Starting phenix.real_space_refine on Mon Sep 30 10:53:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t18_40957/09_2024/8t18_40957.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t18_40957/09_2024/8t18_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t18_40957/09_2024/8t18_40957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t18_40957/09_2024/8t18_40957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t18_40957/09_2024/8t18_40957.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t18_40957/09_2024/8t18_40957.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.71, per 1000 atoms: 0.54 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: 5.97 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.78 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: 9.30 Time building geometry restraints manager: 7.28 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: 0.00 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: 2.420 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: 0.490 Extract box with map and model: 1.110 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 55.620 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.170 ------------------------------------------------------------------------------- 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= 0.878 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (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 TRP 0.026 0.006 TRP J 519 HIS 0.011 0.004 HIS A 520 PHE 0.053 0.011 PHE B 444 TYR 0.102 0.031 TYR G 495 ARG 0.006 0.001 ARG H 517 *********************** 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 fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.063 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: 3.4696 time to fit residues: 818.8994 Evaluate side-chains 191 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 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 505 GLN J 520 HIS K 470 ASN K 520 HIS L 470 ASN L 520 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2184 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= 0.244 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 : 0.58 % Allowed : 6.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (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 TRP 0.010 0.002 TRP K 519 HIS 0.005 0.002 HIS A 520 PHE 0.013 0.002 PHE B 444 TYR 0.009 0.002 TYR L 462 ARG 0.003 0.000 ARG I 410 *********************** 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 211 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 2.081 Fit side-chains REVERT: A 413 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 416 LYS cc_start: 0.8093 (tptt) cc_final: 0.7874 (ttpt) REVERT: A 417 THR cc_start: 0.7341 (m) cc_final: 0.7101 (t) REVERT: A 435 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7940 (mtpt) REVERT: A 436 ILE cc_start: 0.6546 (mt) cc_final: 0.5460 (mp) REVERT: A 454 GLU cc_start: 0.8163 (tt0) cc_final: 0.7898 (tt0) REVERT: B 412 GLN cc_start: 0.7371 (tp40) cc_final: 0.7082 (mm110) REVERT: B 413 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7051 (tm-30) REVERT: B 416 LYS cc_start: 0.8245 (tptt) cc_final: 0.7950 (ttpt) REVERT: B 417 THR cc_start: 0.7382 (m) cc_final: 0.7109 (t) REVERT: B 436 ILE cc_start: 0.6818 (mt) cc_final: 0.5504 (mp) REVERT: B 488 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7570 (pm20) REVERT: C 417 THR cc_start: 0.7583 (m) cc_final: 0.7352 (t) REVERT: C 488 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7405 (pm20) REVERT: C 525 LYS cc_start: 0.7547 (tttp) cc_final: 0.7292 (tmtt) REVERT: D 413 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7168 (tm-30) REVERT: D 417 THR cc_start: 0.7308 (m) cc_final: 0.6982 (t) REVERT: D 436 ILE cc_start: 0.6855 (mt) cc_final: 0.5585 (mp) REVERT: D 454 GLU cc_start: 0.8162 (tt0) cc_final: 0.7868 (tt0) REVERT: D 488 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7442 (pm20) REVERT: E 412 GLN cc_start: 0.7302 (tp40) cc_final: 0.7037 (mm110) REVERT: E 413 GLU cc_start: 0.7328 (tm-30) cc_final: 0.7010 (tm-30) REVERT: E 416 LYS cc_start: 0.8154 (tptt) cc_final: 0.7911 (ttpt) REVERT: E 417 THR cc_start: 0.7463 (m) cc_final: 0.7075 (t) REVERT: E 436 ILE cc_start: 0.6613 (mt) cc_final: 0.5361 (mp) REVERT: E 488 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7524 (pm20) REVERT: F 417 THR cc_start: 0.7556 (m) cc_final: 0.7230 (t) REVERT: F 454 GLU cc_start: 0.8079 (tt0) cc_final: 0.7834 (tt0) REVERT: F 488 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7447 (pm20) REVERT: G 413 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7191 (tm-30) REVERT: G 417 THR cc_start: 0.7407 (m) cc_final: 0.7135 (t) REVERT: G 436 ILE cc_start: 0.6792 (mt) cc_final: 0.5464 (mp) REVERT: G 454 GLU cc_start: 0.8129 (tt0) cc_final: 0.7774 (tt0) REVERT: G 488 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7446 (pm20) REVERT: H 412 GLN cc_start: 0.7370 (tp40) cc_final: 0.7107 (mm110) REVERT: H 413 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7142 (tm-30) REVERT: H 416 LYS cc_start: 0.8181 (tptt) cc_final: 0.7905 (ttpt) REVERT: H 417 THR cc_start: 0.7535 (m) cc_final: 0.7172 (t) REVERT: H 436 ILE cc_start: 0.6700 (mt) cc_final: 0.5537 (mp) REVERT: H 488 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7492 (pm20) REVERT: I 417 THR cc_start: 0.7558 (m) cc_final: 0.7251 (t) REVERT: I 454 GLU cc_start: 0.7970 (tt0) cc_final: 0.7695 (tt0) REVERT: I 488 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7412 (pm20) REVERT: J 413 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7221 (tm-30) REVERT: J 416 LYS cc_start: 0.8121 (tptt) cc_final: 0.7902 (ttpt) REVERT: J 417 THR cc_start: 0.7429 (m) cc_final: 0.7159 (t) REVERT: J 436 ILE cc_start: 0.6696 (mt) cc_final: 0.5557 (mp) REVERT: J 454 GLU cc_start: 0.8141 (tt0) cc_final: 0.7843 (tt0) REVERT: J 488 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7474 (pm20) REVERT: K 412 GLN cc_start: 0.7424 (tp40) cc_final: 0.7084 (mm110) REVERT: K 413 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7123 (tm-30) REVERT: K 416 LYS cc_start: 0.8230 (tptt) cc_final: 0.7970 (ttpt) REVERT: K 417 THR cc_start: 0.7457 (m) cc_final: 0.7183 (t) REVERT: K 436 ILE cc_start: 0.6724 (mt) cc_final: 0.5502 (mp) REVERT: K 488 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7697 (pm20) REVERT: L 417 THR cc_start: 0.7573 (m) cc_final: 0.7313 (t) REVERT: L 488 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7650 (pm20) outliers start: 8 outliers final: 5 residues processed: 205 average time/residue: 3.0353 time to fit residues: 670.7540 Evaluate side-chains 190 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 0.1980 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 E 505 GLN F 505 GLN H 505 GLN I 505 GLN K 505 GLN L 505 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13272 Z= 0.204 Angle : 0.636 5.431 18036 Z= 0.346 Chirality : 0.047 0.147 1920 Planarity : 0.005 0.051 2412 Dihedral : 5.469 18.682 1752 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.09 % Allowed : 8.77 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1596 helix: -0.57 (0.21), residues: 420 sheet: 1.86 (0.22), residues: 588 loop : -0.76 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 519 HIS 0.006 0.002 HIS H 530 PHE 0.016 0.002 PHE J 444 TYR 0.009 0.002 TYR F 462 ARG 0.004 0.000 ARG J 507 *********************** 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 206 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 2.042 Fit side-chains REVERT: A 416 LYS cc_start: 0.8069 (tptt) cc_final: 0.7839 (ttpt) REVERT: A 417 THR cc_start: 0.7431 (m) cc_final: 0.7219 (t) REVERT: B 412 GLN cc_start: 0.7415 (tp40) cc_final: 0.7121 (mm110) REVERT: B 413 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7038 (tm-30) REVERT: B 416 LYS cc_start: 0.8166 (tptt) cc_final: 0.7874 (ttpt) REVERT: B 417 THR cc_start: 0.7445 (m) cc_final: 0.7203 (t) REVERT: B 488 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7516 (pm20) REVERT: C 488 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7317 (pm20) REVERT: C 525 LYS cc_start: 0.7614 (tttp) cc_final: 0.7228 (tmtt) REVERT: D 417 THR cc_start: 0.7406 (m) cc_final: 0.7108 (t) REVERT: D 488 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7409 (pm20) REVERT: E 412 GLN cc_start: 0.7362 (tp40) cc_final: 0.7079 (mm110) REVERT: E 413 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7012 (tm-30) REVERT: E 416 LYS cc_start: 0.8074 (tptt) cc_final: 0.7835 (ttpt) REVERT: E 417 THR cc_start: 0.7532 (m) cc_final: 0.7189 (t) REVERT: E 488 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7470 (pm20) REVERT: F 488 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7406 (pm20) REVERT: G 413 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7184 (tm-30) REVERT: G 417 THR cc_start: 0.7491 (m) cc_final: 0.7204 (t) REVERT: G 488 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7413 (pm20) REVERT: H 412 GLN cc_start: 0.7377 (tp40) cc_final: 0.7104 (mm110) REVERT: H 413 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7074 (tm-30) REVERT: H 416 LYS cc_start: 0.8104 (tptt) cc_final: 0.7833 (ttpt) REVERT: H 417 THR cc_start: 0.7593 (m) cc_final: 0.7250 (t) REVERT: H 436 ILE cc_start: 0.6728 (mt) cc_final: 0.5499 (mp) REVERT: H 488 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7442 (pm20) REVERT: I 454 GLU cc_start: 0.7919 (tt0) cc_final: 0.7657 (tt0) REVERT: I 488 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7366 (pm20) REVERT: J 413 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7221 (tm-30) REVERT: J 416 LYS cc_start: 0.8090 (tptt) cc_final: 0.7860 (ttpt) REVERT: J 417 THR cc_start: 0.7455 (m) cc_final: 0.7180 (t) REVERT: J 488 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7423 (pm20) REVERT: K 412 GLN cc_start: 0.7484 (tp40) cc_final: 0.7191 (mm110) REVERT: K 413 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7132 (tm-30) REVERT: K 416 LYS cc_start: 0.8156 (tptt) cc_final: 0.7897 (ttpt) REVERT: K 417 THR cc_start: 0.7557 (m) cc_final: 0.7288 (t) REVERT: K 436 ILE cc_start: 0.6790 (mt) cc_final: 0.5451 (mp) REVERT: K 488 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7614 (pm20) REVERT: L 488 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7408 (pm20) outliers start: 15 outliers final: 4 residues processed: 200 average time/residue: 3.0744 time to fit residues: 662.5783 Evaluate side-chains 189 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain I 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 140 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2943 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= 0.283 Angle : 0.686 6.751 18036 Z= 0.372 Chirality : 0.048 0.133 1920 Planarity : 0.006 0.041 2412 Dihedral : 5.406 18.724 1752 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.81 % Allowed : 11.52 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1596 helix: -0.97 (0.20), residues: 468 sheet: 1.71 (0.21), residues: 588 loop : -0.98 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 519 HIS 0.007 0.002 HIS F 459 PHE 0.016 0.002 PHE J 444 TYR 0.012 0.002 TYR E 462 ARG 0.003 0.001 ARG C 517 *********************** 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 205 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 2.148 Fit side-chains REVERT: B 412 GLN cc_start: 0.7499 (tp40) cc_final: 0.7164 (mm110) REVERT: B 413 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 416 LYS cc_start: 0.8144 (tptt) cc_final: 0.7875 (ttpt) REVERT: B 488 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7494 (pm20) REVERT: B 515 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8462 (mt-10) REVERT: C 488 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7332 (pm20) REVERT: C 525 LYS cc_start: 0.7575 (tttp) cc_final: 0.7301 (tmtt) REVERT: D 488 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7393 (pm20) REVERT: E 412 GLN cc_start: 0.7453 (tp40) cc_final: 0.7145 (mm110) REVERT: E 413 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6854 (tm-30) REVERT: E 416 LYS cc_start: 0.8058 (tptt) cc_final: 0.7840 (ttpt) REVERT: E 488 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7449 (pm20) REVERT: E 515 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: F 488 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7428 (pm20) REVERT: G 488 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7409 (pm20) REVERT: H 412 GLN cc_start: 0.7515 (tp40) cc_final: 0.7210 (mm110) REVERT: H 416 LYS cc_start: 0.8080 (tptt) cc_final: 0.7844 (ttpt) REVERT: H 436 ILE cc_start: 0.6788 (mt) cc_final: 0.5493 (mp) REVERT: H 488 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7416 (pm20) REVERT: H 515 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8479 (mt-10) REVERT: I 488 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7349 (pm20) REVERT: J 488 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7445 (pm20) REVERT: J 509 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7432 (mtp180) REVERT: K 412 GLN cc_start: 0.7595 (tp40) cc_final: 0.7279 (mm110) REVERT: K 416 LYS cc_start: 0.8134 (tptt) cc_final: 0.7911 (ttpt) REVERT: K 488 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7576 (pm20) REVERT: K 515 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: L 488 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7416 (pm20) outliers start: 25 outliers final: 15 residues processed: 196 average time/residue: 3.1977 time to fit residues: 676.3638 Evaluate side-chains 194 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 505 GLN 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 509 ARG 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 509 ARG 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 125 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13272 Z= 0.210 Angle : 0.609 5.857 18036 Z= 0.328 Chirality : 0.045 0.129 1920 Planarity : 0.006 0.085 2412 Dihedral : 5.171 17.755 1752 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.46 % Allowed : 11.88 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1596 helix: -0.73 (0.20), residues: 468 sheet: 1.74 (0.21), residues: 588 loop : -0.93 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 519 HIS 0.004 0.002 HIS H 530 PHE 0.013 0.002 PHE K 444 TYR 0.009 0.002 TYR C 462 ARG 0.009 0.000 ARG E 521 *********************** 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 212 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 2.276 Fit side-chains REVERT: A 511 SER cc_start: 0.9033 (p) cc_final: 0.8799 (m) REVERT: B 412 GLN cc_start: 0.7560 (tp40) cc_final: 0.7175 (mm110) REVERT: B 416 LYS cc_start: 0.8156 (tptt) cc_final: 0.7861 (ttpt) REVERT: B 488 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7517 (pm20) REVERT: C 488 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7302 (pm20) REVERT: C 509 ARG cc_start: 0.8029 (mmt-90) cc_final: 0.7710 (mmp-170) REVERT: C 525 LYS cc_start: 0.7548 (tttp) cc_final: 0.7277 (tmtt) REVERT: D 454 GLU cc_start: 0.8112 (tt0) cc_final: 0.7832 (tt0) REVERT: D 488 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7372 (pm20) REVERT: D 511 SER cc_start: 0.8945 (p) cc_final: 0.8693 (m) REVERT: E 412 GLN cc_start: 0.7502 (tp40) cc_final: 0.7132 (mm110) REVERT: E 413 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6957 (tm-30) REVERT: E 416 LYS cc_start: 0.8035 (tptt) cc_final: 0.7826 (ttpt) REVERT: E 488 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7443 (pm20) REVERT: F 488 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7394 (pm20) REVERT: G 488 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7522 (pm20) REVERT: G 511 SER cc_start: 0.9031 (p) cc_final: 0.8780 (m) REVERT: H 412 GLN cc_start: 0.7527 (tp40) cc_final: 0.7162 (mm110) REVERT: H 416 LYS cc_start: 0.8063 (tptt) cc_final: 0.7814 (ttpt) REVERT: H 417 THR cc_start: 0.7634 (m) cc_final: 0.7353 (t) REVERT: H 488 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7432 (pm20) REVERT: I 488 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7502 (pm20) REVERT: J 488 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7410 (pm20) REVERT: J 509 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7436 (mtp180) REVERT: J 511 SER cc_start: 0.9031 (p) cc_final: 0.8816 (m) REVERT: K 412 GLN cc_start: 0.7641 (tp40) cc_final: 0.7255 (mm110) REVERT: K 416 LYS cc_start: 0.8123 (tptt) cc_final: 0.7902 (ttpt) REVERT: K 488 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7576 (pm20) REVERT: L 488 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7402 (pm20) REVERT: L 505 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7521 (pt0) outliers start: 34 outliers final: 16 residues processed: 199 average time/residue: 3.0443 time to fit residues: 654.3510 Evaluate side-chains 191 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 441 LEU 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 D residue 474 ILE Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain F residue 436 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain I residue 436 ILE Chi-restraints excluded: chain I residue 505 GLN Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain K residue 436 ILE Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 436 ILE Chi-restraints excluded: chain L residue 505 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 150 optimal weight: 0.0470 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3271 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= 0.247 Angle : 0.636 6.306 18036 Z= 0.344 Chirality : 0.047 0.132 1920 Planarity : 0.006 0.055 2412 Dihedral : 5.089 17.399 1752 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.62 % Allowed : 11.01 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1596 helix: -0.72 (0.20), residues: 468 sheet: 1.71 (0.22), residues: 588 loop : -0.99 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 519 HIS 0.005 0.002 HIS F 459 PHE 0.015 0.002 PHE E 444 TYR 0.010 0.002 TYR E 462 ARG 0.005 0.000 ARG E 521 *********************** 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 224 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 174 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 GLU cc_start: 0.7771 (pt0) cc_final: 0.7464 (pt0) REVERT: A 511 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8818 (m) REVERT: B 412 GLN cc_start: 0.7598 (tp40) cc_final: 0.7200 (mm110) REVERT: B 416 LYS cc_start: 0.8122 (tptt) cc_final: 0.7868 (ttpt) REVERT: B 488 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7493 (pm20) REVERT: B 515 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: C 488 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7491 (pm20) REVERT: C 525 LYS cc_start: 0.7565 (tttp) cc_final: 0.7291 (tmtt) REVERT: D 488 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7501 (pm20) REVERT: D 511 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8707 (m) REVERT: E 412 GLN cc_start: 0.7519 (tp40) cc_final: 0.7141 (mm110) REVERT: E 416 LYS cc_start: 0.8061 (tptt) cc_final: 0.7843 (ttpt) REVERT: E 488 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7428 (pm20) REVERT: E 515 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: F 488 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7602 (pm20) REVERT: G 423 GLU cc_start: 0.7711 (pt0) cc_final: 0.7459 (pt0) REVERT: G 488 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7354 (pm20) REVERT: G 511 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8791 (m) REVERT: H 412 GLN cc_start: 0.7545 (tp40) cc_final: 0.7172 (mm110) REVERT: H 416 LYS cc_start: 0.8089 (tptt) cc_final: 0.7837 (ttpt) REVERT: H 488 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7408 (pm20) REVERT: H 515 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: I 488 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7519 (pm20) REVERT: I 509 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7734 (mmp-170) REVERT: J 423 GLU cc_start: 0.7695 (pt0) cc_final: 0.7440 (pt0) REVERT: J 488 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7526 (pm20) REVERT: J 509 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7443 (mtp180) REVERT: J 511 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8835 (m) REVERT: K 412 GLN cc_start: 0.7656 (tp40) cc_final: 0.7262 (mm110) REVERT: K 413 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7105 (tm-30) REVERT: K 416 LYS cc_start: 0.8146 (tptt) cc_final: 0.7909 (ttpt) REVERT: K 488 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7584 (pm20) REVERT: K 515 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8376 (mt-10) REVERT: L 488 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7567 (pm20) REVERT: L 509 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7720 (mtp180) outliers start: 50 outliers final: 30 residues processed: 205 average time/residue: 2.9290 time to fit residues: 649.2358 Evaluate side-chains 211 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 511 SER 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 505 GLN Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 511 SER 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 474 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 511 SER 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 441 LEU Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 505 GLN Chi-restraints excluded: chain J residue 436 ILE Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain J residue 511 SER 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 Chi-restraints excluded: chain L residue 509 ARG Chi-restraints excluded: chain L residue 516 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13272 Z= 0.265 Angle : 0.646 6.387 18036 Z= 0.350 Chirality : 0.047 0.130 1920 Planarity : 0.006 0.048 2412 Dihedral : 5.088 17.587 1752 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.20 % Allowed : 10.94 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1596 helix: -0.78 (0.20), residues: 468 sheet: 1.67 (0.22), residues: 588 loop : -1.00 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 519 HIS 0.005 0.002 HIS F 459 PHE 0.014 0.002 PHE E 444 TYR 0.011 0.002 TYR G 462 ARG 0.006 0.001 ARG K 521 *********************** 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 232 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 SER cc_start: 0.9036 (p) cc_final: 0.8815 (m) REVERT: B 412 GLN cc_start: 0.7592 (tp40) cc_final: 0.7183 (mm110) REVERT: B 413 GLU cc_start: 0.7505 (tm-30) cc_final: 0.6932 (tm-30) REVERT: B 416 LYS cc_start: 0.8143 (tptt) cc_final: 0.7861 (ttpt) REVERT: B 488 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7519 (pm20) REVERT: B 515 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: C 525 LYS cc_start: 0.7566 (tttp) cc_final: 0.7309 (tmtt) REVERT: D 488 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7378 (pm20) REVERT: D 511 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8718 (m) REVERT: E 412 GLN cc_start: 0.7528 (tp40) cc_final: 0.7142 (mm110) REVERT: E 416 LYS cc_start: 0.8067 (tptt) cc_final: 0.7841 (ttpt) REVERT: E 515 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8387 (mt-10) REVERT: G 488 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7330 (pm20) REVERT: G 511 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8799 (m) REVERT: H 412 GLN cc_start: 0.7553 (tp40) cc_final: 0.7169 (mm110) REVERT: H 413 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6939 (tm-30) REVERT: H 416 LYS cc_start: 0.8092 (tptt) cc_final: 0.7826 (ttpt) REVERT: H 488 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7402 (pm20) REVERT: H 515 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: I 488 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7426 (pm20) REVERT: J 488 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7393 (pm20) REVERT: J 509 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7438 (mtp180) REVERT: J 511 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8850 (m) REVERT: K 412 GLN cc_start: 0.7638 (tp40) cc_final: 0.7227 (mm110) REVERT: K 413 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7096 (tm-30) REVERT: K 416 LYS cc_start: 0.8153 (tptt) cc_final: 0.7908 (ttpt) REVERT: K 488 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7582 (pm20) REVERT: K 505 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7162 (pt0) REVERT: K 515 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: L 488 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7617 (pm20) REVERT: L 509 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7647 (mtp180) outliers start: 58 outliers final: 40 residues processed: 212 average time/residue: 2.8649 time to fit residues: 659.0209 Evaluate side-chains 224 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 174 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 516 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 511 SER 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 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 436 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain G residue 509 ARG Chi-restraints excluded: chain G residue 511 SER 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 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 436 ILE Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 509 ARG Chi-restraints excluded: chain J residue 511 SER 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 509 ARG 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 60 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 420 GLN ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 420 GLN ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13272 Z= 0.233 Angle : 0.619 5.970 18036 Z= 0.335 Chirality : 0.046 0.129 1920 Planarity : 0.005 0.042 2412 Dihedral : 4.969 17.331 1752 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.20 % Allowed : 11.52 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1596 helix: -0.63 (0.21), residues: 468 sheet: 1.70 (0.22), residues: 588 loop : -0.96 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 519 HIS 0.004 0.002 HIS F 459 PHE 0.013 0.002 PHE J 444 TYR 0.010 0.002 TYR G 462 ARG 0.005 0.000 ARG E 521 *********************** 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 233 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 175 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 511 SER cc_start: 0.9028 (p) cc_final: 0.8808 (m) REVERT: B 412 GLN cc_start: 0.7579 (tp40) cc_final: 0.7167 (mm110) REVERT: B 413 GLU cc_start: 0.7579 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 416 LYS cc_start: 0.8136 (tptt) cc_final: 0.7860 (ttpt) REVERT: B 488 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7514 (pm20) REVERT: B 515 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: C 413 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6936 (tm-30) REVERT: C 525 LYS cc_start: 0.7558 (tttp) cc_final: 0.7299 (tmtt) REVERT: D 488 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7393 (pm20) REVERT: D 511 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8710 (m) REVERT: E 412 GLN cc_start: 0.7484 (tp40) cc_final: 0.7095 (mm110) REVERT: E 413 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6931 (tm-30) REVERT: E 416 LYS cc_start: 0.8057 (tptt) cc_final: 0.7830 (ttpt) REVERT: E 515 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: G 488 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7334 (pm20) REVERT: G 511 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8786 (m) REVERT: H 412 GLN cc_start: 0.7505 (tp40) cc_final: 0.7120 (mm110) REVERT: H 413 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7002 (tm-30) REVERT: H 416 LYS cc_start: 0.8088 (tptt) cc_final: 0.7820 (ttpt) REVERT: H 488 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7427 (pm20) REVERT: H 515 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: I 488 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7553 (pm20) REVERT: J 488 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7374 (pm20) REVERT: J 509 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7438 (mtp180) REVERT: K 412 GLN cc_start: 0.7625 (tp40) cc_final: 0.7216 (mm110) REVERT: K 413 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7070 (tm-30) REVERT: K 416 LYS cc_start: 0.8149 (tptt) cc_final: 0.7903 (ttpt) REVERT: K 488 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7575 (pm20) REVERT: K 515 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8350 (mt-10) REVERT: L 488 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7616 (pm20) REVERT: L 509 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7687 (mtp180) outliers start: 58 outliers final: 40 residues processed: 212 average time/residue: 2.7893 time to fit residues: 641.4959 Evaluate side-chains 217 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 516 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 511 SER 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 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 516 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 G residue 511 SER 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 436 ILE Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 509 ARG 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 441 LEU Chi-restraints excluded: chain L residue 505 GLN Chi-restraints excluded: chain L residue 509 ARG Chi-restraints excluded: chain L residue 516 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 GLN ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 GLN L 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13272 Z= 0.207 Angle : 0.593 5.587 18036 Z= 0.319 Chirality : 0.045 0.128 1920 Planarity : 0.005 0.041 2412 Dihedral : 4.817 16.424 1752 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.06 % Allowed : 12.61 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1596 helix: -0.41 (0.21), residues: 468 sheet: 1.93 (0.22), residues: 576 loop : -1.07 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 519 HIS 0.003 0.001 HIS K 530 PHE 0.012 0.001 PHE K 444 TYR 0.009 0.002 TYR G 462 ARG 0.005 0.000 ARG E 521 *********************** 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 231 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 175 time to evaluate : 2.238 Fit side-chains REVERT: A 413 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 412 GLN cc_start: 0.7531 (tp40) cc_final: 0.7114 (mm110) REVERT: B 413 GLU cc_start: 0.7538 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 416 LYS cc_start: 0.8136 (tptt) cc_final: 0.7861 (ttpt) REVERT: B 488 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7518 (pm20) REVERT: B 515 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: C 525 LYS cc_start: 0.7535 (tttp) cc_final: 0.7279 (tmtt) REVERT: D 488 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7379 (pm20) REVERT: D 511 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8695 (m) REVERT: E 412 GLN cc_start: 0.7437 (tp40) cc_final: 0.7037 (mm110) REVERT: E 413 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6896 (tm-30) REVERT: E 416 LYS cc_start: 0.8015 (tptt) cc_final: 0.7779 (ttpt) REVERT: E 515 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: G 488 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7330 (pm20) REVERT: G 511 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8776 (m) REVERT: H 412 GLN cc_start: 0.7493 (tp40) cc_final: 0.7089 (mm110) REVERT: H 413 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7045 (tm-30) REVERT: H 416 LYS cc_start: 0.8043 (tptt) cc_final: 0.7762 (ttpt) REVERT: H 417 THR cc_start: 0.7644 (m) cc_final: 0.7319 (t) REVERT: H 488 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7424 (pm20) REVERT: H 515 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: I 488 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7440 (pm20) REVERT: J 488 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7370 (pm20) REVERT: J 509 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7456 (mtp180) REVERT: K 412 GLN cc_start: 0.7606 (tp40) cc_final: 0.7191 (mm110) REVERT: K 413 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7033 (tm-30) REVERT: K 416 LYS cc_start: 0.8105 (tptt) cc_final: 0.7856 (ttpt) REVERT: K 488 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7589 (pm20) REVERT: K 515 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: L 488 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7491 (pm20) REVERT: L 509 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7656 (mtp180) outliers start: 56 outliers final: 35 residues processed: 210 average time/residue: 2.8239 time to fit residues: 645.2269 Evaluate side-chains 216 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 173 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 474 ILE Chi-restraints excluded: chain D residue 511 SER 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 F residue 516 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 G residue 511 SER 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 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 436 ILE Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 509 ARG 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 509 ARG 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 148 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13272 Z= 0.200 Angle : 0.584 5.549 18036 Z= 0.313 Chirality : 0.045 0.128 1920 Planarity : 0.005 0.041 2412 Dihedral : 4.710 15.851 1752 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.33 % Allowed : 13.91 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1596 helix: -0.24 (0.21), residues: 468 sheet: 1.96 (0.22), residues: 576 loop : -1.00 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 519 HIS 0.003 0.001 HIS F 459 PHE 0.012 0.001 PHE E 444 TYR 0.009 0.002 TYR D 462 ARG 0.005 0.000 ARG K 521 ********************** 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 222 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 1.963 Fit side-chains REVERT: A 413 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 412 GLN cc_start: 0.7494 (tp40) cc_final: 0.7060 (mm110) REVERT: B 416 LYS cc_start: 0.8130 (tptt) cc_final: 0.7853 (ttpt) REVERT: B 488 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7511 (pm20) REVERT: B 515 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: C 525 LYS cc_start: 0.7519 (tttp) cc_final: 0.7269 (tmtt) REVERT: D 488 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7382 (pm20) REVERT: E 412 GLN cc_start: 0.7428 (tp40) cc_final: 0.7019 (mm110) REVERT: E 416 LYS cc_start: 0.8005 (tptt) cc_final: 0.7786 (ttpt) REVERT: E 515 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: G 488 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7331 (pm20) REVERT: H 412 GLN cc_start: 0.7450 (tp40) cc_final: 0.7047 (mm110) REVERT: H 413 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7060 (tm-30) REVERT: H 416 LYS cc_start: 0.8033 (tptt) cc_final: 0.7748 (ttpt) REVERT: H 417 THR cc_start: 0.7637 (m) cc_final: 0.7302 (t) REVERT: H 488 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7418 (pm20) REVERT: H 515 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: I 488 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7551 (pm20) REVERT: J 488 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7370 (pm20) REVERT: J 509 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7462 (mtp180) REVERT: K 412 GLN cc_start: 0.7567 (tp40) cc_final: 0.7142 (mm110) REVERT: K 416 LYS cc_start: 0.8096 (tptt) cc_final: 0.7850 (ttpt) REVERT: K 417 THR cc_start: 0.7596 (m) cc_final: 0.7391 (t) REVERT: K 488 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7595 (pm20) REVERT: K 515 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8287 (mt-10) REVERT: L 488 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7626 (pm20) REVERT: L 509 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7664 (mtp180) outliers start: 46 outliers final: 33 residues processed: 206 average time/residue: 2.7980 time to fit residues: 627.4842 Evaluate side-chains 215 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 516 THR Chi-restraints excluded: chain D residue 474 ILE 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 F residue 474 ILE Chi-restraints excluded: chain F residue 516 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 436 ILE Chi-restraints excluded: chain H residue 441 LEU 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 516 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 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 509 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.215673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189575 restraints weight = 31397.912| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 1.40 r_work: 0.4045 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3943 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3702 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= 0.167 Angle : 0.543 4.925 18036 Z= 0.290 Chirality : 0.044 0.128 1920 Planarity : 0.005 0.038 2412 Dihedral : 4.496 16.078 1752 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.46 % Allowed : 14.71 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1596 helix: 0.09 (0.22), residues: 468 sheet: 2.05 (0.22), residues: 576 loop : -0.87 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 519 HIS 0.003 0.001 HIS K 530 PHE 0.012 0.001 PHE K 444 TYR 0.007 0.001 TYR D 462 ARG 0.005 0.000 ARG K 521 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10524.32 seconds wall clock time: 184 minutes 52.66 seconds (11092.66 seconds total)