Starting phenix.real_space_refine on Fri Jun 27 12:51:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exp_50043/06_2025/9exp_50043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exp_50043/06_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_50043/06_2025/9exp_50043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exp_50043/06_2025/9exp_50043.map" model { file = "/net/cci-nas-00/data/ceres_data/9exp_50043/06_2025/9exp_50043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exp_50043/06_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-5710/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: 12.28, per 1000 atoms: 0.38 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: 8.13 Conformation dependent library (CDL) restraints added in 4.0 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: 4.48 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: 12.99 Time building geometry restraints manager: 9.55 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: 0.28 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 65.800 Find NCS groups from input model: 0.800 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: 0.000 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: 84.650 ------------------------------------------------------------------------------- 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 : 3.717 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: 1.3007 time to fit residues: 591.0059 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 : 3.396 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136874 restraints weight = 33346.086| |-----------------------------------------------------------------------------| 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: 4.29 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 3.830 Fit side-chains REVERT: A 594 MET cc_start: 0.7729 (mtp) cc_final: 0.7476 (mpp) REVERT: A 657 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7239 (mtt-85) REVERT: B 109 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: B 462 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: B 657 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7319 (mtm-85) REVERT: C 450 PHE cc_start: 0.7984 (m-10) cc_final: 0.7780 (m-80) REVERT: C 594 MET cc_start: 0.7761 (mtp) cc_final: 0.7517 (mpp) REVERT: C 657 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7285 (mtt-85) REVERT: D 109 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: D 136 ASP cc_start: 0.7224 (t70) cc_final: 0.6902 (t0) REVERT: D 462 GLU cc_start: 0.8499 (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: 0.7739 (mtp) cc_final: 0.7488 (mpp) REVERT: E 657 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7243 (mtt-85) REVERT: F 109 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: F 462 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: F 657 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7325 (mtm-85) REVERT: G 450 PHE cc_start: 0.7972 (m-10) cc_final: 0.7768 (m-80) REVERT: G 594 MET cc_start: 0.7801 (mtp) cc_final: 0.7554 (mpp) REVERT: G 657 ARG cc_start: 0.8221 (mmm160) cc_final: 0.7289 (mtt-85) REVERT: H 109 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: H 462 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: H 657 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7311 (mtm-85) outliers start: 30 outliers final: 13 residues processed: 346 average time/residue: 1.4371 time to fit residues: 605.9843 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 : 3.593 ------------------------------------------------------------------------------- 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: 3.9990 chunk 64 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 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: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.197788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144998 restraints weight = 33628.218| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.04 r_work: 0.3550 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 32568 Z= 0.148 Angle : 0.576 7.598 44184 Z= 0.276 Chirality : 0.044 0.157 5288 Planarity : 0.004 0.032 5584 Dihedral : 8.932 118.104 4488 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.54 % Allowed : 8.12 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.47 (0.13), residues: 1840 sheet: 1.11 (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 D 477 HIS 0.002 0.001 HIS C 622 PHE 0.012 0.001 PHE F 542 TYR 0.006 0.001 TYR B 705 ARG 0.002 0.000 ARG G 682 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 1640) hydrogen bonds : angle 4.21489 ( 4824) covalent geometry : bond 0.00356 (32568) covalent geometry : angle 0.57640 (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 374 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 3.433 Fit side-chains REVERT: A 136 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: A 594 MET cc_start: 0.7618 (mtp) cc_final: 0.7361 (mpp) REVERT: A 657 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7083 (mtt-85) REVERT: B 109 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: B 136 ASP cc_start: 0.7298 (t70) cc_final: 0.6970 (m-30) REVERT: B 462 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7941 (mt-10) REVERT: B 657 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7116 (mtm-85) REVERT: C 136 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7301 (m-30) REVERT: C 450 PHE cc_start: 0.7790 (m-10) cc_final: 0.7577 (m-80) REVERT: C 657 ARG cc_start: 0.8024 (mmm160) cc_final: 0.7070 (mtt-85) REVERT: D 109 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: D 136 ASP cc_start: 0.6857 (t70) cc_final: 0.6376 (t0) REVERT: D 462 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: D 657 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7128 (mtm-85) REVERT: E 109 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: E 136 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: E 657 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7079 (mtt-85) REVERT: F 109 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: F 136 ASP cc_start: 0.7377 (t70) cc_final: 0.7053 (m-30) REVERT: F 462 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: F 657 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7124 (mtm-85) REVERT: G 109 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: G 136 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: G 450 PHE cc_start: 0.7790 (m-10) cc_final: 0.7585 (m-80) REVERT: G 594 MET cc_start: 0.7613 (mtp) cc_final: 0.7345 (mpp) REVERT: G 657 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7070 (mtt-85) REVERT: H 109 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: H 136 ASP cc_start: 0.7349 (t70) cc_final: 0.7039 (m-30) REVERT: H 462 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: H 657 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7128 (mtm-85) outliers start: 