Starting phenix.real_space_refine on Fri Aug 9 07:54:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/08_2024/8t15_40955.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/08_2024/8t15_40955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/08_2024/8t15_40955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/08_2024/8t15_40955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/08_2024/8t15_40955.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/08_2024/8t15_40955.cif" } resolution = 2.7 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= 0.002 sd= 0.097 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 60 5.16 5 C 8256 2.51 5 N 2340 2.21 5 O 2388 1.98 5 H 12612 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C ASP 424": "OD1" <-> "OD2" Residue "C GLU 425": "OE1" <-> "OE2" Residue "C TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D ASP 424": "OD1" <-> "OD2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 355": "OE1" <-> "OE2" Residue "E GLU 359": "OE1" <-> "OE2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E ASP 424": "OD1" <-> "OD2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "F TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 359": "OE1" <-> "OE2" Residue "G GLU 400": "OE1" <-> "OE2" Residue "G ASP 424": "OD1" <-> "OD2" Residue "G TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 355": "OE1" <-> "OE2" Residue "H GLU 359": "OE1" <-> "OE2" Residue "H GLU 400": "OE1" <-> "OE2" Residue "H ASP 424": "OD1" <-> "OD2" Residue "H GLU 425": "OE1" <-> "OE2" Residue "H TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 400": "OE1" <-> "OE2" Residue "I TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 359": "OE1" <-> "OE2" Residue "J GLU 400": "OE1" <-> "OE2" Residue "J ASP 424": "OD1" <-> "OD2" Residue "J GLU 425": "OE1" <-> "OE2" Residue "J TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 355": "OE1" <-> "OE2" Residue "K GLU 359": "OE1" <-> "OE2" Residue "K GLU 400": "OE1" <-> "OE2" Residue "K TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 400": "OE1" <-> "OE2" Residue "L ASP 424": "OD1" <-> "OD2" Residue "L TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 25656 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "B" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "C" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "E" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "F" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "G" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "H" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "I" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "J" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "K" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "L" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Time building chain proxies: 13.35, per 1000 atoms: 0.52 Number of scatterers: 25656 At special positions: 0 Unit cell: (120.783, 125.229, 70.395, 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 60 16.00 O 2388 8.00 N 2340 7.00 C 8256 6.00 H 12612 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: 20.14 Conformation dependent library (CDL) restraints added in 2.5 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 31.4% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 345 through 363 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 392 through 402 removed outlier: 4.019A pdb=" N PHE B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 363 Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 392 through 402 removed outlier: 4.017A pdb=" N PHE C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR C 398 " --> pdb=" O PHE C 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 363 Processing helix chain 'D' and resid 365 through 372 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE E 350 " --> pdb=" O ARG E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 392 through 402 removed outlier: 4.021A pdb=" N PHE E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 363 Processing helix chain 'F' and resid 365 through 372 Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 392 through 402 removed outlier: 4.017A pdb=" N PHE F 397 " --> pdb=" O ASP F 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 363 Processing helix chain 'G' and resid 365 through 372 Processing helix chain 'G' and resid 381 through 385 Processing helix chain 'G' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE H 350 " --> pdb=" O ARG H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 372 Processing helix chain 'H' and resid 381 through 385 Processing helix chain 'H' and resid 392 through 402 removed outlier: 4.019A pdb=" N PHE H 397 " --> pdb=" O ASP H 393 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 363 Processing helix chain 'I' and resid 365 through 372 Processing helix chain 'I' and resid 381 through 385 Processing helix chain 'I' and resid 392 through 402 removed outlier: 4.017A pdb=" N PHE I 397 " --> pdb=" O ASP I 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 363 Processing helix chain 'J' and resid 365 through 372 Processing helix chain 'J' and resid 381 through 385 Processing helix chain 'J' and resid 392 through 402 removed outlier: 3.989A pdb=" N PHE J 397 " --> pdb=" O ASP J 393 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR J 398 " --> pdb=" O PHE J 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 363 removed outlier: 3.543A pdb=" N ILE K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 372 Processing