Starting phenix.real_space_refine on Fri Sep 19 10:25:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t18_40957/09_2025/8t18_40957.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t18_40957/09_2025/8t18_40957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t18_40957/09_2025/8t18_40957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t18_40957/09_2025/8t18_40957.map" model { file = "/net/cci-nas-00/data/ceres_data/8t18_40957/09_2025/8t18_40957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t18_40957/09_2025/8t18_40957.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 8148 2.51 5 N 2304 2.21 5 O 2436 1.98 5 H 12420 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25356 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "B" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "C" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "D" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "E" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "F" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "G" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "H" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "I" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "J" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "K" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "L" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2113 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Time building chain proxies: 4.82, per 1000 atoms: 0.19 Number of scatterers: 25356 At special positions: 0 Unit cell: (128.766, 120.124, 73.457, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 2436 8.00 N 2304 7.00 C 8148 6.00 H 12420 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 708.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 34.9% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.905A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 449 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.999A pdb=" N PHE A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 463 " --> pdb=" O HIS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'B' and resid 409 through 427 Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.899A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 456 through 466 removed outlier: 4.004A pdb=" N PHE B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 463 " --> pdb=" O HIS B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 Processing helix chain 'C' and resid 409 through 427 Processing helix chain 'C' and resid 429 through 436 removed outlier: 3.941A pdb=" N LYS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 449 Processing helix chain 'C' and resid 456 through 466 removed outlier: 4.003A pdb=" N PHE C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 463 " --> pdb=" O HIS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 525 Processing helix chain 'D' and resid 409 through 427 Processing helix chain 'D' and resid 429 through 436 removed outlier: 3.916A pdb=" N LYS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 449 Processing helix chain 'D' and resid 456 through 466 removed outlier: 4.000A pdb=" N PHE D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 463 " --> pdb=" O HIS D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 525 Processing helix chain 'E' and resid 409 through 427 Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.905A pdb=" N LYS E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 449 Processing helix chain 'E' and resid 456 through 466 removed outlier: 4.000A pdb=" N PHE E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR E 462 " --> pdb=" O PHE E 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE E 463 " --> pdb=" O HIS E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 525 Processing helix chain 'F' and resid 409 through 427 Processing helix chain 'F' and resid 429 through 436 removed outlier: 3.905A pdb=" N LYS F 435 " --> pdb=" O GLU F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 456 through 466 removed outlier: 3.998A pdb=" N PHE F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE F 463 " --> pdb=" O HIS F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 525 Processing helix chain 'G' and resid 409 through 427 Processing helix chain 'G' and resid 429 through 436 removed outlier: 3.931A pdb=" N LYS G 435 " --> pdb=" O GLU G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 449 Processing helix chain 'G' and resid 456 through 466 removed outlier: 3.994A pdb=" N PHE G 461 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE G 463 " --> pdb=" O HIS G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 525 Processing helix chain 'H' and resid 409 through 427 Processing helix chain 'H' and resid 429 through 436 removed outlier: 3.886A pdb=" N LYS H 435 " --> pdb=" O GLU H 431 " (cutoff:3.500A) Processing helix chain 'H' and resid 445 through 449 Processing helix chain 'H' and resid 456 through 466 removed outlier: 3.999A pdb=" N PHE H 461 " --> pdb=" O ASP H 457 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR H 462 " --> pdb=" O PHE H 458 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE H 463 " --> pdb=" O HIS H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 525 Processing helix chain 'I' and resid 409 through 427 Processing helix chain 'I' and resid 429 through 436 removed outlier: 3.939A pdb=" N LYS I 435 " --> pdb=" O GLU I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 449 Processing helix chain 'I' and resid 456 through 466 removed outlier: 4.008A pdb=" N PHE I 461 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR I 462 " --> pdb=" O PHE I 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE I 463 " --> pdb=" O HIS I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 522 through 525 Processing helix chain 'J' and resid 409 through 427 Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.905A pdb=" N LYS J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 449 Processing helix chain 'J' and resid 456 through 466 removed outlier: 4.002A pdb=" N PHE J 461 " --> pdb=" O ASP J 457 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR J 462 " --> pdb=" O PHE J 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE J 463 " --> pdb=" O HIS J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 525 Processing helix chain 'K' and resid 409 through 427 Processing helix chain 'K' and resid 429 through 436 removed outlier: 3.905A pdb=" N LYS K 435 " --> pdb=" O GLU K 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 449 Processing helix chain 'K' and resid 456 through 466 removed outlier: 4.005A pdb=" N PHE K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR K 462 " --> pdb=" O PHE K 458 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE K 463 " --> pdb=" O HIS K 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 522 through 525 Processing helix chain 'L' and resid 409 through 427 Processing helix chain 'L' and resid 429 through 436 removed outlier: 3.950A pdb=" N LYS L 435 " --> pdb=" O GLU L 431 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 Processing helix chain 'L' and resid 456 through 466 removed outlier: 4.001A pdb=" N PHE L 461 " --> pdb=" O ASP L 457 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR L 462 " --> pdb=" O PHE L 458 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE L 463 " --> pdb=" O HIS L 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 522 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 454 removed outlier: 7.679A pdb=" N HIS A 530 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 11.233A pdb=" N GLY A 440 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 