (tp) cc_final: 0.7502 (tt) REVERT: H 109 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: H 136 ASP cc_start: 0.7443 (t70) cc_final: 0.7162 (m-30) REVERT: H 428 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6846 (tt) REVERT: H 462 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: H 657 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7176 (mtm-85) outliers start: 54 outliers final: 15 residues processed: 361 average time/residue: 1.2431 time to fit residues: 547.6078 Evaluate side-chains 342 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 ASP 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 428 ILE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 ASP 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 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 119 VAL 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 428 ILE Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 119 VAL 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 428 ILE Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 594 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 177 optimal weight: 5.9990 chunk 406 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 265 optimal weight: 10.0000 chunk 362 optimal weight: 7.9990 chunk 355 optimal weight: 0.8980 chunk 320 optimal weight: 0.6980 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.202830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153915 restraints weight = 33559.931| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.07 r_work: 0.3517 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32568 Z= 0.101 Angle : 0.522 7.004 44184 Z= 0.250 Chirality : 0.043 0.163 5288 Planarity : 0.003 0.028 5584 Dihedral : 7.986 109.155 4488 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.25 % Allowed : 11.22 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.13), residues: 4072 helix: 1.89 (0.13), residues: 1840 sheet: 1.35 (0.18), residues: 696 loop : -1.59 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 477 HIS 0.001 0.000 HIS F 622 PHE 0.011 0.001 PHE F 542 TYR 0.015 0.001 TYR G 705 ARG 0.004 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1640) hydrogen bonds : angle 3.86681 ( 4824) covalent geometry : bond 0.00226 (32568) covalent geometry : angle 0.52195 (44184) *********************** 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 373 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 329 time to evaluate : 3.431 Fit side-chains REVERT: A 109 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: A 214 SER cc_start: 0.7603 (t) cc_final: 0.6924 (p) REVERT: A 634 GLN cc_start: 0.8494 (mt0) cc_final: 0.7678 (mm-40) REVERT: A 657 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7171 (mtm-85) REVERT: B 92 LEU cc_start: 0.7671 (tp) cc_final: 0.7398 (tt) REVERT: B 105 ASP cc_start: 0.7790 (m-30) cc_final: 0.7299 (m-30) REVERT: B 109 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: B 136 ASP cc_start: 0.7362 (t70) cc_final: 0.6804 (m-30) REVERT: B 428 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6703 (tt) REVERT: B 447 PHE cc_start: 0.6580 (m-10) cc_final: 0.5900 (t80) REVERT: B 462 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: B 657 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7149 (mtm-85) REVERT: C 109 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: C 214 SER cc_start: 0.7612 (t) cc_final: 0.6936 (p) REVERT: C 450 PHE cc_start: 0.7597 (m-10) cc_final: 0.7381 (m-80) REVERT: C 634 GLN cc_start: 0.8493 (mt0) cc_final: 0.7686 (mm-40) REVERT: C 657 ARG cc_start: 0.8084 (mmm160) cc_final: 0.7180 (mtm-85) REVERT: D 92 LEU cc_start: 0.7648 (tp) cc_final: 0.7366 (tt) REVERT: D 105 ASP cc_start: 0.7806 (m-30) cc_final: 0.7314 (m-30) REVERT: D 136 ASP cc_start: 0.6867 (t70) cc_final: 0.6337 (t70) REVERT: D 428 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6719 (tt) REVERT: D 447 PHE cc_start: 0.6580 (m-10) cc_final: 0.5905 (t80) REVERT: D 462 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: D 657 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7172 (mtm-85) REVERT: E 109 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: E 214 SER cc_start: 0.7613 (t) cc_final: 0.6939 (p) REVERT: E 634 GLN cc_start: 0.8492 (mt0) cc_final: 0.7685 (mm-40) REVERT: E 657 ARG cc_start: 0.8066 (mmm160) cc_final: 0.7171 (mtm-85) REVERT: F 92 LEU cc_start: 0.7661 (tp) cc_final: 0.7416 (tt) REVERT: F 105 ASP cc_start: 0.7794 (m-30) cc_final: 0.7287 (m-30) REVERT: F 136 ASP cc_start: 0.7436 (t70) cc_final: 0.6818 (m-30) REVERT: F 428 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6724 (tt) REVERT: F 447 PHE cc_start: 0.6574 (m-10) cc_final: 0.5900 (t80) REVERT: F 462 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: F 657 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7165 (mtm-85) REVERT: G 109 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: G 214 SER cc_start: 0.7622 (t) cc_final: 0.6947 (p) REVERT: G 450 PHE cc_start: 0.7586 (m-10) cc_final: 0.7364 (m-80) REVERT: G 634 GLN cc_start: 0.8495 (mt0) cc_final: 0.7680 (mm-40) REVERT: G 657 ARG cc_start: 0.8073 (mmm160) cc_final: 