Starting phenix.real_space_refine on Mon Aug 25 04:32:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6q_41077/08_2025/8t6q_41077.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6q_41077/08_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_41077/08_2025/8t6q_41077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6q_41077/08_2025/8t6q_41077.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6q_41077/08_2025/8t6q_41077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6q_41077/08_2025/8t6q_41077.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.67, per 1000 atoms: 0.22 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: 2.39 Conformation dependent library (CDL) restraints added in 734.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 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: 0.72 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: 5.89 Time building geometry restraints manager: 3.28 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.180 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- 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 : 6.44 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (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 ARG 0.007 0.000 ARG B 460 TYR 0.011 0.001 TYR L 462 PHE 0.013 0.001 PHE L 461 TRP 0.010 0.001 TRP F 519 HIS 0.008 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00306 (13284) covalent geometry : angle 0.56333 (18036) hydrogen bonds : bond 0.25006 ( 547) hydrogen bonds : angle 8.03599 ( 1506) *********************** 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 : 0.870 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: 0.6047 (tttp) REVERT: I 457 ASP cc_start: 0.8494 (m-30) cc_final: 0.8016 (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: 0.6638 (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: 0.7919 (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: 0.3575 time to fit residues: 100.7152 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 : 0.709 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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** ** 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 = 0.4494 r_free = 0.4494 target = 0.222687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.206688 restraints weight = 45196.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.195022 restraints weight = 67117.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.187625 restraints weight = 55461.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.187580 restraints weight = 63403.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188839 restraints weight = 43439.793| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 13284 Z= 0.146 Angle : 0.602 7.405 18036 Z= 0.330 Chirality : 0.044 0.172 1920 Planarity : 0.004 0.065 2400 Dihedral : 5.115 47.664 1761 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.30 % Allowed : 15.00 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.21), residues: 1596 helix: 0.53 (0.25), residues: 460 sheet: 1.48 (0.24), residues: 499 loop : -0.89 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L 517 TYR 0.016 0.001 TYR A 501 PHE 0.015 0.001 PHE L 461 TRP 0.005 0.001 TRP C 519 HIS 0.011 0.001 HIS F 484 Details of bonding type rmsd covalent geometry : bond 0.00326 (13284) covalent geometry : angle 0.60244 (18036) hydrogen bonds : bond 0.05952 ( 547) hydrogen bonds : angle 6.07423 ( 1506) *********************** 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 183 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.737 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: A 495 TYR cc_start: 0.6286 (p90) cc_final: 0.5880 (p90) REVERT: B 408 LYS cc_start: 0.5156 (pttm) cc_final: 0.4739 (pttm) REVERT: C 464 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5450 (tp30) REVERT: K 486 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7784 (pt) REVERT: L 461 PHE cc_start: 0.4020 (OUTLIER) cc_final: 0.3758 (t80) outliers start: 18 outliers final: 10 residues processed: 176 average time/residue: 0.3096 time to fit residues: 76.5961 Evaluate side-chains 159 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 F residue 476 THR 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 461 PHE 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 28 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.0870 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 426 ASN ** 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 = 0.4473 r_free = 0.4473 target = 0.218834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 136)---------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175487 restraints weight = 45101.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.173245 restraints weight = 80466.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173977 restraints weight = 64678.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.174986 restraints weight = 53975.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.175180 restraints weight = 50272.304| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13284 Z= 0.125 Angle : 0.557 5.873 18036 Z= 0.300 Chirality : 0.043 0.150 1920 Planarity : 0.004 0.044 2400 Dihedral : 4.738 40.641 1756 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.30 % Allowed : 15.14 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.21), residues: 1596 helix: 0.62 (0.25), residues: 461 sheet: 1.44 (0.24), residues: 495 loop : -0.88 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 517 TYR 0.023 0.001 TYR A 501 PHE 0.014 0.001 PHE B 444 TRP 0.005 0.001 TRP F 519 HIS 0.008 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00289 (13284) covalent geometry : angle 0.55664 (18036) hydrogen bonds : bond 0.04714 ( 547) hydrogen bonds : angle 5.53233 ( 1506) *********************** 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 176 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.646 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: 0.6309 (p90) cc_final: 0.5955 (p90) REVERT: B 408 LYS cc_start: 0.5200 (pttm) cc_final: 0.4770 (pttm) REVERT: C 464 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5598 (tp30) REVERT: K 486 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7781 (pt) outliers start: 18 outliers final: 11 residues processed: 171 average time/residue: 0.2954 time to fit residues: 71.4836 Evaluate side-chains 156 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 F residue 425 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain I residue 489 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 500 GLN B 451 ASN ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4436 r_free = 0.4436 target = 0.214865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.182848 restraints weight = 45172.