helix chain 'K' and resid 381 through 385 Processing helix chain 'K' and resid 392 through 402 removed outlier: 4.018A pdb=" N PHE K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR K 398 " --> pdb=" O PHE K 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 363 Processing helix chain 'L' and resid 365 through 372 Processing helix chain 'L' and resid 381 through 385 Processing helix chain 'L' and resid 392 through 402 removed outlier: 4.018A pdb=" N PHE L 397 " --> pdb=" O ASP L 393 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR L 398 " --> pdb=" O PHE L 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 390 removed outlier: 8.917A pdb=" N ASP A 374 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN A 463 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N GLY A 376 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 465 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 454 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 467 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 452 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG A 469 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A 450 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY A 471 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN A 448 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER A 426 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU A 421 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS A 428 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 419 " --> pdb=" O CYS A 428 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 430 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP B 374 " --> pdb=" O LYS B 461 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N GLN B 463 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N GLY B 376 " --> pdb=" O GLN B 463 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 465 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 454 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE B 467 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 452 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG B 469 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 450 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLY B 471 " --> pdb=" O GLN B 448 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLN B 448 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER B 426 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU B 421 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS B 428 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE B 419 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 430 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 389 through 390 removed outlier: 8.929A pdb=" N ASP C 374 " --> pdb=" O LYS C 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN C 463 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLY C 376 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 465 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 454 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE C 467 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR C 452 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG C 469 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU C 450 " --> pdb=" O ARG C 469 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY C 471 " --> pdb=" O GLN C 448 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN C 448 " --> pdb=" O GLY C 471 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER C 426 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU C 421 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS C 428 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE C 419 " --> pdb=" O CYS C 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA C 430 " --> pdb=" O PRO C 417 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 389 through 390 removed outlier: 8.917A pdb=" N ASP D 374 " --> pdb=" O LYS D 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN D 463 " --> pdb=" O ASP D 374 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N GLY D 376 " --> pdb=" O GLN D 463 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL D 465 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL D 454 " --> pdb=" O VAL D 465 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE D 467 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 452 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG D 469 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU D 450 " --> pdb=" O ARG D 469 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY D 471 " --> pdb=" O GLN D 448 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLN D 448 " --> pdb=" O GLY D 471 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER D 426 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU D 421 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS D 428 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE D 419 " --> pdb=" O CYS D 428 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 430 " --> pdb=" O PRO D 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP E 374 " --> pdb=" O LYS E 461 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLN E 463 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N GLY E 376 " --> pdb=" O GLN E 463 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 465 " --> pdb=" O GLY E 376 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL E 454 " --> pdb=" O VAL E 465 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE E 467 