0.7143 (mtt-85) REVERT: H 92 LEU cc_start: 0.7655 (tp) cc_final: 0.7389 (tt) REVERT: H 105 ASP cc_start: 0.7806 (m-30) cc_final: 0.7303 (m-30) REVERT: H 109 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7350 (pm20) REVERT: H 136 ASP cc_start: 0.7402 (t70) cc_final: 0.6837 (m-30) REVERT: H 428 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6728 (tt) REVERT: H 447 PHE cc_start: 0.6578 (m-10) cc_final: 0.5901 (t80) REVERT: H 462 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: H 657 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7153 (mtm-85) outliers start: 44 outliers final: 2 residues processed: 361 average time/residue: 1.2573 time to fit residues: 550.9364 Evaluate side-chains 319 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 303 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain B residue 109 GLN 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 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 428 ILE Chi-restraints excluded: chain F residue 462 GLU 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 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 102 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 183 optimal weight: 4.9990 chunk 359 optimal weight: 2.9990 chunk 383 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 634 GLN C 611 GLN D 634 GLN G 611 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.201259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150786 restraints weight = 33442.748| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.93 r_work: 0.3609 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32568 Z= 0.136 Angle : 0.550 7.263 44184 Z= 0.264 Chirality : 0.044 0.164 5288 Planarity : 0.003 0.030 5584 Dihedral : 8.147 108.485 4488 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.03 % Allowed : 11.59 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.13), residues: 4072 helix: 1.78 (0.13), residues: 1840 sheet: 1.28 (0.18), residues: 664 loop : -1.61 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 477 HIS 0.002 0.001 HIS B 622 PHE 0.013 0.001 PHE F 542 TYR 0.006 0.001 TYR B 658 ARG 0.001 0.000 ARG G 682 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 1640) hydrogen bonds : angle 3.92936 ( 4824) covalent geometry : bond 0.00328 (32568) covalent geometry : angle 0.55026 (44184) *********************** 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 349 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 3.450 Fit side-chains REVERT: A 214 SER cc_start: 0.7717 (t) cc_final: 0.7054 (p) REVERT: A 580 LYS cc_start: 0.7161 (mmtt) cc_final: 0.6944 (mptt) REVERT: A 657 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7234 (mtt-85) REVERT: B 92 LEU cc_start: 0.7868 (tp) cc_final: 0.7596 (tt) REVERT: B 109 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: B 136 ASP cc_start: 0.7458 (t70) cc_final: 0.6855 (m-30) REVERT: B 428 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6928 (tt) REVERT: B 462 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: B 657 ARG cc_start: 0.8137 (mmm160) cc_final: 0.7246 (mtm-85) REVERT: C 214 SER cc_start: 0.7719 (t) cc_final: 0.7055 (p) REVERT: C 580 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6968 (mptt) REVERT: C 657 ARG cc_start: 0.8108 (mmm160) cc_final: 0.7234 (mtt-85) REVERT: D 92 LEU cc_start: 0.7807 (tp) cc_final: 0.7523 (tt) REVERT: D 105 ASP cc_start: 0.7852 (m-30) cc_final: 0.7368 (m-30) REVERT: D 136 ASP cc_start: 0.6994 (t70) cc_final: 0.6430 (t70) REVERT: D 428 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6922 (tt) REVERT: D 462 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: D 657 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7253 (mtm-85) REVERT: E 109 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: E 214 SER cc_start: 0.7723 (t) cc_final: 0.7060 (p) REVERT: E 580 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6961 (mptt) REVERT: E 657 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7240 (mtt-85) REVERT: F 136 ASP cc_start: 0.7543 (t70) cc_final: 0.7224 (m-30) REVERT: F 428 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6938 (tt) REVERT: F 462 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: F 657 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7245 (mtm-85) REVERT: G 109 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: G 580 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6949 (mptt) REVERT: G 657 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7232 (mtt-85) REVERT: H 92 LEU cc_start: 0.7801 (tp) cc_final: 0.7541 (tt) REVERT: H 109 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: H 136 ASP cc_start: 0.7484 (t70) cc_final: 0.6898 (m-30) REVERT: H 428 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6940 (tt) REVERT: H 462 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: H 657 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7249 (mtm-85) outliers start: 36 outliers final: 9 residues processed: 340 average time/residue: 1.2397 time to fit residues: 514.0784 Evaluate side-chains 329 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 3.214 ------------------------------------------------------------------------------- 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 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 428 ILE Chi-restraints excluded: chain D residue 462 GLU 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 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 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 246 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 349 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 383 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 405 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.201094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151651 restraints weight = 33443.581| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.05 r_work: 0.3609 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32568 Z= 0.136 Angle : 0.551 7.405 44184 Z= 0.264 Chirality : 0.044 0.163 5288 Planarity : 0.003 0.030 5584 Dihedral : 8.223 109.650 4488 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.05 % Allowed : 11.50 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.13), residues: 4072 helix: 1.75 (0.13), residues: 1840 sheet: 1.27 (0.18), residues: 696 loop : -1.58 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 477 HIS 0.002 0.001 HIS F 622 PHE 0.013 0.001 PHE F 542 TYR 0.011 0.001 TYR C 705 ARG 0.001 0.000 ARG E 566 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1640) hydrogen bonds : angle 3.93654 ( 4824) covalent geometry : bond 0.00326 (32568) covalent geometry : angle 0.55145 (44184) *********************** 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 344 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 3.167 Fit side-chains REVERT: A 109 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7379 (pm20) REVERT: A 214 SER cc_start: 0.7593 (t) cc_final: 0.6936 (p) REVERT: A 580 LYS cc_start: 0.7102 (mmtt) cc_final: 0.6884 (mptt) REVERT: A 634 GLN cc_start: 0.8496 (mt0) cc_final: 0.7759 (mm-40) REVERT: A 657 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7172 (mtm-85) REVERT: B 92 LEU cc_start: 0.7739 (tp) cc_final: 0.7479 (tt) REVERT: B 105 ASP cc_start: 0.7783 (m-30) cc_final: 0.7280 (m-30) REVERT: B 109 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: B 136 ASP cc_start: 0.7391 (t70) cc_final: 0.6802 (m-30) REVERT: B 428 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6836 (tt) REVERT: B 462 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: B 657 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7166 (mtm-85) REVERT: C 109 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7381 (pm20) REVERT: C 214 SER cc_start: 0.7593 (t) cc_final: 0.6938 (p) REVERT: C 657 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7147 (mtt-85) REVERT: D 92 LEU cc_start: 0.7702 (tp) cc_final: 0.7421 (tt) REVERT: D 109 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: D 136 ASP cc_start: 0.6923 (t70) cc_final: 0.6327 (t70) REVERT: D 428 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6825 (tt) REVERT: D 462 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: D 657 ARG cc_start: 0.8109 (mmm160) cc_final: 0.7173 (mtm-85) REVERT: E 109 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: E 214 SER cc_start: 0.7597 (t) cc_final: 0.6942 (p) REVERT: E 580 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6901 (mptt) REVERT: E 634 GLN cc_start: 0.8491 (mt0) cc_final: 0.7759 (mm-40) REVERT: E 657 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7173 (mtm-85) REVERT: F 109 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: F 136 ASP cc_start: 0.7537 (t70) cc_final: 0.7237 (m-30) REVERT: F 428 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6858 (tt) REVERT: F 462 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: F 657 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7165 (mtm-85) REVERT: G 109 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: G 214 SER cc_start: 0.7635 (t) cc_final: 0.7008 (p) REVERT: G 580 LYS cc_start: 0.7108 (mmtt) cc_final: 0.6890 (mptt) REVERT: G 657 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7142 (mtt-85) REVERT: H 92 LEU cc_start: 0.7710 (tp) cc_final: 0.7455 (tt) REVERT: H 109 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7542 (pm20) REVERT: H 136 ASP cc_start: 0.7452 (t70) cc_final: 0.6843 (m-30) REVERT: H 428 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6839 (tt) REVERT: H 462 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: H 657 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7166 (mtm-85) outliers start: 37 outliers final: 8 residues processed: 337 average time/residue: 1.2596 time to fit residues: 511.2222 Evaluate side-chains 329 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 3.212 ------------------------------------------------------------------------------- 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 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 428 ILE Chi-restraints excluded: chain D residue 462 GLU 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 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 