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.172099 restraints weight = 58713.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.164285 restraints weight = 39093.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.163822 restraints weight = 47702.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.164336 restraints weight = 39503.673| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13284 Z= 0.221 Angle : 0.614 5.933 18036 Z= 0.337 Chirality : 0.045 0.158 1920 Planarity : 0.005 0.063 2400 Dihedral : 4.845 26.819 1753 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.59 % Allowed : 15.00 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.21), residues: 1596 helix: 0.40 (0.24), residues: 466 sheet: 1.17 (0.25), residues: 495 loop : -1.10 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 517 TYR 0.036 0.002 TYR A 501 PHE 0.022 0.002 PHE B 444 TRP 0.008 0.002 TRP F 519 HIS 0.010 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00531 (13284) covalent geometry : angle 0.61425 (18036) hydrogen bonds : bond 0.04690 ( 547) hydrogen bonds : angle 5.44637 ( 1506) *********************** 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 171 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.707 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: 0.6357 (p90) cc_final: 0.5913 (p90) REVERT: B 408 LYS cc_start: 0.5271 (pttm) cc_final: 0.5025 (pttt) REVERT: C 410 ARG cc_start: 0.5666 (mmt-90) cc_final: 0.5143 (ptt90) REVERT: C 464 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6090 (tp30) REVERT: K 486 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7890 (pt) REVERT: N 456 MET cc_start: 0.7729 (mmm) cc_final: 0.7414 (mmm) outliers start: 22 outliers final: 19 residues processed: 164 average time/residue: 0.2814 time to fit residues: 65.1569 Evaluate side-chains 161 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 476 THR 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 496 ILE Chi-restraints excluded: chain H residue 523 ASP Chi-restraints excluded: chain I residue 489 ASP 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 493 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 421 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** H 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 = 0.4465 r_free = 0.4465 target = 0.217794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 130)---------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174214 restraints weight = 44912.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173344 restraints weight = 62279.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174480 restraints weight = 55283.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175156 restraints weight = 46674.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175194 restraints weight = 41876.909| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13284 Z= 0.114 Angle : 0.548 5.552 18036 Z= 0.293 Chirality : 0.043 0.146 1920 Planarity : 0.004 0.054 2400 Dihedral : 4.630 23.967 1753 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.16 % Allowed : 16.16 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.21), residues: 1596 helix: 0.59 (0.25), residues: 466 sheet: 1.23 (0.25), residues: 477 loop : -0.94 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 460 TYR 0.029 0.001 TYR A 501 PHE 0.015 0.001 PHE B 444 TRP 0.006 0.001 TRP C 519 HIS 0.008 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00265 (13284) covalent geometry : angle 0.54762 (18036) hydrogen bonds : bond 0.03878 ( 547) hydrogen bonds : angle 5.11570 ( 1506) *********************** 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: 16 poor density : 149 time to evaluate : 0.701 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: A 495 TYR cc_start: 0.6330 (p90) cc_final: 0.6057 (p90) REVERT: B 408 LYS cc_start: 0.5280 (pttm) cc_final: 0.5013 (pttt) REVERT: C 410 ARG cc_start: 0.5513 (mmt-90) cc_final: 0.5136 (ptt90) REVERT: C 464 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5504 (tp30) REVERT: K 486 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7836 (pt) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.2703 time to fit residues: 61.6778 Evaluate side-chains 151 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 533 CYS Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 492 CYS 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 J residue 484 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 421 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.214271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.176318 restraints weight = 45191.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175185 restraints weight = 67624.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176391 restraints weight = 63642.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.177252 restraints weight = 44545.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177069 restraints weight = 41596.642| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13284 Z= 0.149 Angle : 0.557 5.671 18036 Z= 0.300 Chirality : 0.043 0.159 1920 Planarity : 0.004 0.062 2400 Dihedral : 4.592 21.435 1753 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.52 % Allowed : 15.80 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.22), residues: 1596 helix: 0.62 (0.25), residues: 466 sheet: 1.16 (0.25), residues: 477 loop : -0.99 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 460 TYR 0.035 0.001 TYR A 501 PHE 0.018 0.001 PHE B 444 TRP 0.006 0.001 TRP F 519 HIS 0.008 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00357 (13284) covalent geometry : angle 0.55679 (18036) hydrogen bonds : bond 0.03881 ( 547) hydrogen bonds : angle 4.99765 ( 1506) *********************** 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: 21 poor density : 144 time to evaluate : 0.797 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: A 495 TYR cc_start: 0.6386 (p90) cc_final: 0.6159 (p90) REVERT: C 410 ARG cc_start: 0.5393 (mmt-90) cc_final: 0.5114 (ptt90) REVERT: C 445 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5722 (mp0) REVERT: C 464 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5201 (tp30) REVERT: K 486 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7838 (pt) outliers start: 21 outliers final: 17 residues processed: 160 average time/residue: 0.2952 time to fit residues: 66.5913 Evaluate side-chains 157 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE 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 478 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4441 r_free = 0.4441 target = 0.215324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3923 r_free = 0.3923 target = 0.165815 restraints weight = 45290.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.165315 restraints weight = 45763.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165406 restraints weight = 44692.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165779 restraints weight = 40033.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.165886 restraints weight = 37385.064| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13284 Z= 0.167 Angle : 0.569 5.808 18036 Z= 0.308 Chirality : 0.043 0.165 1920 Planarity : 0.005 0.066 2400 Dihedral : 4.631 20.325 1752 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.81 % Allowed : 16.52 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.21), residues: 1596 helix: 0.57 (0.25), residues: 466 sheet: 1.11 (0.25), residues: 476 loop : -1.03 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 521 TYR 0.033 0.002 TYR A 501 PHE 0.019 0.002 PHE B 444 TRP 0.007 0.001 TRP F 519 HIS 0.008 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00400 (13284) covalent geometry : angle 0.56950 (18036) hydrogen bonds : bond 0.03931 ( 547) hydrogen bonds : angle 4.96376 ( 1506) *********************** 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 168 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.734 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: A 495 TYR cc_start: 0.6475 (p90) cc_final: 0.6106 (p90) REVERT: A 521 ARG cc_start: 0.5671 (ttt90) cc_final: 0.5245 (tpt170) REVERT: C 410 ARG cc_start: 0.5856 (mmt-90) cc_final: 0.5161 (ptt90) REVERT: C 445 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5616 (mp0) REVERT: C 464 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6112 (tp30) REVERT: G 474 ILE cc_start: 0.6803 (pp) cc_final: 0.6564 (pt) REVERT: K 486 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7842 (pt) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 0.2654 time to fit residues: 61.1579 Evaluate side-chains 161 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE 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 H residue 523 ASP 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 456 MET 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 47 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.214629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3831 r_free = 0.3831 target = 0.158364 restraints weight = 45431.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159991 restraints weight = 35950.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160021 restraints weight = 30111.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160023 restraints weight = 29037.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.160023 restraints weight = 29024.810| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13284 Z= 0.136 Angle : 0.543 5.720 18036 Z= 0.292 Chirality : 0.043 0.160 1920 Planarity : 0.005 0.061 2400 Dihedral : 4.530 20.205 1752 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.88 % Allowed : 16.30 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.22), residues: 1596 helix: 0.68 (0.25), residues: 466 sheet: 1.18 (0.25), residues: 476 loop : -0.98 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 460 TYR 0.035 0.001 TYR A 501 PHE 0.017 0.001 PHE B 444 TRP 0.006 0.001 TRP F 519 HIS 0.007 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00325 (13284) covalent geometry : angle 0.54325 (18036) hydrogen bonds : bond 0.03608 ( 547) hydrogen bonds : angle 4.80386 ( 1506) *********************** 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 173 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.659 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: A 495 TYR cc_start: 0.6444 (p90) cc_final: 0.6047 (p90) REVERT: C 410 ARG cc_start: 0.6028 (mmt-90) cc_final: 0.5168 (ptt-90) REVERT: C 445 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5705 (mp0) REVERT: C 464 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6294 (tp30) REVERT: G 474 ILE cc_start: 0.6876 (pp) cc_final: 0.6642 (pt) REVERT: K 486 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7823 (pt) outliers start: 26 outliers final: 20 residues processed: 166 average time/residue: 0.2550 time to fit residues: 60.8897 Evaluate side-chains 166 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE 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 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 456 MET 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 127 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.215510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.191390 restraints weight = 45373.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169759 restraints weight = 60194.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.170650 restraints weight = 53303.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.171535 restraints weight = 43764.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.171567 restraints weight = 39318.953| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13284 Z= 0.155 Angle : 0.558 5.624 18036 Z= 0.301 Chirality : 0.043 0.160 1920 Planarity : 0.004 0.062 2400 Dihedral : 4.562 19.956 1752 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.81 % Allowed : 16.30 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1596 helix: 0.62 (0.25), residues: 466 sheet: 1.13 (0.25), residues: 476 loop : -1.00 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 460 TYR 0.035 0.001 TYR A 501 PHE 0.019 0.001 PHE B 444 TRP 0.007 0.001 TRP F 519 HIS 0.007 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00372 (13284) covalent geometry : angle 0.55758 (18036) hydrogen bonds : bond 0.03731 ( 547) hydrogen bonds : angle 4.80354 ( 1506) *********************** 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 173 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.707 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: 0.6367 (p90) cc_final: 0.5942 (p90) REVERT: C 410 ARG cc_start: 0.6085 (mmt-90) cc_final: 0.5236 (ptt-90) REVERT: C 445 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5590 (mp0) REVERT: C 464 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6408 (tp30) REVERT: G 474 ILE cc_start: 0.6949 (pp) cc_final: 0.6702 (pt) outliers start: 25 outliers final: 23 residues processed: 168 average time/residue: 0.2663 time to fit residues: 64.4683 Evaluate side-chains 169 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 445 GLU Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE 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 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 484 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 456 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.216904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.185809 restraints weight = 44874.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.173303 restraints weight = 61035.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169969 restraints weight = 48389.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170454 restraints weight = 40800.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170294 restraints weight = 35709.756| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13284 Z= 0.106 Angle : 0.526 5.451 18036 Z= 0.280 Chirality : 0.042 0.163 1920 Planarity : 0.004 0.068 2400 Dihedral : 4.408 19.900 1752 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.38 % Allowed : 17.03 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.22), residues: 1596 helix: 0.79 (0.25), residues: 466 sheet: 1.27 (0.25), residues: 476 loop : -0.88 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 521 TYR 0.036 0.001 TYR A 501 PHE 0.015 0.001 PHE B 444 TRP 0.007 0.001 TRP A 519 HIS 0.006 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00250 (13284) covalent geometry : angle 0.52580 (18036) hydrogen bonds : bond 0.03231 ( 547) hydrogen bonds : angle 4.60840 ( 1506) ********************** 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 167 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.739 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: A 495 TYR cc_start: 0.6424 (p90) cc_final: 0.6080 (p90) REVERT: C 410 ARG cc_start: 0.5968 (mmt-90) cc_final: 0.5254 (ptt-90) REVERT: C 464 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6087 (tp30) REVERT: G 474 ILE cc_start: 0.6785 (pp) cc_final: 0.6558 (pt) REVERT: K 486 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7804 (pt) outliers start: 19 outliers final: 16 residues processed: 164 average time/residue: 0.2550 time to fit residues: 60.9380 Evaluate side-chains 162 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 533 CYS 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 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 484 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 456 MET 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 44 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.218232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169294 restraints weight = 45086.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169517 restraints weight = 42810.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169669 restraints weight = 39406.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169675 restraints weight = 35606.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.169675 restraints weight = 35470.781| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13284 Z= 0.102 Angle : 0.521 5.515 18036 Z= 0.277 Chirality : 0.042 0.160 1920 Planarity : 0.004 0.060 2400 Dihedral : 4.330 19.626 1752 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.30 % Allowed : 16.88 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1596 helix: 0.85 (0.25), residues: 466 sheet: 1.33 (0.25), residues: 476 loop : -0.84 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 521 TYR 0.032 0.001 TYR A 501 PHE 0.016 0.001 PHE B 444 TRP 0.006 0.001 TRP A 519 HIS 0.006 0.001 HIS L 530 Details of bonding type rmsd covalent geometry : bond 0.00242 (13284) covalent geometry : angle 0.52086 (18036) hydrogen bonds : bond 0.03137 ( 547) hydrogen bonds : angle 4.52180 ( 1506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.21 seconds wall clock time: 69 minutes 24.13 seconds (4164.13 seconds total)