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR E 452 " --> pdb=" O PHE E 467 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG E 469 " --> pdb=" O GLU E 450 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU E 450 " --> pdb=" O ARG E 469 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY E 471 " --> pdb=" O GLN E 448 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLN E 448 " --> pdb=" O GLY E 471 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N SER E 426 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU E 421 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS E 428 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE E 419 " --> pdb=" O CYS E 428 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA E 430 " --> pdb=" O PRO E 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 389 through 390 removed outlier: 8.927A pdb=" N ASP F 374 " --> pdb=" O LYS F 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN F 463 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLY F 376 " --> pdb=" O GLN F 463 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL F 465 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL F 454 " --> pdb=" O VAL F 465 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE F 467 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR F 452 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG F 469 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU F 450 " --> pdb=" O ARG F 469 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLY F 471 " --> pdb=" O GLN F 448 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLN F 448 " --> pdb=" O GLY F 471 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER F 426 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU F 421 " --> pdb=" O SER F 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS F 428 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE F 419 " --> pdb=" O CYS F 428 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA F 430 " --> pdb=" O PRO F 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 389 through 390 removed outlier: 8.917A pdb=" N ASP G 374 " --> pdb=" O LYS G 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN G 463 " --> pdb=" O ASP G 374 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N GLY G 376 " --> pdb=" O GLN G 463 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL G 465 " --> pdb=" O GLY G 376 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL G 454 " --> pdb=" O VAL G 465 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE G 467 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR G 452 " --> pdb=" O PHE G 467 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG G 469 " --> pdb=" O GLU G 450 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU G 450 " --> pdb=" O ARG G 469 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 471 " --> pdb=" O GLN G 448 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN G 448 " --> pdb=" O GLY G 471 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER G 426 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU G 421 " --> pdb=" O SER G 426 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS G 428 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE G 419 " --> pdb=" O CYS G 428 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA G 430 " --> pdb=" O PRO G 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP H 374 " --> pdb=" O LYS H 461 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N GLN H 463 " --> pdb=" O ASP H 374 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N GLY H 376 " --> pdb=" O GLN H 463 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL H 465 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL H 454 " --> pdb=" O VAL H 465 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE H 467 " --> pdb=" O THR H 452 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR H 452 " --> pdb=" O PHE H 467 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG H 469 " --> pdb=" O GLU H 450 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU H 450 " --> pdb=" O ARG H 469 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY H 471 " --> pdb=" O GLN H 448 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLN H 448 " --> pdb=" O GLY H 471 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N SER H 426 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU H 421 " --> pdb=" O SER H 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS H 428 " --> pdb=" O ILE H 419 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE H 419 " --> pdb=" O CYS H 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA H 430 " --> pdb=" O PRO H 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 389 through 390 removed outlier: 8.929A pdb=" N ASP I 374 " --> pdb=" O LYS I 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN I 463 " --> pdb=" O ASP I 374 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLY I 376 " --> pdb=" O GLN I 463 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL I 465 " --> pdb=" O GLY I 376 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL I 454 " --> pdb=" O VAL I 465 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE I 467 " --> pdb=" O THR I 452 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR I 452 " --> pdb=" O PHE I 467 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG I 469 " --> pdb=" O GLU I 450 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU I 450 " --> pdb=" O ARG I 469 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY I 471 " --> pdb=" O GLN I 448 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN I 448 " --> pdb=" O GLY I 471 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER I 426 " --> pdb=" O LEU I 421 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU I 421 " --> pdb=" O SER I 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS I 428 " --> pdb=" O ILE I 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE I 419 " --> pdb=" O CYS I 428 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA I 430 " --> pdb=" O PRO I 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 389 through 390 removed outlier: 8.916A pdb=" N ASP J 374 " --> pdb=" O LYS J 461 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLN J 463 " --> pdb=" O ASP J 374 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N GLY J 376 " --> pdb=" O GLN J 463 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL J 465 " --> pdb=" O GLY J 376 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL J 454 " --> pdb=" O VAL J 465 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE J 467 " --> pdb=" O THR J 452 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR J 452 " --> pdb=" O PHE J 467 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG J 469 " --> pdb=" O GLU J 450 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU J 450 " --> pdb=" O ARG J 469 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY J 471 " --> pdb=" O GLN J 448 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN J 448 " --> pdb=" O GLY J 471 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER J 426 " --> pdb=" O LEU J 421 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU J 421 " --> pdb=" O SER J 426 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS J 428 " --> pdb=" O ILE J 419 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE J 419 " --> pdb=" O CYS J 428 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA J 430 " --> pdb=" O PRO J 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 389 through 390 removed outlier: 8.879A pdb=" N ASP K 374 " --> pdb=" O LYS K 461 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN K 463 " --> pdb=" O ASP K 374 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLY K 376 " --> pdb=" O GLN K 463 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL K 465 " --> pdb=" O GLY K 376 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL K 454 " --> pdb=" O VAL K 465 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N PHE K 467 " --> pdb=" O THR K 452 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR K 452 " --> pdb=" O PHE K 467 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG K 469 " --> pdb=" O GLU K 450 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU K 450 " --> pdb=" O ARG K 469 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY K 471 " --> pdb=" O GLN K 448 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLN K 448 " --> pdb=" O GLY K 471 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER K 426 " --> pdb=" O LEU K 421 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU K 421 " --> pdb=" O SER K 426 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS K 428 " --> pdb=" O ILE K 419 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE K 419 " --> pdb=" O CYS K 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA K 430 " --> pdb=" O PRO K 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 389 through 390 removed outlier: 8.928A pdb=" N ASP L 374 " --> pdb=" O LYS L 461 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLN L 463 " --> pdb=" O ASP L 374 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N GLY L 376 " --> pdb=" O GLN L 463 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL L 465 " --> pdb=" O GLY L 376 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL L 454 " --> pdb=" O VAL L 465 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE L 467 " --> pdb=" O THR L 452 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR L 452 " --> pdb=" O PHE L 467 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG L 469 " --> pdb=" O GLU L 450 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU L 450 " --> pdb=" O ARG L 469 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY L 471 " --> pdb=" O GLN L 448 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN L 448 " --> pdb=" O GLY L 471 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N SER L 426 " --> pdb=" O LEU L 421 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU L 421 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS L 428 " --> pdb=" O ILE L 419 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE L 419 " --> pdb=" O CYS L 428 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA L 430 " --> pdb=" O PRO L 417 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1755 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: 10.50 Time building geometry restraints manager: 21.20 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: 12588 1.03 - 1.23: 24 1.23 - 1.42: 5856 1.42 - 1.61: 7452 1.61 - 1.81: 96 Bond restraints: 26016 Sorted by residual: bond pdb=" N VAL L 345 " pdb=" CA VAL L 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N VAL B 345 " pdb=" CA VAL B 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N VAL K 345 " pdb=" CA VAL K 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" N VAL E 345 " pdb=" CA VAL E 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" N VAL C 345 " pdb=" CA VAL C 345 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 ... (remaining 26011 not shown) Histogram of bond angle deviations from ideal: 100.65 - 107.32: 900 107.32 - 114.00: 30082 114.00 - 120.67: 8593 120.67 - 127.35: 7009 127.35 - 134.02: 252 Bond angle restraints: 46836 Sorted by residual: angle pdb=" N VAL C 465 " pdb=" CA VAL C 465 " pdb=" C VAL C 465 " ideal model delta sigma weight residual 111.90 109.63 2.27 8.10e-01 1.52e+00 7.84e+00 angle pdb=" N VAL E 465 " pdb=" CA VAL E 465 " pdb=" C VAL E 465 " ideal model delta sigma weight residual 111.90 109.69 2.21 8.10e-01 1.52e+00 7.42e+00 angle pdb=" N VAL I 465 " pdb=" CA VAL I 465 " pdb=" C VAL I 465 " ideal model delta sigma weight residual 111.90 109.70 2.20 8.10e-01 1.52e+00 7.38e+00 angle pdb=" N VAL F 465 " pdb=" CA VAL F 465 " pdb=" C VAL F 465 " ideal model delta sigma weight residual 111.90 109.70 2.20 8.10e-01 1.52e+00 7.38e+00 angle pdb=" N VAL L 465 " pdb=" CA VAL L 465 " pdb=" C VAL L 465 " ideal model delta sigma weight residual 111.90 109.70 2.20 8.10e-01 1.52e+00 7.37e+00 ... (remaining 46831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 11071 17.06 - 34.12: 696 34.12 - 51.18: 374 51.18 - 68.24: 120 68.24 - 85.30: 39 Dihedral angle restraints: 12300 sinusoidal: 6588 harmonic: 5712 Sorted by residual: dihedral pdb=" CA ALA E 379 " pdb=" C ALA E 379 " pdb=" N PHE E 380 " pdb=" CA PHE E 380 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA F 379 " pdb=" C ALA F 379 " pdb=" N PHE F 380 " pdb=" CA PHE F 380 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ALA C 379 " pdb=" C ALA C 379 " pdb=" N PHE C 380 " pdb=" CA PHE C 380 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 12297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1058 0.027 - 0.053: 537 0.053 - 0.080: 161 0.080 - 0.106: 69 0.106 - 0.133: 95 Chirality restraints: 1920 Sorted by residual: chirality pdb=" CA VAL L 345 " pdb=" N VAL L 345 " pdb=" C VAL L 345 " pdb=" CB VAL L 345 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL B 345 " pdb=" N VAL B 345 " pdb=" C VAL B 345 " pdb=" CB VAL B 345 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1917 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 472 " -0.016 5.00e-02 4.00e+02 2.48e-02 9.87e-01 pdb=" N PRO H 473 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO H 473 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO H 473 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 472 " 0.016 5.00e-02 4.00e+02 2.48e-02 9.82e-01 pdb=" N PRO E 473 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO E 473 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 473 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 472 " 0.016 5.00e-02 4.00e+02 2.47e-02 9.76e-01 pdb=" N PRO B 473 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " 0.014 5.00e-02 4.00e+02 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 5240 2.30 - 2.88: 55609 2.88 - 3.45: 64245 3.45 - 4.03: 94103 4.03 - 4.60: 138564 Nonbonded interactions: 357761 Sorted by model distance: nonbonded pdb=" O ILE H 350 " pdb=" HG1 THR H 354 " model vdw 1.727 2.450 nonbonded pdb=" O ILE B 350 " pdb=" HG1 THR B 354 " model vdw 1.727 2.450 nonbonded pdb=" O ILE K 350 " pdb=" HG1 THR K 354 " model vdw 1.727 2.450 nonbonded pdb=" O ILE E 350 " pdb=" HG1 THR E 354 " model vdw 1.728 2.450 nonbonded pdb=" O ILE L 350 " pdb=" HG1 THR L 354 " model vdw 1.733 2.450 ... (remaining 357756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.380 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 83.520 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.002 0.032 13404 Z= 0.162 Angle : 0.533 4.431 18180 Z= 0.319 Chirality : 0.044 0.133 1920 Planarity : 0.004 0.033 2376 Dihedral : 16.278 85.302 4920 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % 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: 1.81 (0.21), residues: 1584 helix: 0.86 (0.25), residues: 408 sheet: 3.25 (0.21), residues: 552 loop : -0.59 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 455 HIS 0.002 0.000 HIS H 420 PHE 0.013 0.002 PHE K 467 TYR 0.005 0.001 TYR K 398 ARG 0.004 0.000 ARG G 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.030 Fit side-chains REVERT: H 424 ASP cc_start: 0.8276 (p0) cc_final: 0.8007 (m-30) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 4.0640 time to fit residues: 930.3151 Evaluate side-chains 198 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13404 Z= 0.305 Angle : 0.561 3.884 18180 Z= 0.317 Chirality : 0.046 0.154 1920 Planarity : 0.005 0.028 2376 Dihedral : 4.571 21.665 1764 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.28 % Allowed : 12.75 % Favored : 86.97 % 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: 1.42 (0.21), residues: 1584 helix: 0.38 (0.24), residues: 456 sheet: 2.97 (0.21), residues: 552 loop : -0.71 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 455 HIS 0.004 0.001 HIS K 468 PHE 0.014 0.002 PHE H 467 TYR 0.009 0.002 TYR B 398 ARG 0.004 0.001 ARG I 405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 2.049 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 191 average time/residue: 3.7729 time to fit residues: 769.7647 Evaluate side-chains 167 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 GLN C 436 GLN E 436 GLN F 436 GLN H 436 GLN K 436 GLN L 436 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13404 Z= 0.315 Angle : 0.559 3.672 18180 Z= 0.316 Chirality : 0.046 0.151 1920 Planarity : 0.005 0.028 2376 Dihedral : 4.644 20.177 1764 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.42 % Allowed : 13.03 % Favored : 85.54 % 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: 1.23 (0.21), residues: 1584 helix: 0.25 (0.24), residues: 456 sheet: 2.82 (0.21), residues: 552 loop : -0.79 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 455 HIS 0.003 0.001 HIS H 468 PHE 0.013 0.002 PHE K 467 TYR 0.008 0.002 TYR H 398 ARG 0.004 0.001 ARG F 405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: E 433 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7885 (ttm170) REVERT: H 433 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7753 (ttm170) REVERT: K 433 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7766 (ttm170) outliers start: 20 outliers final: 4 residues processed: 180 average time/residue: 4.0955 time to fit residues: 781.5685 Evaluate side-chains 180 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.0050 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN D 436 GLN G 436 GLN I 436 GLN J 436 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13404 Z= 0.264 Angle : 0.527 3.607 18180 Z= 0.297 Chirality : 0.045 0.148 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.580 20.296 1764 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.42 % Allowed : 13.60 % Favored : 84.97 % 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: 1.26 (0.21), residues: 1584 helix: 0.28 (0.24), residues: 456 sheet: 2.85 (0.21), residues: 552 loop : -0.79 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 455 HIS 0.002 0.001 HIS E 468 PHE 0.013 0.002 PHE B 467 TYR 0.006 0.001 TYR H 398 ARG 0.002 0.000 ARG J 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: E 433 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7881 (ttm170) REVERT: H 433 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7753 (ttm170) REVERT: K 433 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7765 (ttm170) outliers start: 20 outliers final: 4 residues processed: 173 average time/residue: 3.8928 time to fit residues: 716.2435 Evaluate side-chains 173 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13404 Z= 0.246 Angle : 0.517 3.852 18180 Z= 0.290 Chirality : 0.044 0.148 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.516 20.032 1764 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.42 % Allowed : 14.60 % Favored : 83.97 % 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: 1.33 (0.21), residues: 1584 helix: 0.33 (0.24), residues: 456 sheet: 2.88 (0.21), residues: 552 loop : -0.73 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 455 HIS 0.002 0.001 HIS D 468 PHE 0.014 0.002 PHE B 467 TYR 0.004 0.001 TYR D 398 ARG 0.002 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7843 (ttm170) REVERT: E 433 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7889 (ttm170) REVERT: H 433 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7741 (ttm170) REVERT: K 433 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7756 (ttm170) outliers start: 20 outliers final: 4 residues processed: 172 average time/residue: 3.9632 time to fit residues: 724.6635 Evaluate side-chains 175 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.0770 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13404 Z= 0.177 Angle : 0.480 3.957 18180 Z= 0.268 Chirality : 0.043 0.146 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.372 19.825 1764 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.57 % Allowed : 15.17 % Favored : 84.26 % 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: 1.49 (0.21), residues: 1584 helix: 0.48 (0.23), residues: 456 sheet: 2.94 (0.21), residues: 552 loop : -0.62 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.002 0.001 HIS B 468 PHE 0.014 0.002 PHE L 467 TYR 0.003 0.001 TYR K 398 ARG 0.001 0.000 ARG J 405 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7868 (ttm170) REVERT: E 433 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7910 (ttm170) REVERT: H 433 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7755 (ttm170) REVERT: K 433 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7779 (ttm170) outliers start: 8 outliers final: 4 residues processed: 173 average time/residue: 3.9696 time to fit residues: 730.1618 Evaluate side-chains 169 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13404 Z= 0.238 Angle : 0.507 4.148 18180 Z= 0.284 Chirality : 0.044 0.148 1920 Planarity : 0.004 0.029 2376 Dihedral : 4.427 19.985 1764 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.64 % Allowed : 15.24 % Favored : 84.12 % 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: 1.44 (0.21), residues: 1584 helix: 0.44 (0.24), residues: 456 sheet: 2.91 (0.21), residues: 552 loop : -0.64 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.003 0.001 HIS E 468 PHE 0.014 0.002 PHE L 467 TYR 0.005 0.001 TYR K 398 ARG 0.002 0.000 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7854 (ttm170) REVERT: E 433 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7909 (ttm170) REVERT: H 433 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: J 433 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8010 (ttm170) REVERT: K 433 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7766 (ttm170) outliers start: 9 outliers final: 4 residues processed: 173 average time/residue: 3.9369 time to fit residues: 724.0498 Evaluate side-chains 173 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 433 ARG Chi-restraints excluded: chain J residue 433 ARG Chi-restraints excluded: chain K residue 433 ARG Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: