Starting phenix.real_space_refine on Wed Jul 24 09:30:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/07_2024/8t15_40955.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/07_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_40955/07_2024/8t15_40955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/07_2024/8t15_40955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/07_2024/8t15_40955.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t15_40955/07_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-5388/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: 13.57, per 1000 atoms: 0.53 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: 18.67 Conformation dependent library (CDL) restraints added in 2.4 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: 1.90 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: 9.44 Time building geometry restraints manager: 19.74 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 1.850 nonbonded pdb=" O ILE B 350 " pdb=" HG1 THR B 354 " model vdw 1.727 1.850 nonbonded pdb=" O ILE K 350 " pdb=" HG1 THR K 354 " model vdw 1.727 1.850 nonbonded pdb=" O ILE E 350 " pdb=" HG1 THR E 354 " model vdw 1.728 1.850 nonbonded pdb=" O ILE L 350 " pdb=" HG1 THR L 354 " model vdw 1.733 1.850 ... (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 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: 6.770 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: 0.410 Extract box with map and model: 1.020 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 78.590 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.120 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.490 ------------------------------------------------------------------------------- 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 : 2.045 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: 4.1033 time to fit residues: 938.7183 Evaluate side-chains 198 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7986 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13404 Z= 0.385 Angle : 0.594 3.908 18180 Z= 0.334 Chirality : 0.046 0.150 1920 Planarity : 0.005 0.027 2376 Dihedral : 4.657 20.699 1764 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.28 % Allowed : 13.96 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1584 helix: 0.15 (0.24), residues: 456 sheet: 2.92 (0.21), residues: 552 loop : -0.80 (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 B 468 PHE 0.012 0.003 PHE F 467 TYR 0.009 0.002 TYR E 398 ARG 0.003 0.001 ARG D 433 *********************** 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 192 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 2.087 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 192 average time/residue: 4.0847 time to fit residues: 833.1165 Evaluate side-chains 174 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 436 GLN E 436 GLN H 436 GLN K 436 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13404 Z= 0.297 Angle : 0.549 3.651 18180 Z= 0.309 Chirality : 0.045 0.145 1920 Planarity : 0.005 0.027 2376 Dihedral : 4.597 19.752 1764 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.35 % Allowed : 14.32 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1584 helix: 0.17 (0.24), residues: 456 sheet: 2.86 (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 I 455 HIS 0.003 0.001 HIS J 468 PHE 0.013 0.002 PHE E 467 TYR 0.006 0.001 TYR K 398 ARG 0.003 0.000 ARG L 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 187 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7859 (ttm170) REVERT: E 433 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: H 433 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: K 433 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7770 (ttm170) outliers start: 19 outliers final: 4 residues processed: 185 average time/residue: 4.1330 time to fit residues: 810.3422 Evaluate side-chains 185 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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: 0.6980 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 150 optimal weight: 0.0050 chunk 74 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 436 GLN D 436 GLN F 436 GLN G 436 GLN I 436 GLN L 436 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13404 Z= 0.188 Angle : 0.489 3.661 18180 Z= 0.273 Chirality : 0.044 0.141 1920 Planarity : 0.004 0.027 2376 Dihedral : 4.379 19.491 1764 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.14 % Allowed : 14.53 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.21), residues: 1584 helix: 0.39 (0.23), residues: 456 sheet: 3.06 (0.21), residues: 552 loop : -0.71 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 455 HIS 0.003 0.001 HIS E 420 PHE 0.014 0.002 PHE F 467 TYR 0.005 0.001 TYR K 398 ARG 0.001 0.000 ARG L 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 189 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: E 424 ASP cc_start: 0.8183 (p0) cc_final: 0.7897 (m-30) REVERT: E 433 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7900 (ttm170) REVERT: H 424 ASP cc_start: 0.8263 (p0) cc_final: 0.7995 (m-30) REVERT: H 433 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7741 (ttm170) REVERT: K 433 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7757 (ttm170) outliers start: 16 outliers final: 4 residues processed: 181 average time/residue: 4.0340 time to fit residues: 774.1584 Evaluate side-chains 176 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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: 3.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13404 Z= 0.358 Angle : 0.576 3.880 18180 Z= 0.324 Chirality : 0.046 0.149 1920 Planarity : 0.005 0.028 2376 Dihedral : 4.633 19.679 1764 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.14 % Allowed : 15.74 % 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: 1.16 (0.21), residues: 1584 helix: 0.12 (0.24), residues: 456 sheet: 2.86 (0.21), residues: 552 loop : -0.85 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 455 HIS 0.003 0.001 HIS A 420 PHE 0.013 0.003 PHE B 467 TYR 0.007 0.002 TYR K 398 ARG 0.003 0.000 ARG C 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 184 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7877 (ttm170) REVERT: E 433 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7923 (ttm170) REVERT: H 433 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7777 (ttm170) REVERT: K 433 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7788 (ttm170) outliers start: 16 outliers final: 4 residues processed: 176 average time/residue: 4.0115 time to fit residues: 748.9553 Evaluate side-chains 176 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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: 3.9990 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7976 moved from start: 0.1166 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= 0.231 Angle : 0.509 4.031 18180 Z= 0.286 Chirality : 0.044 0.142 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.479 19.461 1764 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.64 % Allowed : 16.81 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.21), residues: 1584 helix: 0.25 (0.23), residues: 456 sheet: 2.96 (0.21), residues: 552 loop : -0.79 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.003 0.001 HIS H 420 PHE 0.013 0.002 PHE H 467 TYR 0.004 0.001 TYR J 369 ARG 0.001 0.000 ARG H 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 181 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 433 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7884 (ttm170) REVERT: E 433 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7917 (ttm170) REVERT: H 424 ASP cc_start: 0.8269 (p0) cc_final: 0.7987 (m-30) REVERT: H 433 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7781 (ttm170) REVERT: J 433 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8004 (ttm170) REVERT: K 433 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7794 (ttm170) outliers start: 9 outliers final: 4 residues processed: 181 average time/residue: 4.1762 time to fit residues: 801.3715 Evaluate side-chains 181 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 13404 Z= 0.248 Angle : 0.517 4.179 18180 Z= 0.290 Chirality : 0.044 0.145 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.475 19.445 1764 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.07 % Allowed : 15.95 % Favored : 82.98 % 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: 1.32 (0.21), residues: 1584 helix: 0.25 (0.23), residues: 456 sheet: 2.96 (0.21), residues: 552 loop : -0.77 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 455 HIS 0.003 0.001 HIS F 420 PHE 0.014 0.002 PHE F 467 TYR 0.005 0.001 TYR B 398 ARG 0.002 0.000 ARG E 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 187 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 172 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8081 (ttm170) REVERT: A 451 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.9023 (mt-10) REVERT: B 433 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7876 (ttm170) REVERT: D 433 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8200 (ttm170) REVERT: E 433 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7928 (ttm170) REVERT: G 433 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: G 451 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.9042 (mt-10) REVERT: H 424 ASP cc_start: 0.8288 (p0) cc_final: 0.7991 (m-30) REVERT: H 433 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7773 (ttm170) REVERT: J 433 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8047 (ttm170) REVERT: K 433 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7786 (ttm170) outliers start: 15 outliers final: 4 residues processed: 187 average time/residue: 4.2161 time to fit residues: 834.1156 Evaluate side-chains 187 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain D residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain G residue 433 ARG Chi-restraints excluded: chain G residue 451 GLU 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: 6.9990 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7989 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13404 Z= 0.290 Angle : 0.542 4.334 18180 Z= 0.305 Chirality : 0.045 0.147 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.552 19.309 1764 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.50 % Allowed : 15.46 % Favored : 83.05 % 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: 1.19 (0.21), residues: 1584 helix: 0.15 (0.23), residues: 456 sheet: 2.87 (0.21), residues: 552 loop : -0.84 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 455 HIS 0.003 0.001 HIS J 420 PHE 0.013 0.002 PHE H 467 TYR 0.005 0.001 TYR J 369 ARG 0.003 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 8 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 193 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8117 (ttm170) REVERT: B 433 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7896 (ttm170) REVERT: D 433 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8229 (ttm170) REVERT: E 433 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7932 (ttm170) REVERT: G 433 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8061 (ttm170) REVERT: H 424 ASP cc_start: 0.8280 (p0) cc_final: 0.7994 (m-30) REVERT: H 433 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7795 (ttm170) REVERT: J 433 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8045 (ttm170) REVERT: K 433 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7806 (ttm170) outliers start: 21 outliers final: 8 residues processed: 193 average time/residue: 4.0941 time to fit residues: 837.3975 Evaluate side-chains 193 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain D residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 378 THR Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain G residue 433 ARG Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 378 THR 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 378 THR Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7968 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13404 Z= 0.185 Angle : 0.491 4.319 18180 Z= 0.275 Chirality : 0.044 0.141 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.377 19.302 1764 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.28 % Allowed : 15.31 % Favored : 83.40 % 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: 1.47 (0.21), residues: 1584 helix: 0.36 (0.23), residues: 456 sheet: 3.06 (0.21), residues: 552 loop : -0.69 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 455 HIS 0.003 0.001 HIS K 420 PHE 0.014 0.002 PHE I 467 TYR 0.003 0.001 TYR A 369 ARG 0.001 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 9 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 195 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8046 (ttm170) REVERT: A 451 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8997 (mt-10) REVERT: B 433 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7871 (ttm170) REVERT: D 433 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8180 (ttm170) REVERT: E 424 ASP cc_start: 0.8176 (p0) cc_final: 0.7883 (m-30) REVERT: E 433 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7924 (ttm170) REVERT: G 433 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7994 (ttm170) REVERT: G 451 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.9017 (mt-10) REVERT: H 424 ASP cc_start: 0.8289 (p0) cc_final: 0.7989 (m-30) REVERT: H 433 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7767 (ttm170) REVERT: J 433 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8035 (ttm170) REVERT: K 433 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7780 (ttm170) outliers start: 18 outliers final: 8 residues processed: 195 average time/residue: 4.1026 time to fit residues: 851.1778 Evaluate side-chains 190 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain D residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 378 THR Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain G residue 433 ARG Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 378 THR 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 378 THR Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7981 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13404 Z= 0.257 Angle : 0.523 4.378 18180 Z= 0.293 Chirality : 0.044 0.145 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.460 19.533 1764 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1584 helix: 0.31 (0.23), residues: 456 sheet: 3.12 (0.20), residues: 576 loop : -1.00 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.003 0.001 HIS I 420 PHE 0.013 0.002 PHE L 467 TYR 0.005 0.001 TYR B 398 ARG 0.002 0.000 ARG B 405 ********************** REFINEMENT MACRO_CYCLE 10 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 190 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8053 (ttm170) REVERT: A 451 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.9021 (mt-10) REVERT: B 433 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7881 (ttm170) REVERT: D 433 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8197 (ttm170) REVERT: E 424 ASP cc_start: 0.8179 (p0) cc_final: 0.7884 (m-30) REVERT: E 433 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: G 433 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8007 (ttm170) REVERT: G 451 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.9040 (mt-10) REVERT: H 424 ASP cc_start: 0.8278 (p0) cc_final: 0.7983 (m-30) REVERT: H 433 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7779 (ttm170) REVERT: J 433 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8042 (ttm170) REVERT: K 433 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7791 (ttm170) outliers start: 18 outliers final: 8 residues processed: 190 average time/residue: 4.0340 time to fit residues: 812.6275 Evaluate side-chains 190 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 433 ARG Chi-restraints excluded: chain D residue 433 ARG Chi-restraints excluded: chain E residue 433 ARG Chi-restraints excluded: chain F residue 378 THR Chi-restraints excluded: chain F residue 433 ARG Chi-restraints excluded: chain G residue 433 ARG Chi-restraints excluded: chain G residue 451 GLU Chi-restraints excluded: chain H residue 433 ARG Chi-restraints excluded: chain I residue 378 THR 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 378 THR Chi-restraints excluded: chain L residue 433 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.167415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134117 restraints weight = 33635.553| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.79 r_work: 0.3397 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1283 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= 0.195 Angle : 0.494 4.114 18180 Z= 0.276 Chirality : 0.044 0.142 1920 Planarity : 0.004 0.028 2376 Dihedral : 4.364 19.484 1764 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.28 % Allowed : 15.53 % 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: 1.51 (0.21), residues: 1584 helix: 0.42 (0.23), residues: 456 sheet: 3.07 (0.21), residues: 552 loop : -0.68 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 455 HIS 0.003 0.001 HIS B 420 PHE 0.013 0.002 PHE L 467 TYR 0.003 0.001 TYR A 369 ARG 0.001 0.000 ARG K 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12132.55 seconds wall clock time: 209 minutes 48.67 seconds (12588.67 seconds total)