Starting phenix.real_space_refine on Sat May 24 08:53:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6q_41077/05_2025/8t6q_41077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6q_41077/05_2025/8t6q_41077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6q_41077/05_2025/8t6q_41077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6q_41077/05_2025/8t6q_41077.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6q_41077/05_2025/8t6q_41077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6q_41077/05_2025/8t6q_41077.cif" } resolution = 3.5 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= -0.001 sd= 0.020 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 8172 2.51 5 N 2316 2.21 5 O 2412 1.98 5 H 12534 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25482 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "B" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "C" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "D" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "G" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "H" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "I" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "J" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "K" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "L" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "N" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Time building chain proxies: 12.20, per 1000 atoms: 0.48 Number of scatterers: 25482 At special positions: 0 Unit cell: (74.82, 128.14, 140.18, 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 2412 8.00 N 2316 7.00 C 8172 6.00 H 12534 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: 5.72 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: 55 helices and 19 sheets defined 34.0% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 408 through 425 removed outlier: 3.662A pdb=" N GLN A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 455 through 470 removed outlier: 3.557A pdb=" N HIS A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 428 removed outlier: 3.734A pdb=" N GLU B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 removed outlier: 3.655A pdb=" N TYR B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.581A pdb=" N PHE B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 463 " --> pdb=" O HIS B 459 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'C' and resid 410 through 426 Processing helix chain 'C' and resid 430 through 437 Processing helix chain 'C' and resid 445 through 449 Processing helix chain 'C' and resid 456 through 466 removed outlier: 4.136A pdb=" N TYR C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 427 removed outlier: 3.741A pdb=" N ILE D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 436 removed outlier: 3.856A pdb=" N ILE D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 449 Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.914A pdb=" N PHE D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN D 465 " --> pdb=" O PHE D 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 428 Processing helix chain 'F' and resid 429 through 436 Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 463 through 468 removed outlier: 3.626A pdb=" N ALA F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 428 removed outlier: 3.961A pdb=" N ILE G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 437 removed outlier: 4.433A pdb=" N TYR G 433 " --> pdb=" O ASP G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 449 Processing helix chain 'G' and resid 456 through 466 removed outlier: 3.791A pdb=" N PHE G 461 " --> pdb=" O ASP G 457 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 470 Processing helix chain 'H' and resid 409 through 428 removed outlier: 3.833A pdb=" N ILE H 415 " --> pdb=" O LYS H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 437 Processing helix chain 'H' and resid 445 through 449 Processing helix chain 'H' and resid 456 through 470 removed outlier: 3.717A pdb=" N PHE H 461 " --> pdb=" O ASP H 457 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR H 462 " --> pdb=" O PHE H 458 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE H 463 " --> pdb=" O HIS H 459 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU H 467 " --> pdb=" O PHE H 463 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ALA H 468 " --> pdb=" O GLU H 464 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS H 469 " --> pdb=" O ASN H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 525 Processing helix chain 'I' and resid 409 through 428 removed outlier: 3.588A pdb=" N ILE I 415 " --> pdb=" O LYS I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 437 removed outlier: 3.720A pdb=" N TYR I 433 " --> pdb=" O ASP I 429 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 449 Processing helix chain 'I' and resid 456 through 466 removed outlier: 3.927A pdb=" N PHE I 461 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR I 462 " --> pdb=" O PHE I 458 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE I 463 " --> pdb=" O HIS I 459 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU I 464 " --> pdb=" O ARG I 460 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN I 465 " --> pdb=" O PHE I 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 428 removed outlier: 3.526A pdb=" N ILE J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 437 removed outlier: 3.517A pdb=" N LYS J 435 " --> pdb=" O GLU J 431 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE J 436 " --> pdb=" O ALA J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 449 Processing helix chain 'J' and resid 456 through 461 removed outlier: 3.799A pdb=" N PHE J 461 " --> pdb=" O ASP J 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 466 through 470 Processing helix chain 'K' and resid 409 through 428 removed outlier: 3.748A pdb=" N GLU K 413 " --> pdb=" O ALA K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 437 removed outlier: 3.711A pdb=" N ILE K 436 " --> pdb=" O ALA K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 449 Processing helix chain 'K' and resid 456 through 461 removed outlier: 3.519A pdb=" N ARG K 460 " --> pdb=" O MET K 456 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 456 through 461' Processing helix chain 'K' and resid 461 through 466 removed outlier: 3.724A pdb=" N ASN K 465 " --> pdb=" O PHE K 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 409 through 428 Processing helix chain 'L' and resid 429 through 436 removed outlier: 3.596A pdb=" N TYR L 433 " --> pdb=" O ASP L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 445 through 449 Processing helix chain 'L' and resid 456 through 468 Processing helix chain 'L' and resid 469 through 472 Processing helix chain 'N' and resid 409 through 427 removed outlier: 3.637A pdb=" N ILE N 414 " --> pdb=" O ARG N 410 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE N 415 " --> pdb=" O LYS N 411 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 437 removed outlier: 3.882A pdb=" N LYS N 435 " --> pdb=" O GLU N 431 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE N 436 " --> pdb=" O ALA N 432 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS N 437 " --> pdb=" O TYR N 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 445 through 449 Processing helix chain 'N' and resid 456 through 461 removed outlier: 3.933A pdb=" N PHE N 461 " --> pdb=" O ASP N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 466 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 475 through 483 removed outlier: 5.603A pdb=" N THR A 476 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN A 500 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE A 478 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A 498 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASN A 480 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE A 496 " --> pdb=" O ASN A 480 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 495 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 516 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE A 531 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 518 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 453 through 454 removed outlier: 4.103A pdb=" N THR B 442 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 518 " --> pdb=" O VAL B 529 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE B 531 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 516 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS B 533 " --> pdb=" O GLU B 514 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU B 514 " --> pdb=" O CYS B 533 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY B 535 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N GLN B 512 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA B 490 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 485 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS B 492 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 483 " --> pdb=" O CYS B 492 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA B 494 " --> pdb=" O PRO B 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.516A pdb=" N VAL C 453 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 474 through 486 removed outlier: 3.789A pdb=" N ILE C 496 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 494 " --> pdb=" O PRO C 481 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL C 483 " --> pdb=" O CYS C 492 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS C 492 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL C 485 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ALA C 490 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR C 495 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU C 514 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N CYS C 533 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 516 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE C 531 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 518 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 453 through 454 removed outlier: 7.586A pdb=" N HIS D 530 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLY D 440 " --> pdb=" O HIS D 530 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N HIS D 532 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N THR D 442 " --> pdb=" O HIS D 532 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 518 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE D 531 " --> pdb=" O THR D 516 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR D 516 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS D 533 " --> pdb=" O GLU D 514 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU D 514 " --> pdb=" O CYS D 533 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA D 490 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL D 485 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS D 492 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL D 483 " --> pdb=" O CYS D 492 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA D 494 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 496 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 453 through 454 removed outlier: 7.413A pdb=" N HIS F 530 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 10.557A pdb=" N GLY F 440 " --> pdb=" O HIS F 530 " (cutoff:3.500A) removed outlier: 11.294A pdb=" N HIS F 532 " --> pdb=" O GLY F 440 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N THR F 442 " --> pdb=" O HIS F 532 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 518 " --> pdb=" O VAL F 529 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE F 531 " --> pdb=" O THR F 516 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR F 516 " --> pdb=" O PHE F 531 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA F 491 " --> pdb=" O TRP F 519 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA F 490 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL F 485 " --> pdb=" O ALA F 490 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS F 492 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL F 483 " --> pdb=" O CYS F 492 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA F 494 " --> pdb=" O PRO F 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 442 through 443 Processing sheet with id=AA8, first strand: chain 'G' and resid 474 through 486 removed outlier: 3.795A pdb=" N ILE G 496 " --> pdb=" O LEU G 479 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA G 494 " --> pdb=" O PRO G 481 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL G 483 " --> pdb=" O CYS G 492 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS G 492 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL G 485 " --> pdb=" O ALA G 490 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA G 490 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU G 514 " --> pdb=" O CYS G 533 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS G 533 " --> pdb=" O GLU G 514 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR G 516 " --> pdb=" O PHE G 531 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE G 531 " --> pdb=" O THR G 516 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL G 518 " --> pdb=" O VAL G 529 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 474 through 483 removed outlier: 6.690A pdb=" N ALA H 494 " --> pdb=" O PRO H 481 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL H 483 " --> pdb=" O CYS H 492 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS H 492 " --> pdb=" O VAL H 483 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 474 through 483 removed outlier: 6.690A pdb=" N ALA H 494 " --> pdb=" O PRO H 481 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL H 483 " --> pdb=" O CYS H 492 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS H 492 " --> pdb=" O VAL H 483 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR H 516 " --> pdb=" O PHE H 531 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE H 531 " --> pdb=" O THR H 516 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL H 518 " --> pdb=" O VAL H 529 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 442 through 443 Processing sheet with id=AB3, first strand: chain 'I' and resid 474 through 486 removed outlier: 3.509A pdb=" N ILE I 496 " --> pdb=" O LEU I 479 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA I 494 " --> pdb=" O PRO I 481 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL I 483 " --> pdb=" O CYS I 492 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS I 492 " --> pdb=" O VAL I 483 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL I 485 " --> pdb=" O ALA I 490 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA I 490 " --> pdb=" O VAL I 485 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLN I 512 " --> pdb=" O GLY I 535 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLY I 535 " --> pdb=" O GLN I 512 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLU I 514 " --> pdb=" O CYS I 533 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N CYS I 533 " --> pdb=" O GLU I 514 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR I 516 " --> pdb=" O PHE I 531 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE I 531 " --> pdb=" O THR I 516 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL I 518 " --> pdb=" O VAL I 529 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 453 through 454 removed outlier: 3.716A pdb=" N SER J 443 " --> pdb=" O VAL J 453 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR J 442 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL J 518 " --> pdb=" O VAL J 529 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE J 531 " --> pdb=" O THR J 516 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR J 516 " --> pdb=" O PHE J 531 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU J 515 " --> pdb=" O TYR J 495 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR J 495 " --> pdb=" O GLU J 515 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE J 496 " --> pdb=" O ASN J 480 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN J 480 " --> pdb=" O ILE J 496 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU J 498 " --> pdb=" O ILE J 478 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE J 478 " --> pdb=" O LEU J 498 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN J 500 " --> pdb=" O THR J 476 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR J 476 " --> pdb=" O GLN J 500 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE J 502 " --> pdb=" O ILE J 474 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE J 474 " --> pdb=" O ILE J 502 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 442 through 443 Processing sheet with id=AB6, first strand: chain 'K' and resid 474 through 485 removed outlier: 8.270A pdb=" N ILE K 474 " --> pdb=" O ILE K 502 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ILE K 502 " --> pdb=" O ILE K 474 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N THR K 476 " --> pdb=" O GLN K 500 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLN K 500 " --> pdb=" O THR K 476 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE K 478 " --> pdb=" O LEU K 498 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU K 498 " --> pdb=" O ILE K 478 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN K 480 " --> pdb=" O ILE K 496 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE K 496 " --> pdb=" O ASN K 480 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU K 514 " --> pdb=" O CYS K 533 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N CYS K 533 " --> pdb=" O GLU K 514 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR K 516 " --> pdb=" O PHE K 531 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE K 531 " --> pdb=" O THR K 516 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL K 518 " --> pdb=" O VAL K 529 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 437 through 442 removed outlier: 6.863A pdb=" N HIS L 530 " --> pdb=" O ASP L 438 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N GLY L 440 " --> pdb=" O HIS L 530 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 474 through 486 removed outlier: 6.730A pdb=" N ALA L 494 " --> pdb=" O PRO L 481 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL L 483 " --> pdb=" O CYS L 492 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS L 492 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL L 485 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA L 490 " --> pdb=" O VAL L 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 442 through 443 Processing sheet with id=AC1, first strand: chain 'N' and resid 474 through 486 removed outlier: 8.242A pdb=" N ILE N 474 " --> pdb=" O ILE N 502 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE N 502 " --> pdb=" O ILE N 474 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N THR N 476 " --> pdb=" O GLN N 500 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLN N 500 " --> pdb=" O THR N 476 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE N 478 " --> pdb=" O LEU N 498 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU N 498 " --> pdb=" O ILE N 478 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN N 480 " --> pdb=" O ILE N 496 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE N 496 " --> pdb=" O ASN N 480 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA N 490 " --> pdb=" O ILE N 486 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU N 514 " --> pdb=" O CYS N 533 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N CYS N 533 " --> pdb=" O GLU N 514 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR N 516 " --> pdb=" O PHE N 531 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE N 531 " --> pdb=" O THR N 516 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL N 518 " --> pdb=" O VAL N 529 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1506 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: 8.05 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12498 1.03 - 1.23: 36 1.23 - 1.42: 5701 1.42 - 1.62: 7522 1.62 - 1.81: 61 Bond restraints: 25818 Sorted by residual: bond pdb=" CB PRO H 508 " pdb=" CG PRO H 508 " ideal model delta sigma weight residual 1.492 1.659 -0.167 5.00e-02 4.00e+02 1.12e+01 bond pdb=" CG PRO H 508 " pdb=" CD PRO H 508 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.85e+00 bond pdb=" N PRO H 508 " pdb=" CD PRO H 508 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.52e+00 bond pdb=" N LYS D 408 " pdb=" CA LYS D 408 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N LYS B 408 " pdb=" CA LYS B 408 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 ... (remaining 25813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 46459 2.99 - 5.98: 120 5.98 - 8.97: 3 8.97 - 11.95: 1 11.95 - 14.94: 1 Bond angle restraints: 46584 Sorted by residual: angle pdb=" CA PRO H 508 " pdb=" N PRO H 508 " pdb=" CD PRO H 508 " ideal model delta sigma weight residual 112.00 97.06 14.94 1.40e+00 5.10e-01 1.14e+02 angle pdb=" N PRO H 508 " pdb=" CD PRO H 508 " pdb=" CG PRO H 508 " ideal model delta sigma weight residual 103.20 94.40 8.80 1.50e+00 4.44e-01 3.44e+01 angle pdb=" N PRO H 508 " pdb=" CA PRO H 508 " pdb=" C PRO H 508 " ideal model delta sigma weight residual 111.19 117.69 -6.50 1.57e+00 4.06e-01 1.71e+01 angle pdb=" N PRO H 508 " pdb=" CD PRO H 508 " pdb=" HD2 PRO H 508 " ideal model delta sigma weight residual 109.00 120.61 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA PRO H 508 " pdb=" CB PRO H 508 " pdb=" CG PRO H 508 " ideal model delta sigma weight residual 104.50 97.64 6.86 1.90e+00 2.77e-01 1.30e+01 ... (remaining 46579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10893 17.86 - 35.73: 917 35.73 - 53.59: 325 53.59 - 71.46: 70 71.46 - 89.32: 29 Dihedral angle restraints: 12234 sinusoidal: 6600 harmonic: 5634 Sorted by residual: dihedral pdb=" CA LYS L 472 " pdb=" C LYS L 472 " pdb=" N PRO L 473 " pdb=" CA PRO L 473 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER H 443 " pdb=" C SER H 443 " pdb=" N PHE H 444 " pdb=" CA PHE H 444 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU H 514 " pdb=" C GLU H 514 " pdb=" N GLU H 515 " pdb=" CA GLU H 515 " ideal model delta harmonic sigma weight residual 180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 12231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1637 0.056 - 0.112: 223 0.112 - 0.168: 58 0.168 - 0.224: 1 0.224 - 0.280: 1 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CA PRO H 508 " pdb=" N PRO H 508 " pdb=" C PRO H 508 " pdb=" CB PRO H 508 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ILE L 474 " pdb=" N ILE L 474 " pdb=" C ILE L 474 " pdb=" CB ILE L 474 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE A 474 " pdb=" N ILE A 474 " pdb=" C ILE A 474 " pdb=" CB ILE A 474 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 1917 not shown) Planarity restraints: 3912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 507 " -0.105 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO H 508 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO H 508 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO H 508 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 470 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ASN A 470 " 0.033 2.00e-02 2.50e+03 pdb=" O ASN A 470 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 471 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 523 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASP B 523 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP B 523 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 524 " 0.011 2.00e-02 2.50e+03 ... (remaining 