54 outliers final: 16 residues processed: 354 average time/residue: 1.4139 time to fit residues: 609.8400 Evaluate side-chains 334 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 304 time to evaluate : 4.030 ------------------------------------------------------------------------------- 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 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 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 109 GLN 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: 0.9980 chunk 302 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 chunk 384 optimal weight: 4.9990 chunk 372 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.196239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.138860 restraints weight = 33657.464| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.99 r_work: 0.3481 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32568 Z= 0.197 Angle : 0.613 8.370 44184 Z= 0.294 Chirality : 0.046 0.162 5288 Planarity : 0.004 0.037 5584 Dihedral : 9.000 116.668 4488 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.88 % Allowed : 9.14 % Favored : 88.98 % 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: 0.26 (0.13), residues: 4072 helix: 1.30 (0.12), residues: 1840 sheet: 0.99 (0.18), residues: 672 loop : -1.63 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 477 HIS 0.004 0.001 HIS H 622 PHE 0.014 0.002 PHE H 604 TYR 0.009 0.001 TYR D 658 ARG 0.003 0.000 ARG G 682 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 1640) hydrogen bonds : angle 4.28427 ( 4824) covalent geometry : bond 0.00491 (32568) covalent geometry : angle 0.61306 (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 365 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 3.533 Fit side-chains REVERT: A 136 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: A 597 ASP cc_start: 0.7912 (t0) cc_final: 0.7659 (t0) REVERT: A 657 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7317 (mtt-85) REVERT: B 109 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: B 136 ASP cc_start: 0.7443 (t70) cc_final: 0.7147 (m-30) REVERT: B 428 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.7073 (tt) REVERT: B 462 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: B 657 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7333 (mtm-85) REVERT: C 136 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: C 450 PHE cc_start: 0.7971 (m-10) cc_final: 0.7754 (m-80) REVERT: C 597 ASP cc_start: 0.7905 (t0) cc_final: 0.7683 (t0) REVERT: C 657 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7318 (mtt-85) REVERT: D 109 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: D 136 ASP cc_start: 0.7058 (t70) cc_final: 0.6539 (t70) REVERT: D 428 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7090 (tt) REVERT: D 462 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: D 657 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7337 (mtm-85) REVERT: E 136 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: E 597 ASP cc_start: 0.7901 (t0) cc_final: 0.7645 (t0) REVERT: E 657 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7316 (mtt-85) REVERT: F 109 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: F 136 ASP cc_start: 0.7493 (t70) cc_final: 0.7181 (m-30) REVERT: F 428 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7078 (tt) REVERT: F 462 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: F 657 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7347 (mtm-85) REVERT: G 136 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7094 (m-30) REVERT: G 450 PHE cc_start: 0.7962 (m-10) cc_final: 0.7736 (m-80) REVERT: G 597 ASP cc_start: 0.7933 (t0) cc_final: 0.7677 (t0) REVERT: G 657 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7312 (mtt-85) REVERT: H 109 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: H 136 ASP cc_start: 0.7484 (t70) cc_final: 0.7199 (m-30) REVERT: H 428 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7076 (tt) REVERT: H 462 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: H 657 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7337 (mtm-85) outliers start: 66 outliers final: 20 residues processed: 344 average time/residue: 1.3329 time to fit residues: 562.6375 Evaluate side-chains 324 residues out of total 3512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 4.018 ------------------------------------------------------------------------------- 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 F residue 594 MET 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2662 > 50: distance: 8 - 207: 35.552 distance: 11 - 204: 18.210 distance: 22 - 192: 11.974 distance: 25 - 189: 25.556 distance: 80 - 199: 24.636 distance: 83 - 196: 21.520 distance: 96 - 181: 24.656 distance: 99 - 178: 24.752 distance: 131 - 136: 26.836 distance: 136 - 137: 31.579 distance: 137 - 138: 40.427 distance: 137 - 140: 28.047 distance: 138 - 139: 38.472 distance: 138 - 141: 40.809 distance: 141 - 142: 18.658 distance: 142 - 143: 46.115 distance: 142 - 145: 28.924 distance: 143 - 150: 18.246 distance: 145 - 146: 16.425 distance: 147 - 148: 27.324 distance: 148 - 149: 13.736 distance: 150 - 151: 14.727 distance: 150 - 156: 22.715 distance: 151 - 152: 41.348 distance: 151 - 154: 38.834 distance: 152 - 153: 33.100 distance: 152 - 157: 22.646 distance: 154 - 155: 21.786 distance: 155 - 156: 29.115 distance: 157 - 158: 31.938 distance: 158 - 159: 26.419 distance: 159 - 160: 14.443 distance: 159 - 161: 7.886 distance: 161 - 162: 22.371 distance: 162 - 163: 12.282 distance: 162 - 165: 12.597 distance: 163 - 164: 22.722 distance: 163 - 169: 15.572 distance: 165 - 166: 21.070 distance: 166 - 167: 36.399 distance: 166 - 168: 20.648 distance: 169 - 170: 21.779 distance: 170 - 171: 26.600 distance: 170 - 173: 24.529 distance: 171 - 172: 6.816 distance: 171 - 178: 8.939 distance: 173 - 174: 14.723 distance: 174 - 175: 23.305 distance: 175 - 176: 13.216 distance: 175 - 177: 36.877 distance: 179 - 180: 10.610 distance: 179 - 182: 17.719 distance: 180 - 181: 38.453 distance: 180 - 189: 9.584 distance: 182 - 183: 20.651 distance: 183 - 184: 14.900 distance: 183 - 185: 20.329 distance: 184 - 186: 14.795 distance: 185 - 187: 19.764 distance: 186 - 188: 7.578 distance: 187 - 188: 15.365 distance: 189 - 190: 15.480 distance: 190 - 191: 10.410 distance: 190 - 193: 24.165 distance: 191 - 192: 12.531 distance: 191 - 196: 21.600 distance: 193 - 194: 17.087 distance: 193 - 195: 28.699 distance: 196 - 197: 20.678 distance: 197 - 198: 10.787 distance: 197 - 200: 25.285 distance: 198 - 199: 10.447 distance: 198 - 204: 35.365 distance: 200 - 201: 27.562 distance: 200 - 202: 37.572 distance: 201 - 203: 31.640 distance: 204 - 205: 5.299 distance: 205 - 206: 40.360 distance: 205 - 208: 38.146 distance: 206 - 207: 10.795 distance: 206 - 211: 27.125 distance: 208 - 209: 18.646 distance: 208 - 210: 26.645