11.910A pdb=" N HIS A 532 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N THR A 442 " --> pdb=" O HIS A 532 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N SER A 534 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N PHE A 444 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A 518 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 531 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 516 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS A 533 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU A 514 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY A 535 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN A 512 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA A 490 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL A 485 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS A 492 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 483 " --> pdb=" O CYS A 492 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 494 " --> pdb=" O PRO A 481 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 453 through 454 removed outlier: 7.626A pdb=" N HIS B 530 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 11.174A pdb=" N GLY B 440 " --> pdb=" O HIS B 530 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N HIS B 532 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N THR B 442 " --> pdb=" O HIS B 532 " (cutoff:3.500A) removed outlier: 11.994A pdb=" N SER B 534 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N PHE B 444 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 518 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE B 531 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 516 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS B 533 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU B 514 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B 535 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLN B 512 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA B 490 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL B 485 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS B 492 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 483 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 494 " --> pdb=" O PRO B 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 453 through 454 removed outlier: 7.650A pdb=" N HIS C 530 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N GLY C 440 " --> pdb=" O HIS C 530 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N HIS C 532 " --> pdb=" O GLY C 440 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N THR C 442 " --> pdb=" O HIS C 532 " (cutoff:3.500A) removed outlier: 11.979A pdb=" N SER C 534 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 10.877A pdb=" N PHE C 444 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 518 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE C 531 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR C 516 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS C 533 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU C 514 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY C 535 " --> pdb=" O GLN C 512 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN C 512 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA C 490 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL C 485 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS C 492 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 483 " --> pdb=" O CYS C 492 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA C 494 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 453 through 454 removed outlier: 7.649A pdb=" N HIS D 530 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N GLY D 440 " --> pdb=" O HIS D 530 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N HIS D 532 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N THR D 442 " --> pdb=" O HIS D 532 " (cutoff:3.500A) removed outlier: 12.005A pdb=" N SER D 534 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N PHE D 444 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL D 518 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE D 531 " --> pdb=" O THR D 516 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D 516 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS D 533 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU D 514 " --> pdb=" O CYS D 533 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY D 535 " --> pdb=" O GLN D 512 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLN D 512 " --> pdb=" O GLY D 535 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA D 490 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D 485 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS D 492 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 483 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 494 " --> pdb=" O PRO D 481 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 453 through 454 removed outlier: 7.662A pdb=" N HIS E 530 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N GLY E 440 " --> pdb=" O HIS E 530 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N HIS E 532 " --> pdb=" O GLY E 440 " (cutoff:3.500A) removed outlier: 11.346A pdb=" N THR E 442 " --> pdb=" O HIS E 532 " (cutoff:3.500A) removed outlier: 12.015A pdb=" N SER E 534 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N PHE E 444 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL E 518 " --> pdb=" O VAL E 529 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE E 531 " --> pdb=" O THR E 516 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR E 516 " --> pdb=" O PHE E 531 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS E 533 " --> pdb=" O GLU E 514 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU E 514 " --> pdb=" O CYS E 533 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLY E 535 " --> pdb=" O GLN E 512 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN E 512 " --> pdb=" O GLY E 535 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA E 490 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL E 485 " --> pdb=" O ALA E 490 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS E 492 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL E 483 " --> pdb=" O CYS E 492 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA E 494 " --> pdb=" O PRO E 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 453 through 454 removed outlier: 7.659A pdb=" N HIS F 530 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N GLY F 440 " --> pdb=" O HIS F 530 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N HIS F 532 " --> pdb=" O GLY F 440 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N THR F 442 " --> pdb=" O HIS F 532 " (cutoff:3.500A) removed outlier: 12.006A pdb=" N SER F 534 " --> pdb=" O THR F 442 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N PHE F 444 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL F 518 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE F 531 " --> pdb=" O THR F 516 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR F 516 " --> pdb=" O PHE F 531 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS F 533 " --> pdb=" O GLU F 514 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU F 514 " --> pdb=" O CYS F 533 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY F 535 " --> pdb=" O GLN F 512 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN F 512 " --> pdb=" O GLY F 535 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA F 490 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL F 485 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS F 492 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL F 483 " --> pdb=" O CYS F 492 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA F 494 " --> pdb=" O PRO F 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 453 through 454 removed outlier: 7.661A pdb=" N HIS G 530 " --> pdb=" O ASP G 438 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N GLY G 440 " --> pdb=" O HIS G 530 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N HIS G 532 " --> pdb=" O GLY G 440 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N THR G 442 " --> pdb=" O HIS G 532 " (cutoff:3.500A) removed outlier: 12.016A pdb=" N SER G 534 " --> pdb=" O THR G 442 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N PHE G 444 " --> pdb=" O SER G 534 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL G 518 " --> pdb=" O VAL G 529 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE G 531 " --> pdb=" O THR G 516 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR G 516 " --> pdb=" O PHE G 531 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS G 533 " --> pdb=" O GLU G 514 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU G 514 " --> pdb=" O CYS G 533 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N GLY G 535 " --> pdb=" O GLN G 512 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN G 512 " --> pdb=" O GLY G 535 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA G 490 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL G 485 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS G 492 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL G 483 " --> pdb=" O CYS G 492 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA G 494 " --> pdb=" O PRO G 481 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 453 through 454 removed outlier: 7.649A pdb=" N HIS H 530 " --> pdb=" O ASP H 438 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N GLY H 440 " --> pdb=" O HIS H 530 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N HIS H 532 " --> pdb=" O GLY H 440 " (cutoff:3.500A) removed outlier: 11.322A pdb=" N THR H 442 " --> pdb=" O HIS H 532 " (cutoff:3.500A) removed outlier: 11.997A pdb=" N SER H 534 " --> pdb=" O THR H 442 " (cutoff:3.500A) removed outlier: 10.944A pdb=" N PHE H 444 " --> pdb=" O SER H 534 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL H 518 " --> pdb=" O VAL H 529 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE H 531 " --> pdb=" O THR H 516 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR H 516 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS H 533 " --> pdb=" O GLU H 514 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU H 514 " --> pdb=" O CYS H 533 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLY H 535 " --> pdb=" O GLN H 512 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN H 512 " --> pdb=" O GLY H 535 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA H 490 " --> pdb=" O VAL H 485 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL H 485 " --> pdb=" O ALA H 490 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS H 492 " --> pdb=" O VAL H 483 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL H 483 " --> pdb=" O CYS H 492 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA H 494 " --> pdb=" O PRO H 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 453 through 454 removed outlier: 7.662A pdb=" N HIS I 530 " --> pdb=" O ASP I 438 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N GLY I 440 " --> pdb=" O HIS I 530 " (cutoff:3.500A) removed outlier: 11.938A pdb=" N HIS I 532 " --> pdb=" O GLY I 440 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N THR I 442 " --> pdb=" O HIS I 532 " (cutoff:3.500A) removed outlier: 11.985A pdb=" N SER I 534 " --> pdb=" O THR I 442 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N PHE I 444 " --> pdb=" O SER I 534 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL I 518 " --> pdb=" O VAL I 529 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE I 531 " --> pdb=" O THR I 516 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR I 516 " --> pdb=" O PHE I 531 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS I 533 " --> pdb=" O GLU I 514 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU I 514 " --> pdb=" O CYS I 533 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY I 535 " --> pdb=" O GLN I 512 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN I 512 " --> pdb=" O GLY I 535 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ALA I 490 " --> pdb=" O VAL I 485 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL I 485 " --> pdb=" O ALA I 490 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS I 492 " --> pdb=" O VAL I 483 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL I 483 " --> pdb=" O CYS I 492 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA I 494 " --> pdb=" O PRO I 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 453 through 454 removed outlier: 7.671A pdb=" N HIS J 530 " --> pdb=" O ASP J 438 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N GLY J 440 " --> pdb=" O HIS J 530 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N HIS J 532 " --> pdb=" O GLY J 440 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N THR J 442 " --> pdb=" O HIS J 532 " (cutoff:3.500A) removed outlier: 12.014A pdb=" N SER J 534 " --> pdb=" O THR J 442 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N PHE J 444 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL J 518 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE J 531 " --> pdb=" O THR J 516 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR J 516 " --> pdb=" O PHE J 531 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS J 533 " --> pdb=" O GLU J 514 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU J 514 " --> pdb=" O CYS J 533 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY J 535 " --> pdb=" O GLN J 512 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN J 512 " --> pdb=" O GLY J 535 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA J 490 " --> pdb=" O VAL J 485 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL J 485 " --> pdb=" O ALA J 490 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS J 492 " --> pdb=" O VAL J 483 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL J 483 " --> pdb=" O CYS J 492 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA J 494 " --> pdb=" O PRO J 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 453 through 454 removed outlier: 7.649A pdb=" N HIS K 530 " --> pdb=" O ASP K 438 " (cutoff:3.500A) removed outlier: 11.209A pdb=" N GLY K 440 " --> pdb=" O HIS K 530 " (cutoff:3.500A) removed outlier: 11.891A pdb=" N HIS K 532 " --> pdb=" O GLY K 440 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N THR K 442 " --> pdb=" O HIS K 532 " (cutoff:3.500A) removed outlier: 12.014A pdb=" N SER K 534 " --> pdb=" O THR K 442 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE K 444 " --> pdb=" O SER K 534 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL K 518 " --> pdb=" O VAL K 529 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE K 531 " --> pdb=" O THR K 516 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR K 516 " --> pdb=" O PHE K 531 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS K 533 " --> pdb=" O GLU K 514 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU K 514 " --> pdb=" O CYS K 533 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY K 535 " --> pdb=" O GLN K 512 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLN K 512 " --> pdb=" O GLY K 535 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ALA K 490 " --> pdb=" O VAL K 485 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL K 485 " --> pdb=" O ALA K 490 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS K 492 " --> pdb=" O VAL K 483 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL K 483 " --> pdb=" O CYS K 492 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA K 494 " --> pdb=" O PRO K 481 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 453 through 454 removed outlier: 7.647A pdb=" N HIS L 530 " --> pdb=" O ASP L 438 " (cutoff:3.500A) removed outlier: 11.200A pdb=" N GLY L 440 " --> pdb=" O HIS L 530 " (cutoff:3.500A) removed outlier: 11.925A pdb=" N HIS L 532 " --> pdb=" O GLY L 440 " (cutoff:3.500A) removed outlier: 11.337A pdb=" N THR L 442 " --> pdb=" O HIS L 532 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N SER L 534 " --> pdb=" O THR L 442 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N PHE L 444 " --> pdb=" O SER L 534 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL L 518 " --> pdb=" O VAL L 529 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE L 531 " --> pdb=" O THR L 516 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR L 516 " --> pdb=" O PHE L 531 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS L 533 " --> pdb=" O GLU L 514 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU L 514 " --> pdb=" O CYS L 533 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY L 535 " --> pdb=" O GLN L 512 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN L 512 " --> pdb=" O GLY L 535 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA L 490 " --> pdb=" O VAL L 485 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL L 485 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS L 492 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL L 483 " --> pdb=" O CYS L 492 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA L 494 " --> pdb=" O PRO L 481 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.76 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 12384 1.12 - 1.30: 2306 1.30 - 1.47: 4609 1.47 - 1.64: 6333 1.64 - 1.81: 60 Bond restraints: 25692 Sorted by residual: bond pdb=" CZ PHE I 430 " pdb=" HZ PHE I 430 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CZ PHE C 430 " pdb=" HZ PHE C 430 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLU L 423 " pdb=" H GLU L 423 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LEU C 452 " pdb=" H LEU C 452 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" ND2 ASN I 465 " pdb="HD21 ASN I 465 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 25687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 37410 2.46 - 4.92: 7123 4.92 - 7.37: 1619 7.37 - 9.83: 132 9.83 - 12.29: 36 Bond angle restraints: 46320 Sorted by residual: angle pdb=" CA HIS B 532 " pdb=" CB HIS B 532 " pdb=" CG HIS B 532 " ideal model delta sigma weight residual 113.80 119.79 -5.99 1.00e+00 1.00e+00 3.58e+01 angle pdb=" CA HIS H 532 " pdb=" CB HIS H 532 " pdb=" CG HIS H 532 " ideal model delta sigma weight residual 113.80 119.76 -5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" CA HIS E 532 " pdb=" CB HIS E 532 " pdb=" CG HIS E 532 " ideal model delta sigma weight residual 113.80 119.74 -5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CA HIS J 532 " pdb=" CB HIS J 532 " pdb=" CG HIS J 532 " ideal model delta sigma weight residual 113.80 119.72 -5.92 1.00e+00 1.00e+00 3.51e+01 angle pdb=" CA HIS L 532 " pdb=" CB HIS L 532 " pdb=" CG HIS L 532 " ideal model delta sigma weight residual 113.80 119.64 -5.84 1.00e+00 1.00e+00 3.41e+01 ... (remaining 46315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 11255 17.43 - 34.86: 658 34.86 - 52.29: 129 52.29 - 69.72: 137 69.72 - 87.15: 13 Dihedral angle restraints: 12192 sinusoidal: 6564 harmonic: 5628 Sorted by residual: dihedral pdb=" CA LEU J 466 " pdb=" C LEU J 466 " pdb=" N LEU J 467 " pdb=" CA LEU J 467 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LEU B 466 " pdb=" C LEU B 466 " pdb=" N LEU B 467 " pdb=" CA LEU B 467 " ideal model delta harmonic sigma weight residual -180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA LEU C 466 " pdb=" C LEU C 466 " pdb=" N LEU C 467 " pdb=" CA LEU C 467 " ideal model delta harmonic sigma weight residual -180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 12189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1068 0.066 - 0.132: 548 0.132 - 0.197: 209 0.197 - 0.263: 83 0.263 - 0.329: 12 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CA ASN E 426 " pdb=" N ASN E 426 " pdb=" C ASN E 426 " pdb=" CB ASN E 426 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA ASN K 426 " pdb=" N ASN K 426 " pdb=" C ASN K 426 " pdb=" CB ASN K 426 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA ASN C 426 " pdb=" N ASN C 426 " pdb=" C ASN C 426 " pdb=" CB ASN C 426 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 1917 not shown) Planarity restraints: 3924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 495 " 0.118 2.00e-02 2.50e+03 4.91e-02 7.23e+01 pdb=" CG TYR G 495 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR G 495 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR G 495 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR G 495 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR G 495 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR G 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR G 495 " 0.096 2.00e-02 2.50e+03 pdb=" HD1 TYR G 495 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 TYR G 495 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 TYR G 495 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR G 495 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 495 " 0.117 2.00e-02 2.50e+03 4.83e-02 7.00e+01 pdb=" CG TYR H 495 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR H 495 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR H 495 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR H 495 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR H 495 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR H 495 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR H 495 " 0.091 2.00e-02 2.50e+03 pdb=" HD1 TYR H 495 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 TYR H 495 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TYR H 495 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR H 495 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 495 " 0.114 2.00e-02 2.50e+03 4.75e-02 6.77e+01 pdb=" CG TYR I 495 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR I 495 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR I 495 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR I 495 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR I 495 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR I 495 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR I 495 " 0.093 2.00e-02 2.50e+03 pdb=" HD1 TYR I 495 " -0.030 2.00e-02 2.50e+03 pdb=" HD2 TYR I 495 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TYR I 495 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR I 495 " -0.009 2.00e-02 2.50e+03 ... (remaining 3921 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1940 2.21 - 2.81: 43174 2.81 - 3.40: 67060 3.40 - 4.00: 91837 4.00 - 4.60: 133162 Nonbonded interactions: 337173 Sorted by model distance: nonbonded pdb=" HG SER D 443 " pdb=" OE2 GLU D 445 " model vdw 1.612 2.450 nonbonded pdb=" HG SER F 443 " pdb=" OE2 GLU F 445 " model vdw 1.624 2.450 nonbonded pdb=" HG SER E 443 " pdb=" OE2 GLU E 445 " model vdw 1.628 2.450 nonbonded pdb=" HG SER H 443 " pdb=" OE2 GLU H 445 " model vdw 1.631 2.450 nonbonded pdb=" HG SER G 443 " pdb=" OE2 GLU G 445 " model vdw 1.632 2.450 ... (remaining 337168 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 3.910 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: 0.160 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.130 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.013 0.039 13272 Z= 0.834 Angle : 1.910 8.856 18036 Z= 1.299 Chirality : 0.093 0.329 1920 Planarity : 0.013 0.069 2412 Dihedral : 13.014 87.147 4872 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.21), residues: 1596 helix: -2.44 (0.16), residues: 480 sheet: 3.81 (0.20), residues: 492 loop : -0.50 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 517 TYR 0.102 0.031 TYR G 495 PHE 0.053 0.011 PHE B 444 TRP 0.026 0.006 TRP J 519 HIS 0.011 0.004 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.01336 (13272) covalent geometry : angle 1.90959 (18036) hydrogen bonds : bond 0.19914 ( 589) hydrogen bonds : angle 6.40048 ( 1587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 416 LYS cc_start: 0.8279 (tptt) cc_final: 0.7975 (ttpt) REVERT: A 417 THR cc_start: 0.7496 (m) cc_final: 0.7229 (t) REVERT: A 423 GLU cc_start: 0.8062 (pt0) cc_final: 0.7645 (pt0) REVERT: A 436 ILE cc_start: 0.6782 (mt) cc_final: 0.5706 (mp) REVERT: B 412 GLN cc_start: 0.7338 (tp40) cc_final: 0.7103 (mm110) REVERT: B 413 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6977 (tm-30) REVERT: B 416 LYS cc_start: 0.8347 (tptt) cc_final: 0.8024 (ttpt) REVERT: B 417 THR cc_start: 0.7534 (m) cc_final: 0.7267 (t) REVERT: B 436 ILE cc_start: 0.6926 (mt) cc_final: 0.5541 (mp) REVERT: B 454 GLU cc_start: 0.8254 (tt0) cc_final: 0.7905 (tt0) REVERT: B 488 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7542 (pm20) REVERT: C 416 LYS cc_start: 0.8254 (tptt) cc_final: 0.8043 (ttpt) REVERT: C 417 THR cc_start: 0.7651 (m) cc_final: 0.7445 (t) REVERT: C 423 GLU cc_start: 0.8160 (pt0) cc_final: 0.7879 (pt0) REVERT: C 488 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7406 (pm20) REVERT: C 497 ARG cc_start: 0.8407 (ttt180) cc_final: 0.7995 (ttm-80) REVERT: C 525 LYS cc_start: 0.7655 (tttp) cc_final: 0.7392 (tmtt) REVERT: D 413 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7058 (tm-30) REVERT: D 416 LYS cc_start: 0.8143 (tptt) cc_final: 0.7913 (ttpt) REVERT: D 417 THR cc_start: 0.7474 (m) cc_final: 0.7070 (t) REVERT: D 423 GLU cc_start: 0.8125 (pt0) cc_final: 0.7844 (pt0) REVERT: D 436 ILE cc_start: 0.7074 (mt) cc_final: 0.5775 (mp) REVERT: D 488 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7679 (pm20) REVERT: E 412 GLN cc_start: 0.7283 (tp40) cc_final: 0.7074 (mm110) REVERT: E 413 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6922 (tm-30) REVERT: E 416 LYS cc_start: 0.8285 (tptt) cc_final: 0.7984 (ttpt) REVERT: E 417 THR cc_start: 0.7668 (m) cc_final: 0.7242 (t) REVERT: E 436 ILE cc_start: 0.6834 (mt) cc_final: 0.5516 (mp) REVERT: E 488 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7413 (pm20) REVERT: F 417 THR cc_start: 0.7682 (m) cc_final: 0.7386 (t) REVERT: F 423 GLU cc_start: 0.8065 (pt0) cc_final: 0.7727 (pt0) REVERT: F 454 GLU cc_start: 0.8291 (tt0) cc_final: 0.8054 (tt0) REVERT: F 488 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7424 (pm20) REVERT: F 497 ARG cc_start: 0.8469 (ttt180) cc_final: 0.8048 (ttm-80) REVERT: G 413 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7056 (tm-30) REVERT: G 416 LYS cc_start: 0.8227 (tptt) cc_final: 0.7970 (ttpt) REVERT: G 417 THR cc_start: 0.7614 (m) cc_final: 0.7293 (t) REVERT: G 423 GLU cc_start: 0.8008 (pt0) cc_final: 0.7656 (pt0) REVERT: G 436 ILE cc_start: 0.7015 (mt) cc_final: 0.5645 (mp) REVERT: G 488 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7661 (pm20) REVERT: H 412 GLN cc_start: 0.7319 (tp40) cc_final: 0.7101 (mm110) REVERT: H 413 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7017 (tm-30) REVERT: H 416 LYS cc_start: 0.8302 (tptt) cc_final: 0.7998 (ttpt) REVERT: H 417 THR cc_start: 0.7687 (m) cc_final: 0.7297 (t) REVERT: H 423 GLU cc_start: 0.8101 (pt0) cc_final: 0.7731 (pt0) REVERT: H 436 ILE cc_start: 0.6798 (mt) cc_final: 0.5591 (mp) REVERT: H 454 GLU cc_start: 0.8196 (tt0) cc_final: 0.7851 (tt0) REVERT: H 488 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7612 (pm20) REVERT: I 416 LYS cc_start: 0.8245 (tptt) cc_final: 0.8009 (ttpt) REVERT: I 417 THR cc_start: 0.7687 (m) cc_final: 0.7389 (t) REVERT: I 423 GLU cc_start: 0.8023 (pt0) cc_final: 0.7697 (pt0) REVERT: I 454 GLU cc_start: 0.8145 (tt0) cc_final: 0.7859 (tt0) REVERT: I 488 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7525 (pm20) REVERT: I 497 ARG cc_start: 0.8410 (ttt180) cc_final: 0.8036 (ttm-80) REVERT: J 413 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7096 (tm-30) REVERT: J 416 LYS cc_start: 0.8313 (tptt) cc_final: 0.8008 (ttpt) REVERT: J 417 THR cc_start: 0.7570 (m) cc_final: 0.7254 (t) REVERT: J 423 GLU cc_start: 0.8078 (pt0) cc_final: 0.7723 (pt0) REVERT: J 436 ILE cc_start: 0.6853 (mt) cc_final: 0.5709 (mp) REVERT: J 488 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7653 (pm20) REVERT: K 412 GLN cc_start: 0.7375 (tp40) cc_final: 0.7142 (mm110) REVERT: K 413 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7071 (tm-30) REVERT: K 416 LYS cc_start: 0.8334 (tptt) cc_final: 0.8017 (ttpt) REVERT: K 417 THR cc_start: 0.7632 (m) cc_final: 0.7356 (t) REVERT: K 436 ILE cc_start: 0.6881 (mt) cc_final: 0.5612 (mp) REVERT: K 488 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7611 (pm20) REVERT: L 417 THR cc_start: 0.7646 (m) cc_final: 0.7423 (t) REVERT: L 423 GLU cc_start: 0.8089 (pt0) cc_final: 0.7795 (pt0) REVERT: L 488 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7490 (pm20) REVERT: L 497 ARG cc_start: 0.8384 (ttt180) cc_final: 0.7991 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 1.8742 time to fit residues: 440.6039 Evaluate side-chains 191 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 ASN A 520 HIS B 470 ASN B 520 HIS C 470 ASN C 520 HIS D 470 ASN D 520 HIS E 470 ASN E 520 HIS F 470 ASN F 520 HIS G 470 ASN G 505 GLN G 520 HIS H 470 ASN H 520 HIS I 470 ASN I 520 HIS J 470 ASN J 520 HIS K 470 ASN K 520 HIS L 470 ASN L 520 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.216351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.190151 restraints weight = 32002.641| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.41 r_work: 0.4051 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13272 Z= 0.182 Angle : 0.729 6.116 18036 Z= 0.404 Chirality : 0.048 0.139 1920 Planarity : 0.005 0.046 2412 Dihedral : 6.038 20.644 1752 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.51 % Allowed : 7.03 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.20), residues: 1596 helix: -1.05 (0.22), residues: 432 sheet: 2.11 (0.21), residues: 588 loop : -0.41 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 410 TYR 0.009 0.002 TYR L 462 PHE 0.013 0.002 PHE B 444 TRP 0.010 0.002 TRP K 519 HIS 0.005 0.002 HIS A 520 Details of bonding type rmsd covalent geometry : bond 0.00370 (13272) covalent geometry : angle 0.72914 (18036) hydrogen bonds : bond 0.06566 ( 589) hydrogen bonds : angle 5.74980 ( 1587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.684 Fit side-chains REVERT: A 435 LYS cc_start: 0.7658 (mtpp) cc_final: 0.7431 (mtpt) REVERT: A 436 ILE cc_start: 0.5894 (mt) cc_final: 0.5024 (mp) REVERT: B 413 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 436 ILE cc_start: 0.5965 (mt) cc_final: 0.5012 (mp) REVERT: D 436 ILE cc_start: 0.5969 (mt) cc_final: 0.5100 (mp) REVERT: E 413 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6719 (tm-30) REVERT: E 436 ILE cc_start: 0.5982 (mt) cc_final: 0.5079 (mp) REVERT: G 436 ILE cc_start: 0.6009 (mt) cc_final: 0.5004 (mp) REVERT: H 436 ILE cc_start: 0.5987 (mt) cc_final: 0.5080 (mp) REVERT: J 435 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7457 (mtpt) REVERT: J 436 ILE cc_start: 0.5986 (mt) cc_final: 0.5059 (mp) REVERT: K 413 GLU cc_start: 0.6974 (tm-30) cc_final: 0.6725 (tm-30) REVERT: K 436 ILE cc_start: 0.6017 (mt) cc_final: 0.5126 (mp) outliers start: 7 outliers final: 5 residues processed: 204 average time/residue: 1.5309 time to fit residues: 335.7795 Evaluate side-chains 167 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN C 505 GLN D 505 GLN F 505 GLN H 505 GLN I 505 GLN J 505 GLN K 505 GLN L 505 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.203990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174516 restraints weight = 29737.469| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.52 r_work: 0.3836 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13272 Z= 0.188 Angle : 0.704 6.390 18036 Z= 0.384 Chirality : 0.049 0.137 1920 Planarity : 0.006 0.047 2412 Dihedral : 5.658 19.504 1752 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.54 % Allowed : 10.07 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1596 helix: -0.82 (0.21), residues: 420 sheet: 2.18 (0.21), residues: 552 loop : -1.19 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 509 TYR 0.011 0.002 TYR C 462 PHE 0.017 0.002 PHE E 444 TRP 0.009 0.002 TRP C 519 HIS 0.007 0.002 HIS C 530 Details of bonding type rmsd covalent geometry : bond 0.00403 (13272) covalent geometry : angle 0.70423 (18036) hydrogen bonds : bond 0.06119 ( 589) hydrogen bonds : angle 5.42355 ( 1587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 LYS cc_start: 0.7864 (mtpp) cc_final: 0.7617 (mtpt) REVERT: H 436 ILE cc_start: 0.5898 (mt) cc_final: 0.4908 (mp) REVERT: J 435 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7669 (mtpt) REVERT: K 436 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5037 (mp) outliers start: 35 outliers final: 13 residues processed: 196 average time/residue: 1.5612 time to fit residues: 328.7040 Evaluate side-chains 184 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain L residue 436 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 GLN E 505 GLN F 420 GLN L 420 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.203389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174871 restraints weight = 29812.656| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.49 r_work: 0.3848 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13272 Z= 0.157 Angle : 0.632 5.799 18036 Z= 0.341 Chirality : 0.046 0.129 1920 Planarity : 0.005 0.038 2412 Dihedral : 5.253 18.269 1752 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.75 % Allowed : 12.25 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.21), residues: 1596 helix: -0.85 (0.20), residues: 468 sheet: 1.74 (0.22), residues: 588 loop : -0.93 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 517 TYR 0.010 0.002 TYR L 462 PHE 0.014 0.002 PHE J 444 TRP 0.007 0.001 TRP F 519 HIS 0.005 0.002 HIS C 530 Details of bonding type rmsd covalent geometry : bond 0.00339 (13272) covalent geometry : angle 0.63156 (18036) hydrogen bonds : bond 0.05158 ( 589) hydrogen bonds : angle 5.23888 ( 1587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 435 LYS cc_start: 0.7864 (mttp) cc_final: 0.7621 (mtpt) REVERT: B 515 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: D 416 LYS cc_start: 0.7602 (ttpt) cc_final: 0.7375 (ttpp) REVERT: E 515 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: G 416 LYS cc_start: 0.7607 (ttpt) cc_final: 0.7384 (ttpp) REVERT: H 515 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: I 509 ARG cc_start: 0.7259 (mmt-90) cc_final: 0.6987 (mmt180) REVERT: J 416 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7402 (ttpp) REVERT: J 435 LYS cc_start: 0.7886 (mttp) cc_final: 0.7640 (mtpt) REVERT: J 509 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6563 (mtp180) REVERT: K 515 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: L 509 ARG cc_start: 0.7290 (mmt-90) cc_final: 0.7016 (mmp-170) outliers start: 38 outliers final: 22 residues processed: 197 average time/residue: 1.5613 time to fit residues: 331.1156 Evaluate side-chains 196 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain I residue 505 GLN Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 505 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.200358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171441 restraints weight = 29500.376| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.49 r_work: 0.3814 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13272 Z= 0.226 Angle : 0.734 7.251 18036 Z= 0.399 Chirality : 0.050 0.136 1920 Planarity : 0.007 0.094 2412 Dihedral : 5.451 19.025 1752 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.06 % Allowed : 12.25 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1596 helix: -1.10 (0.20), residues: 468 sheet: 1.62 (0.21), residues: 588 loop : -1.17 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 521 TYR 0.012 0.003 TYR E 462 PHE 0.016 0.002 PHE E 444 TRP 0.009 0.002 TRP C 519 HIS 0.007 0.002 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00508 (13272) covalent geometry : angle 0.73399 (18036) hydrogen bonds : bond 0.06465 ( 589) hydrogen bonds : angle 5.31544 ( 1587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LYS cc_start: 0.7932 (mttp) cc_final: 0.7703 (mtpt) REVERT: B 515 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: C 410 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6370 (mtp85) REVERT: E 515 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: H 515 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: J 416 LYS cc_start: 0.7736 (ttpt) cc_final: 0.7521 (ttpp) REVERT: J 435 LYS cc_start: 0.7955 (mttp) cc_final: 0.7720 (mtpt) REVERT: J 509 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6575 (mtp180) REVERT: K 515 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: L 505 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6781 (pt0) outliers start: 56 outliers final: 33 residues processed: 221 average time/residue: 1.5612 time to fit residues: 371.5879 Evaluate side-chains 207 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 505 GLN Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 505 GLN Chi-restraints excluded: chain L residue 516 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.202461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.174236 restraints weight = 29775.516| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.47 r_work: 0.3849 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13272 Z= 0.146 Angle : 0.615 5.686 18036 Z= 0.332 Chirality : 0.045 0.128 1920 Planarity : 0.005 0.058 2412 Dihedral : 5.087 18.160 1752 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.13 % Allowed : 13.55 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.21), residues: 1596 helix: -0.72 (0.21), residues: 468 sheet: 1.71 (0.22), residues: 588 loop : -1.01 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 521 TYR 0.010 0.002 TYR J 462 PHE 0.012 0.001 PHE K 444 TRP 0.006 0.001 TRP C 519 HIS 0.004 0.001 HIS K 530 Details of bonding type rmsd covalent geometry : bond 0.00317 (13272) covalent geometry : angle 0.61460 (18036) hydrogen bonds : bond 0.04907 ( 589) hydrogen bonds : angle 5.13700 ( 1587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 LYS cc_start: 0.7692 (ttpt) cc_final: 0.7469 (ttpp) REVERT: A 435 LYS cc_start: 0.7867 (mttp) cc_final: 0.7645 (mtpt) REVERT: A 511 SER cc_start: 0.8957 (p) cc_final: 0.8712 (m) REVERT: B 515 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: D 416 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7464 (ttpp) REVERT: D 511 SER cc_start: 0.8942 (p) cc_final: 0.8701 (m) REVERT: E 413 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6300 (tm-30) REVERT: E 505 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6358 (pt0) REVERT: E 515 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: G 416 LYS cc_start: 0.7681 (ttpt) cc_final: 0.7458 (ttpp) REVERT: G 511 SER cc_start: 0.8957 (p) cc_final: 0.8708 (m) REVERT: H 515 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: J 416 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7486 (ttpp) REVERT: J 435 LYS cc_start: 0.7885 (mttp) cc_final: 0.7662 (mtpt) REVERT: J 509 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6563 (mtp180) REVERT: J 511 SER cc_start: 0.8944 (p) cc_final: 0.8700 (m) REVERT: K 413 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6301 (tm-30) REVERT: K 515 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7969 (mt-10) outliers start: 57 outliers final: 38 residues processed: 211 average time/residue: 1.5041 time to fit residues: 343.1825 Evaluate side-chains 217 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 456 MET Chi-restraints excluded: chain E residue 505 GLN Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 456 MET Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain K residue 456 MET Chi-restraints excluded: chain K residue 474 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 505 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.201447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172678 restraints weight = 29636.303| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.50 r_work: 0.3829 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13272 Z= 0.166 Angle : 0.630 6.096 18036 Z= 0.341 Chirality : 0.046 0.131 1920 Planarity : 0.006 0.048 2412 Dihedral : 5.037 17.766 1752 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.49 % Allowed : 13.19 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1596 helix: -0.68 (0.21), residues: 468 sheet: 1.65 (0.22), residues: 588 loop : -1.01 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 521 TYR 0.010 0.002 TYR G 462 PHE 0.013 0.002 PHE K 444 TRP 0.007 0.001 TRP C 519 HIS 0.004 0.002 HIS F 459 Details of bonding type rmsd covalent geometry : bond 0.00366 (13272) covalent geometry : angle 0.62973 (18036) hydrogen bonds : bond 0.05267 ( 589) hydrogen bonds : angle 5.11559 ( 1587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 416 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7493 (ttpp) REVERT: A 435 LYS cc_start: 0.7938 (mttp) cc_final: 0.7720 (mtpt) REVERT: A 511 SER cc_start: 0.8954 (p) cc_final: 0.8721 (m) REVERT: B 413 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6381 (tm-30) REVERT: B 515 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: D 416 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7499 (ttpp) REVERT: D 511 SER cc_start: 0.8967 (p) cc_final: 0.8736 (m) REVERT: E 413 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6374 (tm-30) REVERT: E 505 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6344 (pt0) REVERT: E 515 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: G 416 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7495 (ttpp) REVERT: G 511 SER cc_start: 0.8974 (p) cc_final: 0.8740 (m) REVERT: H 515 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: J 416 LYS cc_start: 0.7718 (ttpt) cc_final: 0.7501 (ttpp) REVERT: J 435 LYS cc_start: 0.7952 (mttp) cc_final: 0.7727 (mtpt) REVERT: J 509 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6592 (mtp180) REVERT: J 511 SER cc_start: 0.8942 (p) cc_final: 0.8712 (m) REVERT: K 505 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6462 (pt0) REVERT: K 515 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7990 (mt-10) outliers start: 62 outliers final: 48 residues processed: 220 average time/residue: 1.4553 time to fit residues: 347.0644 Evaluate side-chains 231 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 456 MET Chi-restraints excluded: chain E residue 505 GLN Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 505 GLN Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 456 MET Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 505 GLN Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain K residue 456 MET Chi-restraints excluded: chain K residue 474 ILE Chi-restraints excluded: chain K residue 505 GLN Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 505 GLN Chi-restraints excluded: chain L residue 516 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.201873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.173646 restraints weight = 29755.312| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.47 r_work: 0.3833 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13272 Z= 0.153 Angle : 0.610 5.792 18036 Z= 0.330 Chirality : 0.045 0.128 1920 Planarity : 0.005 0.041 2412 Dihedral : 4.917 17.095 1752 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.49 % Allowed : 13.62 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.21), residues: 1596 helix: -0.57 (0.21), residues: 468 sheet: 1.69 (0.22), residues: 588 loop : -0.94 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 521 TYR 0.010 0.002 TYR J 462 PHE 0.012 0.002 PHE E 444 TRP 0.006 0.001 TRP I 519 HIS 0.004 0.001 HIS K 530 Details of bonding type rmsd covalent geometry : bond 0.00336 (13272) covalent geometry : angle 0.60998 (18036) hydrogen bonds : bond 0.04954 ( 589) hydrogen bonds : angle 5.05321 ( 1587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 0.757 Fit side-chains REVERT: A 416 LYS cc_start: 0.7695 (ttpt) cc_final: 0.7468 (ttpp) REVERT: A 435 LYS cc_start: 0.7920 (mttp) cc_final: 0.7702 (mtpt) REVERT: A 511 SER cc_start: 0.8939 (p) cc_final: 0.8722 (m) REVERT: B 413 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6482 (tm-30) REVERT: B 488 GLU cc_start: 0.7395 (tt0) cc_final: 0.7169 (tt0) REVERT: B 515 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: D 416 LYS cc_start: 0.7725 (ttpt) cc_final: 0.7500 (ttpp) REVERT: D 511 SER cc_start: 0.8938 (p) cc_final: 0.8730 (m) REVERT: E 413 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6452 (tm-30) REVERT: E 488 GLU cc_start: 0.7402 (tt0) cc_final: 0.7167 (tt0) REVERT: E 505 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6253 (pt0) REVERT: E 515 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: G 416 LYS cc_start: 0.7718 (ttpt) cc_final: 0.7493 (ttpp) REVERT: G 511 SER cc_start: 0.8948 (p) cc_final: 0.8733 (m) REVERT: H 488 GLU cc_start: 0.7404 (tt0) cc_final: 0.7133 (tt0) REVERT: H 505 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.6257 (pt0) REVERT: H 515 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: J 416 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7508 (ttpp) REVERT: J 435 LYS cc_start: 0.7928 (mttp) cc_final: 0.7707 (mtpt) REVERT: J 509 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6583 (mtp180) REVERT: J 511 SER cc_start: 0.8925 (p) cc_final: 0.8710 (m) REVERT: K 413 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6424 (tm-30) REVERT: K 488 GLU cc_start: 0.7378 (tt0) cc_final: 0.7137 (tt0) REVERT: K 515 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7954 (mt-10) outliers start: 62 outliers final: 43 residues processed: 227 average time/residue: 1.3934 time to fit residues: 343.5891 Evaluate side-chains 231 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 GLN Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 505 GLN Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain H residue 505 GLN Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 441 LEU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 505 GLN Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain K residue 474 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 505 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 123 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175961 restraints weight = 29648.816| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.50 r_work: 0.3859 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13272 Z= 0.119 Angle : 0.554 5.033 18036 Z= 0.297 Chirality : 0.044 0.127 1920 Planarity : 0.005 0.038 2412 Dihedral : 4.670 15.932 1752 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.84 % Allowed : 15.36 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.21), residues: 1596 helix: -0.23 (0.21), residues: 468 sheet: 1.82 (0.22), residues: 588 loop : -0.81 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 521 TYR 0.008 0.001 TYR J 462 PHE 0.011 0.001 PHE K 444 TRP 0.006 0.001 TRP H 519 HIS 0.003 0.001 HIS K 530 Details of bonding type rmsd covalent geometry : bond 0.00254 (13272) covalent geometry : angle 0.55428 (18036) hydrogen bonds : bond 0.04092 ( 589) hydrogen bonds : angle 4.87207 ( 1587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.604 Fit side-chains REVERT: A 416 LYS cc_start: 0.7675 (ttpt) cc_final: 0.7452 (ttpp) REVERT: A 435 LYS cc_start: 0.7890 (mttp) cc_final: 0.7681 (mtpt) REVERT: B 413 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6436 (tm-30) REVERT: B 488 GLU cc_start: 0.7394 (tt0) cc_final: 0.7148 (tt0) REVERT: B 515 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: D 416 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7459 (ttpp) REVERT: E 413 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6436 (tm-30) REVERT: E 488 GLU cc_start: 0.7405 (tt0) cc_final: 0.7146 (tt0) REVERT: E 505 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.6156 (pt0) REVERT: E 515 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: G 416 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7455 (ttpp) REVERT: H 488 GLU cc_start: 0.7403 (tt0) cc_final: 0.7180 (tt0) REVERT: H 515 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: I 505 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: J 416 LYS cc_start: 0.7690 (ttpt) cc_final: 0.7456 (ttpp) REVERT: J 435 LYS cc_start: 0.7909 (mttp) cc_final: 0.7693 (mtpt) REVERT: J 509 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6543 (mtp180) REVERT: K 413 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6389 (tm-30) REVERT: K 488 GLU cc_start: 0.7376 (tt0) cc_final: 0.7114 (tt0) REVERT: K 515 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7864 (mt-10) outliers start: 53 outliers final: 34 residues processed: 228 average time/residue: 1.4305 time to fit residues: 353.7739 Evaluate side-chains 234 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 GLN Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 505 GLN Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain K residue 474 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 505 GLN Chi-restraints excluded: chain L residue 516 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.201725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172548 restraints weight = 29179.880| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.50 r_work: 0.3822 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13272 Z= 0.193 Angle : 0.660 6.542 18036 Z= 0.358 Chirality : 0.047 0.130 1920 Planarity : 0.006 0.044 2412 Dihedral : 4.888 16.421 1752 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.70 % Allowed : 15.87 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.21), residues: 1596 helix: -0.55 (0.21), residues: 468 sheet: 1.79 (0.22), residues: 576 loop : -1.15 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 521 TYR 0.011 0.003 TYR G 462 PHE 0.014 0.002 PHE A 444 TRP 0.008 0.001 TRP L 519 HIS 0.005 0.002 HIS E 532 Details of bonding type rmsd covalent geometry : bond 0.00434 (13272) covalent geometry : angle 0.65985 (18036) hydrogen bonds : bond 0.05571 ( 589) hydrogen bonds : angle 5.07147 ( 1587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.754 Fit side-chains REVERT: A 416 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7482 (ttpp) REVERT: A 435 LYS cc_start: 0.7926 (mttp) cc_final: 0.7721 (mtpt) REVERT: B 413 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6462 (tm-30) REVERT: B 488 GLU cc_start: 0.7364 (tt0) cc_final: 0.7160 (tt0) REVERT: B 515 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: D 416 LYS cc_start: 0.7735 (ttpt) cc_final: 0.7505 (ttpp) REVERT: E 413 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6417 (tm-30) REVERT: E 488 GLU cc_start: 0.7357 (tt0) cc_final: 0.7145 (tt0) REVERT: E 505 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.6200 (pt0) REVERT: E 515 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: G 416 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7507 (ttpp) REVERT: H 488 GLU cc_start: 0.7386 (tt0) cc_final: 0.7182 (tt0) REVERT: H 515 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: J 416 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7501 (ttpp) REVERT: J 435 LYS cc_start: 0.7923 (mttp) cc_final: 0.7712 (mtpt) REVERT: J 509 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6584 (mtp180) REVERT: K 413 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6398 (tm-30) REVERT: K 488 GLU cc_start: 0.7355 (tt0) cc_final: 0.7136 (tt0) REVERT: K 515 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: L 505 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6825 (pt0) outliers start: 51 outliers final: 39 residues processed: 226 average time/residue: 1.4740 time to fit residues: 360.8937 Evaluate side-chains 230 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain D residue 417 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 GLN Chi-restraints excluded: chain E residue 515 GLU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain F residue 474 ILE Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain G residue 417 THR Chi-restraints excluded: chain G residue 436 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 436 ILE Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 515 GLU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 516 THR Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 417 THR Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain K residue 474 ILE Chi-restraints excluded: chain K residue 515 GLU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 505 GLN Chi-restraints excluded: chain L residue 516 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.203680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.175029 restraints weight = 29505.882| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.49 r_work: 0.3857 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13272 Z= 0.126 Angle : 0.568 5.304 18036 Z= 0.305 Chirality : 0.044 0.128 1920 Planarity : 0.005 0.039 2412 Dihedral : 4.643 15.828 1752 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.55 % Allowed : 16.01 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.21), residues: 1596 helix: -0.15 (0.22), residues: 468 sheet: 1.98 (0.22), residues: 576 loop : -0.97 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 521 TYR 0.008 0.001 TYR J 462 PHE 0.011 0.001 PHE K 444 TRP 0.006 0.001 TRP C 519 HIS 0.003 0.001 HIS K 530 Details of bonding type rmsd covalent geometry : bond 0.00270 (13272) covalent geometry : angle 0.56793 (18036) hydrogen bonds : bond 0.04265 ( 589) hydrogen bonds : angle 4.89712 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9354.16 seconds wall clock time: 159 minutes 2.19 seconds (9542.19 seconds total)