3909 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1220 2.18 - 2.78: 49401 2.78 - 3.39: 67666 3.39 - 3.99: 85827 3.99 - 4.60: 132756 Nonbonded interactions: 336870 Sorted by model distance: nonbonded pdb=" OE1 GLU N 447 " pdb=" H GLU N 447 " model vdw 1.575 2.450 nonbonded pdb=" OD1 ASP G 503 " pdb=" H ARG G 507 " model vdw 1.588 2.450 nonbonded pdb=" OE1 GLU F 431 " pdb=" H GLU F 431 " model vdw 1.609 2.450 nonbonded pdb="HE21 GLN A 512 " pdb=" OE2 GLU A 514 " model vdw 1.612 2.450 nonbonded pdb=" OD1 ASP I 438 " pdb=" H GLY I 440 " model vdw 1.625 2.450 ... (remaining 336865 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 408 through 531 or (resid 532 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 533 through 542)) selection = (chain 'B' and (resid 408 through 531 or (resid 532 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 533 through 542)) selection = (chain 'C' and (resid 408 through 531 or (resid 532 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 533 through 542)) selection = (chain 'D' and (resid 408 through 531 or (resid 532 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 533 through 542)) selection = (chain 'F' and (resid 408 through 531 or (resid 532 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 533 through 542)) selection = (chain 'G' and (resid 408 through 531 or (resid 532 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 533 through 542)) selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' } 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 group one per residue 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: 1.880 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: 0.400 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.080 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 : 0.003 0.167 13284 Z= 0.131 Angle : 0.563 14.942 18036 Z= 0.315 Chirality : 0.043 0.280 1920 Planarity : 0.005 0.144 2400 Dihedral : 15.872 89.320 4896 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.51 % Allowed : 15.51 % Favored : 83.99 % 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: 0.34 (0.22), residues: 1596 helix: 0.29 (0.25), residues: 458 sheet: 1.54 (0.24), residues: 495 loop : -0.85 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 519 HIS 0.008 0.001 HIS L 530 PHE 0.013 0.001 PHE L 461 TYR 0.011 0.001 TYR L 462 ARG 0.007 0.000 ARG B 460 Details of bonding type rmsd hydrogen bonds : bond 0.25006 ( 547) hydrogen bonds : angle 8.03599 ( 1506) covalent geometry : bond 0.00306 (13284) covalent geometry : angle 0.56333 (18036) *********************** 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 211 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 1.976 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: 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 461 PHE cc_start: 0.6233 (t80) cc_final: 0.5662 (t80) REVERT: B 408 LYS cc_start: 0.6252 (pttm) cc_final: 0.5839 (pttm) REVERT: C 410 ARG cc_start: 0.6094 (mmt-90) cc_final: 0.5339 (ptt-90) REVERT: G 408 LYS cc_start: 0.7031 (ptpp) cc_final: 0.6651 (tptt) REVERT: G 488 GLU cc_start: 0.8645 (pp20) cc_final: 0.8250 (mt-10) REVERT: G 489 ASP cc_start: 0.8596 (p0) cc_final: 0.8178 (p0) REVERT: I 408 LYS cc_start: 0.6315 (pttm) cc_final: 0.6046 (tttp) REVERT: I 457 ASP cc_start: 0.8494 (m-30) cc_final: 0.8015 (m-30) REVERT: I 523 ASP cc_start: 0.7661 (p0) cc_final: 0.7398 (m-30) REVERT: J 464 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6648 (mp0) REVERT: K 460 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.8046 (ttp80) REVERT: K 503 ASP cc_start: 0.8234 (p0) cc_final: 0.8015 (p0) REVERT: L 416 LYS cc_start: 0.8416 (tptp) cc_final: 0.8095 (tptp) REVERT: L 419 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6603 (tm-30) REVERT: N 420 GLN cc_start: 0.8154 (mt0) cc_final: 0.7920 (mt0) REVERT: N 505 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8564 (mp10) outliers start: 7 outliers final: 5 residues processed: 210 average time/residue: 0.7020 time to fit residues: 197.8163 Evaluate side-chains 159 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain I residue 534 SER Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain L residue 461 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 HIS ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN ** F 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.220563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.204499 restraints weight = 45043.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.203422 restraints weight = 62959.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.202373 restraints weight = 60093.841| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13284 Z= 0.188 Angle : 0.632 7.201 18036 Z= 0.348 Chirality : 0.045 0.177 1920 Planarity : 0.005 0.065 2400 Dihedral : 5.241 48.273 1761 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.67 % Allowed : 15.14 % Favored : 83.19 % 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: 0.24 (0.21), residues: 1596 helix: 0.42 (0.25), residues: 460 sheet: 1.40 (0.24), residues: 495 loop : -1.03 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 519 HIS 0.013 0.001 HIS F 484 PHE 0.020 0.002 PHE B 444 TYR 0.022 0.002 TYR A 501 ARG 0.015 0.001 ARG L 517 Details of bonding type rmsd hydrogen bonds : bond 0.05902 ( 547) hydrogen bonds : angle 6.13197 ( 1506) covalent geometry : bond 0.00441 (13284) covalent geometry : angle 0.63246 (18036) *********************** 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 186 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.880 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6070 (p90) cc_final: 0.5835 (p90) REVERT: B 408 LYS cc_start: 0.5248 (pttm) cc_final: 0.4831 (pttm) REVERT: C 464 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4418 (tp30) REVERT: K 486 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7727 (pt) outliers start: 23 outliers final: 15 residues processed: 179 average time/residue: 0.6001 time to fit residues: 150.3312 Evaluate side-chains 164 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain H residue 457 ASP Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 489 ASP Chi-restraints excluded: chain I residue 534 SER Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 472 LYS Chi-restraints excluded: chain L residue 493 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 ASN ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.214901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.191200 restraints weight = 45077.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.172626 restraints weight = 59333.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.168651 restraints weight = 50762.569| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13284 Z= 0.198 Angle : 0.612 5.862 18036 Z= 0.335 Chirality : 0.045 0.160 1920 Planarity : 0.004 0.049 2400 Dihedral : 5.124 40.596 1757 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.88 % Allowed : 15.22 % Favored : 82.90 % 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: 0.01 (0.21), residues: 1596 helix: 0.36 (0.24), residues: 464 sheet: 1.17 (0.25), residues: 478 loop : -1.12 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 519 HIS 0.009 0.001 HIS F 484 PHE 0.019 0.002 PHE B 444 TYR 0.030 0.002 TYR A 501 ARG 0.007 0.000 ARG L 517 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 547) hydrogen bonds : angle 5.72092 ( 1506) covalent geometry : bond 0.00472 (13284) covalent geometry : angle 0.61211 (18036) *********************** 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 182 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.756 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6337 (p90) cc_final: 0.5796 (p90) REVERT: B 408 LYS cc_start: 0.5354 (pttm) cc_final: 0.5093 (pttt) REVERT: C 464 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6291 (tp30) REVERT: K 486 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7824 (pt) outliers start: 26 outliers final: 22 residues processed: 174 average time/residue: 0.5574 time to fit residues: 138.7157 Evaluate side-chains 165 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain G residue 492 CYS Chi-restraints excluded: chain H residue 457 ASP Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 489 ASP Chi-restraints excluded: chain I residue 534 SER Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 484 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 465 ASN Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 421 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 22 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.217391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166857 restraints weight = 45255.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167992 restraints weight = 38248.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.168039 restraints weight = 34483.012| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13284 Z= 0.118 Angle : 0.550 5.791 18036 Z= 0.296 Chirality : 0.043 0.146 1920 Planarity : 0.004 0.050 2400 Dihedral : 4.855 32.655 1757 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.45 % Allowed : 15.80 % 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: 0.19 (0.21), residues: 1596 helix: 0.50 (0.25), residues: 466 sheet: 1.29 (0.25), residues: 474 loop : -1.01 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 519 HIS 0.007 0.001 HIS L 530 PHE 0.016 0.001 PHE B 444 TYR 0.034 0.001 TYR A 501 ARG 0.006 0.000 ARG L 517 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 547) hydrogen bonds : angle 5.30623 ( 1506) covalent geometry : bond 0.00276 (13284) covalent geometry : angle 0.55032 (18036) *********************** 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 174 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.913 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6306 (p90) cc_final: 0.5881 (p90) REVERT: B 408 LYS cc_start: 0.5286 (pttm) cc_final: 0.5018 (pttt) REVERT: C 464 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6151 (tp30) REVERT: K 486 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7798 (pt) REVERT: L 503 ASP cc_start: 0.7462 (p0) cc_final: 0.7257 (p0) outliers start: 20 outliers final: 15 residues processed: 167 average time/residue: 0.5561 time to fit residues: 132.8032 Evaluate side-chains 163 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 462 TYR Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 484 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 492 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** 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 = 0.4455 r_free = 0.4455 target = 0.216912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3889 r_free = 0.3889 target = 0.165857 restraints weight = 45135.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.166080 restraints weight = 39503.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.165714 restraints weight = 40696.848| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13284 Z= 0.103 Angle : 0.526 5.526 18036 Z= 0.280 Chirality : 0.042 0.156 1920 Planarity : 0.004 0.059 2400 Dihedral : 4.607 30.418 1756 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.23 % Allowed : 16.01 % 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: 0.39 (0.22), residues: 1596 helix: 0.71 (0.25), residues: 466 sheet: 1.36 (0.25), residues: 479 loop : -0.91 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 519 HIS 0.008 0.001 HIS L 530 PHE 0.015 0.001 PHE B 444 TYR 0.032 0.001 TYR A 501 ARG 0.005 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 547) hydrogen bonds : angle 4.98172 ( 1506) covalent geometry : bond 0.00239 (13284) covalent geometry : angle 0.52640 (18036) *********************** 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 165 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 2.198 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6252 (p90) cc_final: 0.5773 (p90) REVERT: A 497 ARG cc_start: 0.6889 (ttp80) cc_final: 0.6616 (ttp80) REVERT: B 408 LYS cc_start: 0.5191 (pttm) cc_final: 0.4958 (pttt) REVERT: C 464 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6445 (tp30) REVERT: K 486 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7793 (pt) outliers start: 17 outliers final: 10 residues processed: 160 average time/residue: 0.5727 time to fit residues: 131.4383 Evaluate side-chains 150 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 533 CYS Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 525 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** 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 = 0.4455 r_free = 0.4455 target = 0.216960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.182688 restraints weight = 44981.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166622 restraints weight = 59452.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.169463 restraints weight = 52249.539| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13284 Z= 0.100 Angle : 0.518 5.428 18036 Z= 0.276 Chirality : 0.042 0.161 1920 Planarity : 0.004 0.053 2400 Dihedral : 4.521 29.660 1756 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.16 % Allowed : 16.09 % 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: 0.48 (0.22), residues: 1596 helix: 0.80 (0.25), residues: 466 sheet: 1.41 (0.25), residues: 476 loop : -0.85 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 526 HIS 0.006 0.001 HIS L 530 PHE 0.014 0.001 PHE B 444 TYR 0.030 0.001 TYR A 501 ARG 0.007 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 547) hydrogen bonds : angle 4.82376 ( 1506) covalent geometry : bond 0.00235 (13284) covalent geometry : angle 0.51818 (18036) *********************** 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 165 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.973 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6315 (p90) cc_final: 0.5935 (p90) REVERT: B 408 LYS cc_start: 0.5287 (pttm) cc_final: 0.5071 (pttt) REVERT: C 464 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6157 (tp30) REVERT: K 486 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7796 (pt) outliers start: 16 outliers final: 11 residues processed: 161 average time/residue: 0.5747 time to fit residues: 131.7006 Evaluate side-chains 160 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 492 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 520 HIS ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.214728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 130)---------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163048 restraints weight = 45364.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.163031 restraints weight = 39487.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162235 restraints weight = 38975.107| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13284 Z= 0.136 Angle : 0.539 5.634 18036 Z= 0.289 Chirality : 0.043 0.164 1920 Planarity : 0.004 0.060 2400 Dihedral : 4.574 31.988 1755 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.52 % Allowed : 16.09 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.22), residues: 1596 helix: 0.80 (0.25), residues: 466 sheet: 1.36 (0.25), residues: 481 loop : -0.90 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 519 HIS 0.005 0.001 HIS L 530 PHE 0.017 0.001 PHE B 444 TYR 0.033 0.001 TYR A 501 ARG 0.006 0.000 ARG A 521 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 547) hydrogen bonds : angle 4.80988 ( 1506) covalent geometry : bond 0.00325 (13284) covalent geometry : angle 0.53869 (18036) *********************** 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 169 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 2.551 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6258 (p90) cc_final: 0.5821 (p90) REVERT: C 464 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6610 (tp30) REVERT: K 486 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7798 (pt) outliers start: 21 outliers final: 17 residues processed: 165 average time/residue: 0.5895 time to fit residues: 140.7227 Evaluate side-chains 163 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 533 CYS Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain H residue 478 ILE Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 492 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** 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 = 0.4432 r_free = 0.4432 target = 0.214858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158829 restraints weight = 45313.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160130 restraints weight = 36944.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161216 restraints weight = 30576.944| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13284 Z= 0.138 Angle : 0.542 5.711 18036 Z= 0.291 Chirality : 0.043 0.166 1920 Planarity : 0.004 0.062 2400 Dihedral : 4.592 32.015 1755 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.59 % Allowed : 16.52 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1596 helix: 0.77 (0.25), residues: 466 sheet: 1.32 (0.25), residues: 481 loop : -0.91 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 519 HIS 0.005 0.001 HIS A 530 PHE 0.017 0.001 PHE B 444 TYR 0.033 0.002 TYR A 501 ARG 0.015 0.000 ARG I 507 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 547) hydrogen bonds : angle 4.77187 ( 1506) covalent geometry : bond 0.00330 (13284) covalent geometry : angle 0.54197 (18036) *********************** 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 171 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 2.256 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.6395 (p90) cc_final: 0.6032 (p90) REVERT: C 464 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: G 456 MET cc_start: 0.7898 (tpt) cc_final: 0.7430 (tpt) REVERT: H 488 GLU cc_start: 0.6089 (tp30) cc_final: 0.5864 (tp30) REVERT: K 486 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7805 (pt) outliers start: 22 outliers final: 18 residues processed: 167 average time/residue: 0.5777 time to fit residues: 137.9495 Evaluate side-chains 164 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 533 CYS Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 492 CYS Chi-restraints excluded: chain H residue 478 ILE Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 492 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** 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 = 0.4445 r_free = 0.4445 target = 0.216253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.177215 restraints weight = 45343.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175531 restraints weight = 68094.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177426 restraints weight = 49199.562| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13284 Z= 0.106 Angle : 0.520 5.408 18036 Z= 0.277 Chirality : 0.042 0.166 1920 Planarity : 0.004 0.093 2400 Dihedral : 4.494 29.532 1755 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.52 % Allowed : 16.30 % Favored : 82.17 % 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: 0.53 (0.22), residues: 1596 helix: 0.84 (0.25), residues: 466 sheet: 1.44 (0.25), residues: 479 loop : -0.84 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 519 HIS 0.005 0.001 HIS A 530 PHE 0.015 0.001 PHE B 444 TYR 0.031 0.001 TYR C 462 ARG 0.012 0.000 ARG H 410 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 547) hydrogen bonds : angle 4.63555 ( 1506) covalent geometry : bond 0.00250 (13284) covalent geometry : angle 0.52011 (18036) *********************** 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 170 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.800 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 464 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5208 (tp30) REVERT: G 456 MET cc_start: 0.7837 (tpt) cc_final: 0.7376 (tpt) REVERT: K 486 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7729 (pt) outliers start: 21 outliers final: 19 residues processed: 166 average time/residue: 0.6096 time to fit residues: 142.7837 Evaluate side-chains 165 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 492 CYS Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 533 CYS Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 492 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.216715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.183622 restraints weight = 45529.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168311 restraints weight = 62494.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166043 restraints weight = 48477.878| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13284 Z= 0.133 Angle : 0.536 5.838 18036 Z= 0.287 Chirality : 0.042 0.162 1920 Planarity : 0.004 0.064 2400 Dihedral : 4.541 32.329 1755 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.52 % Allowed : 16.30 % Favored : 82.17 % 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 (0.22), residues: 1596 helix: 0.80 (0.25), residues: 466 sheet: 1.39 (0.25), residues: 481 loop : -0.88 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 519 HIS 0.005 0.001 HIS L 530 PHE 0.018 0.001 PHE B 444 TYR 0.027 0.001 TYR A 501 ARG 0.007 0.000 ARG H 410 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 547) hydrogen bonds : angle 4.65253 ( 1506) covalent geometry : bond 0.00318 (13284) covalent geometry : angle 0.53635 (18036) ********************** 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 168 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.864 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 464 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6226 (tp30) REVERT: G 474 ILE cc_start: 0.6788 (pp) cc_final: 0.6565 (pt) REVERT: K 486 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7758 (pt) outliers start: 21 outliers final: 19 residues processed: 165 average time/residue: 0.5807 time to fit residues: 135.9778 Evaluate side-chains 166 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 492 CYS Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain C residue 533 CYS Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 517 ARG Chi-restraints excluded: chain G residue 492 CYS Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 485 VAL Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 464 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 492 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 104 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 480 ASN ** 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 = 0.4444 r_free = 0.4444 target = 0.215784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.190299 restraints weight = 45426.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.173618 restraints weight = 65271.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172115 restraints weight = 49273.526| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13284 Z= 0.151 Angle : 0.551 5.513 18036 Z= 0.296 Chirality : 0.043 0.159 1920 Planarity : 0.004 0.064 2400 Dihedral : 4.633 34.652 1755 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.52 % Allowed : 16.30 % Favored : 82.17 % 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: 0.34 (0.22), residues: 1596 helix: 0.75 (0.25), residues: 466 sheet: 1.26 (0.25), residues: 472 loop : -0.92 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 519 HIS 0.005 0.001 HIS I 530 PHE 0.018 0.001 PHE B 444 TYR 0.035 0.002 TYR A 501 ARG 0.009 0.000 ARG H 410 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 547) hydrogen bonds : angle 4.70152 ( 1506) covalent geometry : bond 0.00363 (13284) covalent geometry : angle 0.55082 (18036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7309.55 seconds wall clock time: 127 minutes 21.85 seconds (7641.85 seconds total)