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 86 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 377 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148391 restraints weight = 33553.730| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.00 r_work: 0.3570 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32568 Z= 0.209 Angle : 0.616 8.506 44184 Z= 0.296 Chirality : 0.046 0.165 5288 Planarity : 0.004 0.037 5584 Dihedral : 8.763 116.013 4488 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.03 % Allowed : 11.70 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 4072 helix: 1.45 (0.12), residues: 1832 sheet: 1.14 (0.19), residues: 664 loop : -1.59 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 477 HIS 0.005 0.001 HIS F 622 PHE 0.016 0.002 PHE F 542 TYR 0.010 0.001 TYR F 606 ARG 0.002 0.000 ARG E 682 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 1640) hydrogen bonds : angle 4.14248 ( 4824) covalent geometry : bond 0.00522 (32568) covalent geometry : angle 0.61588 (44184) ********************** 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 335 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 299 time to evaluate : 3.335 Fit side-chains REVERT: A 136 ASP cc_start: 0.7525 (m-30) cc_final: 0.6893 (m-30) REVERT: A 580 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6892 (mptt) REVERT: A 657 ARG cc_start: 0.8084 (mmm160) cc_final: 0.7175 (mtt-85) REVERT: B 109 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: B 136 ASP cc_start: 0.7493 (t70) cc_final: 0.7138 (m-30) REVERT: B 428 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6890 (tt) REVERT: B 462 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: B 657 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7188 (mtm-85) REVERT: C 657 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7167 (mtt-85) REVERT: D 109 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: D 136 ASP cc_start: 0.7001 (t70) cc_final: 0.6388 (t70) REVERT: D 428 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6882 (tt) REVERT: D 462 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: D 657 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7190 (mtm-85) REVERT: E 580 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6909 (mptt) REVERT: E 657 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7191 (mtt-85) REVERT: F 109 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: F 136 ASP cc_start: 0.7560 (t70) cc_final: 0.7249 (m-30) REVERT: F 428 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6897 (tt) REVERT: F 462 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: F 657 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7187 (mtm-85) REVERT: G 580 LYS cc_start: 0.7126 (mmtt) cc_final: 0.6896 (mptt) REVERT: G 657 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7167 (mtt-85) REVERT: H 109 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: H 136 ASP cc_start: 0.7518 (t70) cc_final: 0.7213 (m-30) REVERT: H 428 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6910 (tt) REVERT: H 462 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: H 657 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7188 (mtm-85) outliers start: 36 outliers final: 14 residues processed: 327 average time/residue: 1.2221 time to fit residues: 483.3933 Evaluate side-chains 322 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 119 VAL 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 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 428 ILE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 119 VAL 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 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 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 217 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 112 optimal weight: 0.0070 chunk 260 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 303 optimal weight: 0.7980 chunk 193 optimal weight: 0.6980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.202759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152839 restraints weight = 33370.782| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.93 r_work: 0.3649 rms_B_bonded: 2.35 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: 0.7930 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 0.031 32568 Z= 0.098 Angle : 0.522 7.113 44184 Z= 0.252 Chirality : 0.043 0.159 5288 Planarity : 0.003 0.033 5584 Dihedral : 8.169 112.716 4488 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.74 % Allowed : 11.87 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4072 helix: 1.84 (0.13), residues: 1840 sheet: 1.31 (0.18), residues: 696 loop : -1.54 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 477 HIS 0.002 0.001 HIS G 622 PHE 0.010 0.001 PHE F 542 TYR 0.016 0.001 TYR C 705 ARG 0.001 0.000 ARG B 609 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 1640) hydrogen bonds : angle 3.88263 ( 4824) covalent geometry : bond 0.00214 (32568) covalent geometry : angle 0.52242 (44184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23779.99 seconds wall clock time: 410 minutes 42.93 seconds (24642.93 seconds total)