Starting phenix.real_space_refine on Fri Aug 9 06:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6q_41077/08_2024/8t6q_41077.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6q_41077/08_2024/8t6q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6q_41077/08_2024/8t6q_41077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6q_41077/08_2024/8t6q_41077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6q_41077/08_2024/8t6q_41077.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6q_41077/08_2024/8t6q_41077.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 8172 2.51 5 N 2316 2.21 5 O 2412 1.98 5 H 12534 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 523": "OD1" <-> "OD2" Residue "F GLU 413": "OE1" <-> "OE2" Residue "F GLU 419": "OE1" <-> "OE2" Residue "F GLU 423": "OE1" <-> "OE2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "F GLU 464": "OE1" <-> "OE2" Residue "F GLU 515": "OE1" <-> "OE2" Residue "G GLU 464": "OE1" <-> "OE2" Residue "I GLU 488": "OE1" <-> "OE2" Residue "J TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 457": "OD1" <-> "OD2" Residue "L PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 523": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25482 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "B" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "C" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "D" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "G" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2124 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "H" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "I" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "J" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "K" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "L" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "N" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2123 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 126} Time building chain proxies: 11.89, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 19.27 Conformation dependent library (CDL) restraints added in 2.6 seconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 19 sheets defined 34.0% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 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: 9.09 Time building geometry restraints manager: 20.36 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: 94.40 - 102.31: 14 102.31 - 110.23: 24176 110.23 - 118.14: 10140 118.14 - 126.06: 11810 126.06 - 133.97: 444 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: 0.00 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: 2.110 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: 0.340 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 78.820 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.090 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.630 ------------------------------------------------------------------------------- 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= 0.198 Angle : 0.563 14.942 18036 Z= 0.315 Chirality : 0.043 0.280 1920 Planarity : 0.005 0.144 2400 Dihedral : 15.872 89.320 4896 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.51 % Allowed : 15.51 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1596 helix: 0.29 (0.25), residues: 458 sheet: 1.54 (0.24), residues: 495 loop : -0.85 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 519 HIS 0.008 0.001 HIS L 530 PHE 0.013 0.001 PHE L 461 TYR 0.011 0.001 TYR L 462 ARG 0.007 0.000 ARG B 460 *********************** 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 fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 PHE cc_start: 0.6233 (t80) cc_final: 0.5662 (t80) REVERT: B 408 LYS cc_start: 0.6252 (pttm) cc_final: 0.5839 (pttm) REVERT: C 410 ARG cc_start: 0.6094 (mmt-90) cc_final: 0.5339 (ptt-90) REVERT: G 408 LYS cc_start: 0.7031 (ptpp) cc_final: 0.6651 (tptt) REVERT: G 488 GLU cc_start: 0.8645 (pp20) cc_final: 0.8250 (mt-10) REVERT: G 489 ASP cc_start: 0.8596 (p0) cc_final: 0.8178 (p0) REVERT: I 408 LYS cc_start: 0.6315 (pttm) cc_final: 0.6046 (tttp) REVERT: I 457 ASP cc_start: 0.8494 (m-30) cc_final: 0.8015 (m-30) REVERT: I 523 ASP cc_start: 0.7661 (p0) cc_final: 0.7398 (m-30) REVERT: J 464 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6648 (mp0) REVERT: K 460 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.8046 (ttp80) REVERT: K 503 ASP cc_start: 0.8234 (p0) cc_final: 0.8015 (p0) REVERT: L 416 LYS cc_start: 0.8416 (tptp) cc_final: 0.8095 (tptp) REVERT: L 419 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6603 (tm-30) REVERT: N 420 GLN cc_start: 0.8154 (mt0) cc_final: 0.7920 (mt0) REVERT: N 505 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8564 (mp10) outliers start: 7 outliers final: 5 residues processed: 210 average time/residue: 0.7148 time to fit residues: 202.4123 Evaluate side-chains 159 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain I residue 534 SER Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain L residue 461 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 HIS ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN ** F 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13284 Z= 0.294 Angle : 0.632 7.201 18036 Z= 0.348 Chirality : 0.045 0.177 1920 Planarity : 0.005 0.065 2400 Dihedral : 5.241 48.273 1761 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.67 % Allowed : 15.14 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.21), residues: 1596 helix: 0.42 (0.25), residues: 460 sheet: 1.40 (0.24), residues: 495 loop : -1.03 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 519 HIS 0.013 0.001 HIS F 484 PHE 0.020 0.002 PHE B 444 TYR 0.022 0.002 TYR A 501 ARG 0.015 0.001 ARG L 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 PHE cc_start: 0.5993 (t80) cc_final: 0.5569 (t80) REVERT: A 495 TYR cc_start: 0.6935 (p90) cc_final: 0.6448 (p90) REVERT: B 408 LYS cc_start: 0.6408 (pttm) cc_final: 0.5980 (pttm) REVERT: C 410 ARG cc_start: 0.6090 (mmt-90) cc_final: 0.5172 (ptt90) REVERT: C 464 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: F 463 PHE cc_start: 0.6796 (m-80) cc_final: 0.6549 (m-10) REVERT: G 408 LYS cc_start: 0.7212 (ptpp) cc_final: 0.6715 (tptt) REVERT: G 429 ASP cc_start: 0.8069 (t0) cc_final: 0.7852 (t0) REVERT: G 488 GLU cc_start: 0.8639 (pp20) cc_final: 0.8318 (mt-10) REVERT: G 489 ASP cc_start: 0.8759 (p0) cc_final: 0.8424 (p0) REVERT: I 408 LYS cc_start: 0.6487 (pttm) cc_final: 0.6108 (tttp) REVERT: I 457 ASP cc_start: 0.8598 (m-30) cc_final: 0.8185 (m-30) REVERT: J 464 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6663 (mp0) REVERT: J 518 VAL cc_start: 0.5620 (t) cc_final: 0.5381 (t) REVERT: K 460 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8057 (ttp80) REVERT: K 486 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8301 (pt) REVERT: K 503 ASP cc_start: 0.8285 (p0) cc_final: 0.7670 (p0) REVERT: L 416 LYS cc_start: 0.8330 (tptp) cc_final: 0.8038 (mmmt) REVERT: L 420 GLN cc_start: 0.8829 (mt0) cc_final: 0.8304 (mm-40) REVERT: L 461 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.5339 (t80) REVERT: N 420 GLN cc_start: 0.8343 (mt0) cc_final: 0.8013 (mt0) REVERT: N 505 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8564 (mp10) outliers start: 23 outliers final: 15 residues processed: 179 average time/residue: 0.6132 time to fit residues: 153.1369 Evaluate side-chains 172 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain H residue 457 ASP Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 489 ASP Chi-restraints excluded: chain I residue 534 SER Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 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 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN ** C 520 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 ASN ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13284 Z= 0.320 Angle : 0.610 5.773 18036 Z= 0.334 Chirality : 0.045 0.160 1920 Planarity : 0.004 0.049 2400 Dihedral : 5.237 41.136 1759 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.96 % Allowed : 14.93 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1596 helix: 0.35 (0.24), residues: 464 sheet: 1.15 (0.25), residues: 478 loop : -1.16 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 519 HIS 0.009 0.001 HIS F 484 PHE 0.020 0.002 PHE B 444 TYR 0.034 0.002 TYR A 501 ARG 0.007 0.000 ARG L 517 *********************** 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 191 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 2.084 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 461 PHE cc_start: 0.6003 (t80) cc_final: 0.5624 (t80) REVERT: A 495 TYR cc_start: 0.7005 (p90) cc_final: 0.6558 (p90) REVERT: B 408 LYS cc_start: 0.6511 (pttm) cc_final: 0.6192 (pttt) REVERT: C 464 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: D 488 GLU cc_start: 0.8853 (mp0) cc_final: 0.8451 (mp0) REVERT: G 408 LYS cc_start: 0.7238 (ptpp) cc_final: 0.6838 (tptt) REVERT: G 488 GLU cc_start: 0.8635 (pp20) cc_final: 0.8365 (mt-10) REVERT: G 489 ASP cc_start: 0.8783 (p0) cc_final: 0.8431 (p0) REVERT: I 408 LYS cc_start: 0.6492 (pttm) cc_final: 0.6111 (tttp) REVERT: J 464 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6650 (mp0) REVERT: J 518 VAL cc_start: 0.5456 (t) cc_final: 0.5236 (t) REVERT: K 423 GLU cc_start: 0.8294 (tp30) cc_final: 0.8058 (tp30) REVERT: K 460 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7983 (ttp80) REVERT: K 486 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (pt) REVERT: L 461 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5396 (t80) REVERT: N 420 GLN cc_start: 0.8454 (mt0) cc_final: 0.8253 (mt0) REVERT: N 456 MET cc_start: 0.8549 (mmm) cc_final: 0.8234 (mmm) REVERT: N 505 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8647 (mp10) outliers start: 27 outliers final: 22 residues processed: 183 average time/residue: 0.6096 time to fit residues: 157.2981 Evaluate side-chains 179 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain C residue 462 TYR Chi-restraints excluded: chain C residue 464 GLU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 492 CYS Chi-restraints excluded: chain G residue 492 CYS Chi-restraints excluded: chain H residue 457 ASP Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 489 ASP Chi-restraints excluded: chain I residue 534 SER Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 484 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 461 PHE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 525 LYS Chi-restraints excluded: chain N residue 421 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13284 Z= 0.247 Angle : 0.576 6.252 18036 Z= 0.312 Chirality : 0.043 0.150 1920 Planarity : 0.004 0.058 2400 Dihedral : 5.110 40.968 1759 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.74 % Allowed : 15.43 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.21), residues: 1596 helix: 0.37 (0.24), residues: 466 sheet: 1.16 (0.25), residues: 474 loop : -1.13 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 519 HIS 0.007 0.001 HIS L 530 PHE 0.018 0.002 PHE B 444 TYR 0.041 0.002 TYR A 501 ARG 0.006 0.000 ARG L 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 2.117 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 461 PHE cc_start: 0.6007 (t80) cc_final: 0.5648 (t80) REVERT: A 495 TYR cc_start: 0.6958 (p90) cc_final: 0.6562 (p90) REVERT: B 408 LYS cc_start: 0.6450 (pttm) cc_final: 0.6187 (pttt) REVERT: C 464 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: D 488 GLU cc_start: 0.8797 (mp0) cc_final: 0.8440 (mp0) REVERT: G 408 LYS cc_start: 0.7208 (ptpp) cc_final: 0.6811 (tptt) REVERT: G 488 GLU cc_start: 0.8621 (pp20) cc_final: 0.8379 (mt-10) REVERT: G 489 ASP cc_start: 0.8815 (p0) cc_final: 0.8464 (p0) REVERT: H 489 ASP cc_start: 0.8075 (p0) cc_final: 0.7847 (p0) REVERT: I 408 LYS cc_start: 0.6491 (pttm) cc_final: 0.6119 (tttp) REVERT: J 464 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6611 (mp0) REVERT: K 457 ASP cc_start: 0.8586 (t0) cc_final: 0.8299 (t0) REVERT: K 460 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.7957 (ttp80) REVERT: K 486 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8288 (pt) REVERT: L 461 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.5490 (t80) REVERT: N 420 GLN cc_start: 0.8467 (mt0) cc_final: 0.8264 (mt0) REVERT: N 505 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8666 (mp10) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.6011 time to fit residues: 145.9833 Evaluate side-chains 173 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 493 ILE Chi-restraints excluded: chain C residue 514 GLU Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 484 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 461 PHE Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain N residue 421 LEU Chi-restraints excluded: chain N residue 492 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13284 Z= 0.286 Angle : 0.586 5.711 18036 Z= 0.318 Chirality : 0.044 0.151 1920 Planarity : 0.004 0.067 2400 Dihedral : 5.094 40.695 1758 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.17 % Allowed : 16.09 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1596 helix: 0.38 (0.24), residues: 466 sheet: 1.01 (0.25), residues: 477 loop : -1.18 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 519 HIS 0.007 0.001 HIS F 484 PHE 0.020 0.002 PHE B 444 TYR 0.033 0.002 TYR A 501 ARG 0.005 0.000 ARG A 521 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.837 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: A 461 PHE cc_start: 0.6003 (t80) cc_final: 0.5665 (t80) REVERT: A 495 TYR cc_start: 0.7008 (p90) cc_final: 0.6617 (p90) REVERT: B 408 LYS cc_start: 0.6510 (pttm) cc_final: 0.6299 (pttt) REVERT: C 410 ARG cc_start: 0.6114 (mmt-90) cc_final: 0.5309 (ptt90) REVERT: C 445 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: C 464 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7296 (tp30) REVERT: D 488 GLU cc_start: 0.8850 (mp0) cc_final: 0.8509 (mp0) REVERT: G 408 LYS cc_start: 0.7263 (ptpp) cc_final: 0.6863 (tptt) REVERT: G 488 GLU cc_start: 0.8616 (pp20) cc_final: 0.8398 (mt-10) REVERT: G 489 ASP cc_start: 0.8824 (p0) cc_final: 0.8488 (p0) REVERT: H 489 ASP cc_start: 0.8049 (p0) cc_final: 0.7751 (p0) REVERT: I 408 LYS cc_start: 0.6586 (pttm) cc_final: 0.6156 (tttp) REVERT: J 464 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6662 (mp0) REVERT: K 457 ASP cc_start: 0.8591 (t0) cc_final: 0.8291 (t0) REVERT: K 460 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.7949 (ttp80) REVERT: K 486 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8312 (pt) REVERT: L 461 PHE cc_start: 0.5657 (OUTLIER) cc_final: 0.5445 (t80) REVERT: N 420 GLN cc_start: 0.8514 (mt0) cc_final: 0.8298 (mt0) REVERT: N 505 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8695 (mp10) outliers start: 30 outliers final: 24 residues processed: 184 average time/residue: 0.6164 time to fit residues: 159.0512 Evaluate side-chains 180 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 514 GLU 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 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 457 ASP Chi-restraints excluded: chain H residue 478 ILE Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 413 GLU 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 K residue 486 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 461 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.0170 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- 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** G 520 HIS ** I 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13284 Z= 0.187 Angle : 0.543 5.556 18036 Z= 0.291 Chirality : 0.043 0.162 1920 Planarity : 0.004 0.055 2400 Dihedral : 4.914 40.383 1758 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.96 % Allowed : 16.30 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1596 helix: 0.55 (0.25), residues: 466 sheet: 1.10 (0.25), residues: 477 loop : -1.05 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 519 HIS 0.006 0.001 HIS L 530 PHE 0.016 0.001 PHE B 444 TYR 0.033 0.001 TYR A 501 ARG 0.005 0.000 ARG B 460 *********************** 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 189 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 2.013 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 461 PHE cc_start: 0.5999 (t80) cc_final: 0.5676 (t80) REVERT: A 495 TYR cc_start: 0.6952 (p90) cc_final: 0.6620 (p90) REVERT: A 521 ARG cc_start: 0.7054 (ttt90) cc_final: 0.6727 (tpt170) REVERT: C 464 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: D 488 GLU cc_start: 0.8801 (mp0) cc_final: 0.8485 (mp0) REVERT: G 408 LYS cc_start: 0.7141 (ptpp) cc_final: 0.6693 (tptt) REVERT: G 489 ASP cc_start: 0.8778 (p0) cc_final: 0.8404 (p0) REVERT: H 489 ASP cc_start: 0.8120 (p0) cc_final: 0.7747 (p0) REVERT: H 497 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7698 (ttp-170) REVERT: I 408 LYS cc_start: 0.6728 (pttm) cc_final: 0.6225 (tttp) REVERT: J 464 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6616 (mp0) REVERT: K 457 ASP cc_start: 0.8562 (t0) cc_final: 0.8278 (t0) REVERT: K 460 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7938 (ttp80) REVERT: K 486 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8209 (pt) REVERT: L 507 ARG cc_start: 0.6491 (mtp180) cc_final: 0.6063 (ptt180) REVERT: N 420 GLN cc_start: 0.8496 (mt0) cc_final: 0.8240 (mt0) REVERT: N 505 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8693 (mp10) outliers start: 27 outliers final: 21 residues processed: 183 average time/residue: 0.6007 time to fit residues: 154.4643 Evaluate side-chains 175 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 514 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 H residue 478 ILE Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain I residue 413 GLU Chi-restraints excluded: chain I residue 492 CYS Chi-restraints excluded: chain J residue 445 GLU Chi-restraints excluded: chain J residue 475 HIS Chi-restraints excluded: chain J residue 484 HIS Chi-restraints excluded: chain J residue 533 CYS Chi-restraints excluded: chain K residue 486 ILE Chi-restraints excluded: chain L residue 415 ILE Chi-restraints excluded: chain L residue 441 LEU Chi-restraints excluded: chain L residue 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 145 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 84 optimal weight: 0.4980 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: